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both report SD. Indexed primary SPR Methods supply residues 263–398 and buffer, but the full PDF was unavailable. 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Full NanoBRET construct and conditions were not inspected. The 1.4 uM direct tracer-engagement endpoint is separate from this histone PPI assay.", "replicates": "3 independent replicates (Figure 4e; also Supplementary Table 7)", "role": "reported_chemical_probe", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S03", "source_measurement_key": "d81f07907c62c71d3be8efb70d36d0f87a02e504c926113d8e3f019f1e1a7478", "source_original": { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP:ASSAY:0009", "assay_type": "NanoBRET IC50", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": null, "ccd_id": "EJE", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "BI-9321", "conditions": "{\"cell_line\": \"U2OS\"}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:Q9BZ95:PWWP1", "endpoint_label_status": null, "evidence_class": "cellular_interaction_response", "evidence_location": "SGC probe developer report: Overview", "evidence_url": "https://www.thesgc.org/chemical-probes/bi-9321", "gene": "NSD3", "interpretation": null, "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": null, "pdb_id": "6G2O", "preparation_id": "PREP:BI-9321", "protein_id": "UP:Q9BZ95", "qualitative_result": null, "reference_id": "PMID:31285596", "remaining_uncertainty": "The value 1.2 ± 0.06 uM, SD and n=3 were verified in the actual Supplementary Table 7. Full NanoBRET construct and conditions were not inspected. The 1.4 uM direct tracer-engagement endpoint is separate from this histone PPI assay.", "replicates": "3 independent replicates (Figure 4e; also Supplementary Table 7)", "role": "reported_chemical_probe", "source_component_url": null, "source_id": "S03", "source_reported_uncertainty": "0.06", "source_reported_units": "µM", "source_reported_value": "1.2", "source_verification_scope": "Phase 3 actual publisher Supplementary Table 7 and official Figure 3/4 captions; selected indexed accepted-manuscript Methods, full PDF unavailable (403); developer identity page", "temperature_C": null, "uncertainty": 0.06, "uncertainty_type": "SD", "uncertainty_uM": 0.06, "unit_conversion": null, "units": "µM", "value": 1.2, "value_operator": "=", "value_uM": 1.2, "verification_level": "primary_developer_assay_report_verified" }, "source_reported_uncertainty": "0.06", "source_reported_units": "µM", "source_reported_value": "1.2", "source_verification_scope": "Phase 3 actual publisher Supplementary Table 7 and official Figure 3/4 captions; selected indexed accepted-manuscript Methods, full PDF unavailable (403); developer identity page", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 0.06, "uncertainty_type": "SD", "uncertainty_uM": 0.06, "unit_conversion": null, "units": "µM", "value": 1.2, "value_operator": "=", "value_uM": 1.2, "verification_level": "primary_developer_assay_report_verified" }, { "DMSO_percent": 1, "assay_construct_end": 402, "assay_construct_start": 247, "assay_context": "purified_domain", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0001", "assay_type": "ITC Kd", "assay_value_transferred_to_modeled_stereoisomers": false, "buffer": "50 mM Tris-HCl; 150 mM NaCl; 1% DMSO; 3% NMP", "ccd_id": null, "chemical_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N", "compound_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N", "compound_name": "BI-9321", "conditions": { "buffer": "50 mM Tris-HCl; 150 mM NaCl; 1% DMSO; 3% NMP", "compound_syringe_concentration_uM": 200, "construct": "NSD3 247–402 in pNICBio2, E. coli expressed", "first_injection_removed": true, "model": "single binding site", "pH": 6.8, "protein_concentration_uM": 20, "temperature_C": 15 }, "curation_version": "phase5-1.0.0", "domain": "PWWP1", "domain_id": "UP:Q9BZ95:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_location": "Results and Figure 2B-D; STAR Methods: ITC", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8882712/", "gene": "NSD3", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_measured": true, "is_negative": false, "method": "ITC", "normalized_exact_uM": 1.7, "numeric_transcription_status": "source_preserved", "numeric_value_inferred_from_structure": false, "organism": "Homo sapiens", "pH": 6.8, "pdb_id": null, "preparation_id": "PREP:BI-9321", "protein_id": "UP:Q9BZ95", "publication_year": 2022, "reference_id": "PMID:34469831", "remaining_uncertainty": "Primary manuscript and Methods inspected; individual raw titration files not re-fitted. BI-9321 is a distinct study-specific ITC measurement, not the original 2019 SPR result.", "replicates": "2 independent measurements", "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_database": "Primary literature (Phase 5)", "source_id": "P5:S:XU2022", "source_measurement_key": "7a5643332d9884d1ebb0e010bd63f15485c8df4e1297f1a9aeeeea672f48b98f", "source_original": { "DMSO_percent": 1, "assay_construct_end": 402, "assay_construct_start": 247, "assay_context": "purified_domain", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0001", "assay_type": "ITC Kd", "assay_value_transferred_to_modeled_stereoisomers": false, "buffer": "50 mM Tris-HCl; 150 mM NaCl; 1% DMSO; 3% NMP", "ccd_id": null, "chemical_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N", "compound_name": "BI-9321", "conditions": { "buffer": "50 mM Tris-HCl; 150 mM NaCl; 1% DMSO; 3% NMP", "compound_syringe_concentration_uM": 200, "construct": "NSD3 247–402 in pNICBio2, E. coli expressed", "first_injection_removed": true, "model": "single binding site", "pH": 6.8, "protein_concentration_uM": 20, "temperature_C": 15 }, "domain": "PWWP1", "domain_id": "UP:Q9BZ95:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_location": "Results and Figure 2B-D; STAR Methods: ITC", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8882712/", "gene": "NSD3", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_negative": false, "numeric_transcription_status": "source_preserved", "numeric_value_inferred_from_structure": false, "pH": 6.8, "pdb_id": null, "preparation_id": "PREP:BI-9321", "protein_id": "UP:Q9BZ95", "publication_year": 2022, "reference_id": "PMID:34469831", "remaining_uncertainty": "Primary manuscript and Methods inspected; individual raw titration files not re-fitted. 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\"A\", \"minimum_distance_angstrom\": 3.6582, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"367\", \"component\": \"GLN\", \"entity_position\": 105, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 2.8252, \"uniprot_position\": null}]", "pose_kind": "deposited_source_coordinates", "reference_model": "1", "source_coordinate_file": "Structures/NSD3__HUMAN__Q9BZ95/Co-Crystals/6G2O/original.cif", "source_coordinate_sha256": "74d2d63c67c68d75cd98a65a67771b43791e1d61b52c6fd985805899f9c8ecfa", "unique_heavy_atom_names": 27 }, "ligand_instance_id": "PDB:6G2O:LIG:B:EJE:401:.", "ligand_label_asym_id": "B", "minimum_Pfam_distance_angstrom": 2.8197, "minimum_chain_distance_angstrom": 2.8197, "minimum_core_distance_angstrom": 2.8197, "multiple_contacting_mapped_chains": 0, "pdb_id": "6G2O", "protein_id": "UP:Q9BZ95", "protein_label_asym_id": "A", "rank_interpretation": "Distance rank among mapped chains only; crystal packing and biological site assignment require separate review.", "role": "experimentally studied ligand", "role_category": "functional", "site_id": "PDB:6G2O:LIG:B:EJE:401:.:SITE:UP:Q9BZ95:PWWP1:A", "source_coordinate_sha256": "74d2d63c67c68d75cd98a65a67771b43791e1d61b52c6fd985805899f9c8ecfa" } ], "context_assay_count": 3, "context_measured_count": 3, "context_bound_count": 1, "context_pdb_count": 1, "context_negative_count": 0, "context_is_probe": true, "context_bioactivity_only": false, "context_kind": "Measured + bound structure", "science": { "studied_compound": true, "measured_count": 3, "structural_research_ligand": true, "research_pdb_count": 1, "other_component": false, "component_site_count": 0, "verification_queue": true, "positive_direct_binder": true, "reported_probe": true, "reported_control": false, "cellular_activity": true, "protein_degradation": false, "bioactivity_only": false, "research_site_count": 1, "unknown_site_count": 0, "annotation_roles": [ "studied", "structural", "unresolved" ] }, "science_label": "Studied + deposited research ligand", "science_profile": { "annotation_roles": [ "studied", "structural", "unresolved" ], "cellular_activity": true, "chemical_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N", "compound_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N", "entity_kind": "chemical_identity", "identity_resolved": true, "measured_observation_count": 3, "name": "BI-9321", "other_pdb_component": false, "other_site_count": 0, "positive_direct_binder": true, "primary_view": "studied", "protein_degradation": false, "reported_control": false, "reported_probe": true, "rule": "Independent source observations + per-site coordinate role, not universal pharmacology", "source_observation_ids": [ "PWWP5:ASSAY:0001", "PWWP:ASSAY:0008", "PWWP:ASSAY:0009" ], "source_site_ids": [ "PDB:6G2O:LIG:B:EJE:401:.:SITE:UP:Q9BZ95:PWWP1:A" ], "structural_research_ligand": true, "structural_research_site_count": 1, "studied_compound": true, "total_observation_count": 3, "uncertain_site_count": 0, "uncertainty": "Classification is evidence- and experiment-scoped; missing assays do not prove nonbinding.", "verification_queue": true, "verification_status": "source_scoped_mixed" }, "science_site_roles": { "PDB:6G2O:LIG:B:EJE:401:.:SITE:UP:Q9BZ95:PWWP1:A": { "ccd_url": "https://www.rcsb.org/ligand/EJE", "chemical_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N", "compound_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N", "contact_class": "native_annotation_core_contact", "coordinate_sha256": "74d2d63c67c68d75cd98a65a67771b43791e1d61b52c6fd985805899f9c8ecfa", "domain_id": "UP:Q9BZ95:PWWP1", "exact_pwwp_contact": true, "ligand_instance_id": "PDB:6G2O:LIG:B:EJE:401:.", "observed_other_component": false, "pdb_id": "6G2O", "protein_id": "UP:Q9BZ95", "role_code": "reported_studied_structural_ligand", "role_group": "research_ligand", "rule": "Phase5 exact deposited site role, measured heavy-atom contacts and native-domain scope", "site_id": "PDB:6G2O:LIG:B:EJE:401:.:SITE:UP:Q9BZ95:PWWP1:A", "source_role": "experimentally studied ligand", "source_url": "https://www.rcsb.org/structure/6G2O", "structural_research_ligand": true, "uncertainty": "Role is source-annotated; deposited proximity alone does not establish solution binding or biological activity.", "verification_status": "phase5_derived_deposited_geometry" } }, "science_assay_roles": { "PWWP:ASSAY:0008": { "chemical_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N", "compound_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N", "domain_id": "UP:Q9BZ95:PWWP1", "endpoint": "Kd", "evidence_type": "direct_binding", "explicitly_negative": false, "measured": true, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP:ASSAY:0008", "operator": "=", "positive_direct_binder": true, "preparation_id": "PREP:BI-9321", "protein_id": "UP:Q9BZ95", "remaining_uncertainty": "Primary replicate conflict: Figure 3a states n=3 independent experiments, while Supplementary Table 7 states SPR n=4; both report SD. Indexed primary SPR Methods supply residues 263–398 and buffer, but the full PDF was unavailable. Exact assay temperature, mutations and per-dose contact times remain not inspected.", "reported_cellular": false, "reported_control": false, "reported_probe": true, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "S03", "source_location": "SGC probe developer report: Overview", "source_role": "reported_chemical_probe", "source_url": "https://www.thesgc.org/chemical-probes/bi-9321", "source_verification_scope": "Phase 3 actual publisher Supplementary Table 7 and official Figure 3/4 captions; selected indexed accepted-manuscript Methods, full PDF unavailable (403); developer identity page", "studied_compound": true, "target_scope": "domain_specific", "target_variant": null, "units": "nM", "value": 166.0, "verification_status": "primary_developer_assay_report_verified" }, "PWWP:ASSAY:0009": { "chemical_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N", "compound_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N", "domain_id": "UP:Q9BZ95:PWWP1", "endpoint": "IC50", "evidence_type": "cellular_activity", "explicitly_negative": false, "measured": true, "method": "NanoBRET", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP:ASSAY:0009", "operator": "=", "positive_direct_binder": false, "preparation_id": "PREP:BI-9321", "protein_id": "UP:Q9BZ95", "remaining_uncertainty": "The value 1.2 ± 0.06 uM, SD and n=3 were verified in the actual Supplementary Table 7. Full NanoBRET construct and conditions were not inspected. The 1.4 uM direct tracer-engagement endpoint is separate from this histone PPI assay.", "reported_cellular": true, "reported_control": false, "reported_probe": true, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "S03", "source_location": "SGC probe developer report: Overview", "source_role": "reported_chemical_probe", "source_url": "https://www.thesgc.org/chemical-probes/bi-9321", "source_verification_scope": "Phase 3 actual publisher Supplementary Table 7 and official Figure 3/4 captions; selected indexed accepted-manuscript Methods, full PDF unavailable (403); developer identity page", "studied_compound": true, "target_scope": "domain_specific", "target_variant": null, "units": "µM", "value": 1.2, "verification_status": "primary_developer_assay_report_verified" }, "PWWP5:ASSAY:0001": { "chemical_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N", "compound_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N", "domain_id": "UP:Q9BZ95:PWWP1", "endpoint": "Kd", "evidence_type": "direct_binding", "explicitly_negative": false, "measured": true, "method": "ITC", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP5:ASSAY:0001", "operator": "=", "positive_direct_binder": true, "preparation_id": "PREP:BI-9321", "protein_id": "UP:Q9BZ95", "remaining_uncertainty": "Primary manuscript and Methods inspected; individual raw titration files not re-fitted. BI-9321 is a distinct study-specific ITC measurement, not the original 2019 SPR result.", "reported_cellular": false, "reported_control": false, "reported_probe": false, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "P5:S:XU2022", "source_location": "Results and Figure 2B-D; STAR Methods: ITC", "source_role": "experimentally_studied_ligand", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8882712/", "source_verification_scope": "NCBI BioC primary full text; Results, ITC Methods and Figure 2/3 captions inspected", "studied_compound": true, "target_scope": "domain_specific", "target_variant": null, "units": "µM", "value": 1.7, "verification_status": "primary_source_verified" } }, "example": { "DMSO_percent": 2.0, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 398, "assay_construct_start": 263, "assay_record_id": "PWWP:ASSAY:0008", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "50 mM Tris; 150 mM NaCl; 1 mM TCEP; 0.005% Tween-20; 2% DMSO", "ccd_id": "EJE", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N", "compound_name": "BI-9321", "conditions": "{}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:Q9BZ95:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "SGC probe developer report: Overview", "evidence_url": "https://www.thesgc.org/chemical-probes/bi-9321", "gene": "NSD3", "interpretation": "Primary developer website; original full article assay table was not retrieved.", "is_measured": true, "is_negative": false, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 0.166, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": 8.0, "pdb_id": "6G2O", "preparation_id": "PREP:BI-9321", "protein_id": "UP:Q9BZ95", "publication_year": 2019, "qualitative_result": null, "reference_id": "PMID:31285596", "remaining_uncertainty": "Primary replicate conflict: Figure 3a states n=3 independent experiments, while Supplementary Table 7 states SPR n=4; both report SD. Indexed primary SPR Methods supply residues 263–398 and buffer, but the full PDF was unavailable. 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not an experimental measurement", "files": { "dark": "ae706cf1837c8edc9b9b-dark.svg", "light": "ae706cf1837c8edc9b9b-light.svg" }, "rdkit_version": "2025.09.3", "status": "verified_smiles_full_inchikey_match" }, "development_status": "Not independently curated", "domain_ids": [ "UP:O96028:PWWP1", "UP:Q9BZ95:PWWP1" ], "entity_kind": "chemical_identity", "genes": [ "NSD2", "NSD3" ], "has_bioactivity_only": false, "has_source_conflict": false, "identity": { "aliases": [ "N-cyclopropyl-3-oxo-N-({4-[(pyrimidin-4-yl)carbamoyl]phenyl}methyl)-3,4-dihydro-2H-1,4-benzoxazine-7-carboxamide" ], "ccd_ids": [ "V01" ], "ccd_names": "[\"N-cyclopropyl-3-oxo-N-({4-[(pyrimidin-4-yl)carbamoyl]phenyl}methyl)-3,4-dihydro-2H-1,4-benzoxazine-7-carboxamide\"]", "ccd_types": "[\"non-polymer\"]", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "connectivity_block": "KOZGEDUWAQFVAV", "curated_source_sha256": null, "curation_version": "frozen-v1.2", "external_identifiers": {}, "formal_charge_by_ccd": "{\"V01\": 0}", "formulae": "[\"C24 H21 N5 O4\"]", "geometry_note": "CCD ideal SDF is a reference chemical geometry, not a deposited bound pose.", "identity_status": "complete_deposited_InChIKey", "inchikey": "KOZGEDUWAQFVAV-UHFFFAOYSA-N", "inventory_origin": "v1_CCD_inventory", "isomeric_smiles": "c1cc(ccc1CN(C2CC2)C(=O)c3ccc4c(c3)OCC(=O)N4)C(=O)Nc5ccncn5", "primary_name": "N-cyclopropyl-3-oxo-N-({4-[(pyrimidin-4-yl)carbamoyl]phenyl}methyl)-3,4-dihydro-2H-1,4-benzoxazine-7-carboxamide", "retrieval_date": "2026-10-24", "smiles_stereo_by_ccd": "{\"V01\": \"c1cc(ccc1CN(C2CC2)C(=O)c3ccc4c(c3)OCC(=O)N4)C(=O)Nc5ccncn5\"}", "source_metadata_sha256": "{\"V01\": \"ced5ef4acd208273eb85fecdbbc375b05202a622e993dc4571d4354dcab003ca\"}", "source_urls": [ "https://www.rcsb.org/ligand/V01" ] }, "identity_note": "Complete deposited identity retained; no connectivity-only or name-only merge.", "identity_resolved": true, "is_control": false, "is_probe": true, "measured_observation_count": 6, "name": "UNC6934", "negative_count": 1, "observation_ids": [ "PWWP:ASSAY:0004", "PWWP:ASSAY:0005", "PWWP:ASSAY:0006", "PWWP:ASSAY:0014", "PWWP:ASSAY:0021", "PWWP11:ASSAY:0001" ], "pdb_structure_count": 1, "preparation_count": 1, "preparation_ids": [ "PREP:UNC6934" ], "protein_ids": [ "UP:O96028", "UP:Q9BZ95" ], "relationships": [ { "direction": "inverse", "object_id": "INCHIKEY:HUIINGSTUYTZJL-UHFFFAOYSA-N", "object_preparation_id": "PREP:UNC6934", "original_object_id": "PREP:UNC6934", "original_subject_id": "PREP:UNC7145", "predicate": "negative_control_for", "relationship": "has negative control for", "relationship_id": "P5:REL:UNC7145", "retrieval_date": "2026-10-26", "scope": "NSD2-PWWP1 probe negative control", "source_id": "P5:S:DILWORTH2021", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "subject_id": "INCHIKEY:HUIINGSTUYTZJL-UHFFFAOYSA-N", "subject_preparation_id": "PREP:UNC7145", "version": "phase5.chemical_curation.1.1.0" } ], "relevant": true, "search_text": "unc6934 inchikey:kozgeduwaqfvav-uhfffaoysa-n n-cyclopropyl-3-oxo-n-({4-[(pyrimidin-4-yl)carbamoyl]phenyl}methyl)-3,4-dihydro-2h-1,4-benzoxazine-7-carboxamide unc6934 nsd2 nsd3 up:o96028:pwwp1 up:q9bz95:pwwp1 6xcg {\"aliases\":[\"n-cyclopropyl-3-oxo-n-({4-[(pyrimidin-4-yl)carbamoyl]phenyl}methyl)-3,4-dihydro-2h-1,4-benzoxazine-7-carboxamide\"],\"ccd_ids\":[\"v01\"],\"ccd_names\":\"[\\\"n-cyclopropyl-3-oxo-n-({4-[(pyrimidin-4-yl)carbamoyl]phenyl}methyl)-3,4-dihydro-2h-1,4-benzoxazine-7-carboxamide\\\"]\",\"ccd_types\":\"[\\\"non-polymer\\\"]\",\"chemical_id\":\"inchikey:kozgeduwaqfvav-uhfffaoysa-n\",\"connectivity_block\":\"kozgeduwaqfvav\",\"curated_source_sha256\":null,\"curation_version\":\"frozen-v1.2\",\"external_identifiers\":{},\"formal_charge_by_ccd\":\"{\\\"v01\\\": 0}\",\"formulae\":\"[\\\"c24 h21 n5 o4\\\"]\",\"geometry_note\":\"ccd ideal sdf is a reference chemical geometry, not a deposited bound pose.\",\"identity_status\":\"complete_deposited_inchikey\",\"inchikey\":\"kozgeduwaqfvav-uhfffaoysa-n\",\"inventory_origin\":\"v1_ccd_inventory\",\"isomeric_smiles\":\"c1cc(ccc1cn(c2cc2)c(=o)c3ccc4c(c3)occ(=o)n4)c(=o)nc5ccncn5\",\"primary_name\":\"n-cyclopropyl-3-oxo-n-({4-[(pyrimidin-4-yl)carbamoyl]phenyl}methyl)-3,4-dihydro-2h-1,4-benzoxazine-7-carboxamide\",\"retrieval_date\":\"2026-10-24\",\"smiles_stereo_by_ccd\":\"{\\\"v01\\\": \\\"c1cc(ccc1cn(c2cc2)c(=o)c3ccc4c(c3)occ(=o)n4)c(=o)nc5ccncn5\\\"}\",\"source_metadata_sha256\":\"{\\\"v01\\\": \\\"ced5ef4acd208273eb85fecdbbc375b05202a622e993dc4571d4354dcab003ca\\\"}\",\"source_urls\":[\"https://www.rcsb.org/ligand/v01\"]} pmid:34782742 2022 https://pmc.ncbi.nlm.nih.gov/articles/pmc9189931/ pmid:34782742 2022 https://pmc.ncbi.nlm.nih.gov/articles/pmc9189931/ pmid:34782742 2022 https://pmc.ncbi.nlm.nih.gov/articles/pmc9189931/ pmid:40959233 2025 https://pmc.ncbi.nlm.nih.gov/articles/pmc12434523/ pmid:40959233 2025 https://pmc.ncbi.nlm.nih.gov/articles/pmc12434523/ pmid:40959233 2025 https://pmc.ncbi.nlm.nih.gov/articles/pmc12434523/", "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "https://www.rcsb.org/ligand/V01" ], "verification_pending": false, "context_observations": [ { "DMSO_percent": 0.5, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0004", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.05% Tween-20; 0.5% DMSO", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_name": "UNC6934", "conditions": "{\"phase3_verification\": \"SV02A\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"AviTag/NSD2(208–368)/polyhistidine; biotinylated\", \"source_protocol_highest_concentration_uM\": 2}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Results; Figures 1–2", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": null, "is_measured": true, "is_negative": false, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 0.091, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": 7.4, "pdb_id": "6XCG", "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "publication_year": 2022, "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "SPR temperature and exact uncertainty definition are not specified in the inspected assay-specific source. Triplicate experiments reported. Preparation/assay construct differs from crystallization 211–350.", "replicates": "3 (triplicate experiments; independence level not specified)", "role": "reported_chemical_probe", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S02", "source_measurement_key": "7c16700328b32cfd3cd5e66dec0c4ccaa8b2dca48c21be5b56df68be8add7388", "source_original": { "DMSO_percent": 0.5, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0004", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.05% Tween-20; 0.5% DMSO", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "UNC6934", "conditions": "{\"phase3_verification\": \"SV02A\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"AviTag/NSD2(208–368)/polyhistidine; biotinylated\", \"source_protocol_highest_concentration_uM\": 2}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Results; Figures 1–2", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": null, "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": 7.4, "pdb_id": "6XCG", "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "SPR temperature and exact uncertainty definition are not specified in the inspected assay-specific source. Triplicate experiments reported. Preparation/assay construct differs from crystallization 211–350.", "replicates": "3 (triplicate experiments; independence level not specified)", "role": "reported_chemical_probe", "source_component_url": null, "source_id": "S02", "source_reported_uncertainty": "8", "source_reported_units": "nM", "source_reported_value": "91", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "temperature_C": null, "uncertainty": 8.0, "uncertainty_type": null, "uncertainty_uM": 0.008, "unit_conversion": null, "units": "nM", "value": 91.0, "value_operator": "=", "value_uM": 0.091, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "8", "source_reported_units": "nM", "source_reported_value": "91", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 8.0, "uncertainty_type": null, "uncertainty_uM": 0.008, "unit_conversion": null, "units": "nM", "value": 91.0, "value_operator": "=", "value_uM": 0.091, "verification_level": "primary_full_text_sections_verified" }, { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0005", "assay_type": "AlphaScreen IC50", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "150 mM NaCl; 20 mM Tris; 0.01% BSA; 0.01% NP-40; 1 mM DTT (DTT omitted from bead buffer)", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_name": "UNC6934", "conditions": "{\"phase3_verification\": \"SV02A\", \"protein_construct\": \"NSD2 208–368\", \"readout\": \"His-NSD2-PWWP1 binding to H3K36me2 designer nucleosome\", \"tag\": \"6His\", \"temperature_scope\": \"23°C compound/protein and nucleosome preincubation; bead incubation room temperature\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint": "IC50", "endpoint_label_status": null, "evidence_class": "biochemical_interaction_inhibition", "evidence_location": "Discussion; biochemical characterization", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": "Binding-interaction assay, not a direct catalytic SET-domain inhibition measurement.", "is_measured": true, "is_negative": false, "method": "AlphaScreen", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 0.10400000000000001, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": 7.5, "pdb_id": "6XCG", "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "publication_year": 2022, "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "23°C is the antagonist preincubation temperature, not a verified readout temperature. Final DMSO fraction and SD-versus-SEM definition for ±13 nM are not explicit in the inspected assay-specific text.", "replicates": "3 independent experiments; each 10-point curve in duplicate", "role": "reported_chemical_probe", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S02", "source_measurement_key": "ebb1bfa66d69be833d6a30c211d24a8fda7200d43b65ab3b9be6418909d92987", "source_original": { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0005", "assay_type": "AlphaScreen IC50", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "150 mM NaCl; 20 mM Tris; 0.01% BSA; 0.01% NP-40; 1 mM DTT (DTT omitted from bead buffer)", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "UNC6934", "conditions": "{\"phase3_verification\": \"SV02A\", \"protein_construct\": \"NSD2 208–368\", \"readout\": \"His-NSD2-PWWP1 binding to H3K36me2 designer nucleosome\", \"tag\": \"6His\", \"temperature_scope\": \"23°C compound/protein and nucleosome preincubation; bead incubation room temperature\"}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": null, "evidence_class": "biochemical_interaction_inhibition", "evidence_location": "Discussion; biochemical characterization", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": "Binding-interaction assay, not a direct catalytic SET-domain inhibition measurement.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": 7.5, "pdb_id": "6XCG", "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "23°C is the antagonist preincubation temperature, not a verified readout temperature. Final DMSO fraction and SD-versus-SEM definition for ±13 nM are not explicit in the inspected assay-specific text.", "replicates": "3 independent experiments; each 10-point curve in duplicate", "role": "reported_chemical_probe", "source_component_url": null, "source_id": "S02", "source_reported_uncertainty": "13", "source_reported_units": "nM", "source_reported_value": "104", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "temperature_C": 23, "uncertainty": 13.0, "uncertainty_type": null, "uncertainty_uM": 0.013, "unit_conversion": null, "units": "nM", "value": 104.0, "value_operator": "=", "value_uM": 0.104, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "13", "source_reported_units": "nM", "source_reported_value": "104", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "target_scope": "domain_specific", "temperature_C": 23, "uncertainty": 13.0, "uncertainty_type": null, "uncertainty_uM": 0.013, "unit_conversion": null, "units": "nM", "value": 104.0, "value_operator": "=", "value_uM": 0.104, "verification_level": "primary_full_text_sections_verified" }, { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP:ASSAY:0006", "assay_type": "NanoBRET PPI half-response", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "DMEM/F12 without phenol red; 4% FBS; 100 U/mL penicillin; 100 ug/mL streptomycin", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_name": "UNC6934", "conditions": "{\"cell_line\": \"U2OS\", \"readout\": \"NSD2 PWWP1–histone H3.3 interaction\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint": "Unstandardized half-response concentration", "endpoint_label_status": "Results/Figure use EC50, Discussion uses IC50; neutral half-response retained", "evidence_class": "cellular_interaction_response", "evidence_location": "Results: cellular target engagement; Figure 4d", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": "Main Results calls this EC50; Discussion calls it IC50. Original value retained without conflating it with Kd.", "is_measured": true, "is_negative": false, "method": "NanoBRET PPI half-response", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": null, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": null, "pdb_id": "6XCG", "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "publication_year": 2022, "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "NanoLuc construct boundaries, readout temperature and SD-versus-SEM are not explicit in the inspected source. Results say EC50 while Discussion says IC50; neutral half-response label retained.", "replicates": "3 independent replicates", "role": "reported_chemical_probe", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S02", "source_measurement_key": "73dd58f0b5956416fa5d2f849b2939bcaf1b614b24b1131628947441ac92994c", "source_original": { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP:ASSAY:0006", "assay_type": "NanoBRET PPI half-response", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "DMEM/F12 without phenol red; 4% FBS; 100 U/mL penicillin; 100 ug/mL streptomycin", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "UNC6934", "conditions": "{\"cell_line\": \"U2OS\", \"readout\": \"NSD2 PWWP1–histone H3.3 interaction\"}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": "Results/Figure use EC50, Discussion uses IC50; neutral half-response retained", "evidence_class": "cellular_interaction_response", "evidence_location": "Results: cellular target engagement; Figure 4d", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": "Main Results calls this EC50; Discussion calls it IC50. Original value retained without conflating it with Kd.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": null, "pdb_id": "6XCG", "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "NanoLuc construct boundaries, readout temperature and SD-versus-SEM are not explicit in the inspected source. Results say EC50 while Discussion says IC50; neutral half-response label retained.", "replicates": "3 independent replicates", "role": "reported_chemical_probe", "source_component_url": null, "source_id": "S02", "source_reported_uncertainty": "0.25", "source_reported_units": "µM", "source_reported_value": "1.23", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "temperature_C": null, "uncertainty": 0.25, "uncertainty_type": null, "uncertainty_uM": 0.25, "unit_conversion": null, "units": "µM", "value": 1.23, "value_operator": "=", "value_uM": 1.23, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "0.25", "source_reported_units": "µM", "source_reported_value": "1.23", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 0.25, "uncertainty_type": null, "uncertainty_uM": 0.25, "unit_conversion": null, "units": "µM", "value": 1.23, "value_operator": "=", "value_uM": 1.23, "verification_level": "primary_full_text_sections_verified" }, { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0014", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_name": "UNC6934", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Table 1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD2", "interpretation": "Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.", "is_measured": true, "is_negative": false, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 0.24, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": 7.5, "pdb_id": null, "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "publication_year": 2025, "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "role": "reported_chemical_probe", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S05", "source_measurement_key": "b6a422c24a429b6fecbccb8c4722557675fbd65bfeca995764913f27fe18a750", "source_original": { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0014", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "UNC6934", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Table 1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD2", "interpretation": "Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": 7.5, "pdb_id": null, "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "role": "reported_chemical_probe", "source_component_url": null, "source_id": "S05", "source_reported_uncertainty": "0.03", "source_reported_units": "µM", "source_reported_value": "0.24", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "temperature_C": 25, "uncertainty": 0.03, "uncertainty_type": "SD", "uncertainty_uM": 0.03, "unit_conversion": null, "units": "µM", "value": 0.24, "value_operator": "=", "value_uM": 0.24, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "0.03", "source_reported_units": "µM", "source_reported_value": "0.24", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.03, "uncertainty_type": "SD", "uncertainty_uM": 0.03, "unit_conversion": null, "units": "µM", "value": 0.24, "value_operator": "=", "value_uM": 0.24, "verification_level": "primary_full_text_sections_verified" }, { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 350, "assay_construct_start": 211, "assay_record_id": "PWWP:ASSAY:0021", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_name": "UNC6934", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 211–350\", \"purified_tags\": \"N-terminal GS remnant; C-terminal Avi; biotinylated after GST/6His removal\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Table 1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD2", "interpretation": "Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.", "is_measured": true, "is_negative": false, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 1.33, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": 7.5, "pdb_id": null, "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "publication_year": 2025, "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "role": "reported_chemical_probe", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S05", "source_measurement_key": "5c3b0577823f4dad06be18dce48cded60d31905a2adf864071aa56e64dcad6a9", "source_original": { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 350, "assay_construct_start": 211, "assay_record_id": "PWWP:ASSAY:0021", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "UNC6934", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 211–350\", \"purified_tags\": \"N-terminal GS remnant; C-terminal Avi; biotinylated after GST/6His removal\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Table 1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD2", "interpretation": "Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": 7.5, "pdb_id": null, "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "role": "reported_chemical_probe", "source_component_url": null, "source_id": "S05", "source_reported_uncertainty": "0.19", "source_reported_units": "µM", "source_reported_value": "1.33", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "temperature_C": 25, "uncertainty": 0.19, "uncertainty_type": "SD", "uncertainty_uM": 0.19, "unit_conversion": null, "units": "µM", "value": 1.33, "value_operator": "=", "value_uM": 1.33, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "0.19", "source_reported_units": "µM", "source_reported_value": "1.33", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.19, "uncertainty_type": "SD", "uncertainty_uM": 0.19, "unit_conversion": null, "units": "µM", "value": 1.33, "value_operator": "=", "value_uM": 1.33, "verification_level": "primary_full_text_sections_verified" }, { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 398, "assay_construct_start": 263, "assay_record_id": "PWWP11:ASSAY:0001", "assay_type": "SPR Kd counter-screen", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": null, "baseline_assay_record": 0, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "V01", "ccd_mapping_source": null, "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_name": "UNC6934", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD3 263–398\", \"purified_tags\": \"N-terminal 6His-TEV retained\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:Q9BZ95:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "censored_binding_limit", "evidence_location": "Table 1 NSD3 (263–398) column", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD3", "interpretation": "Single counter-target experiment; not evidence of proteome-wide selectivity. No-binding rows have no inferred numerical threshold.", "is_measured": true, "is_negative": true, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": null, "numeric_transcription_status": "matches_primary_table", "numeric_value_inferred_from_structure": null, "organism": "Homo sapiens", "pH": 7.5, "pdb_id": null, "preparation_id": "PREP:UNC6934", "protein_id": "UP:Q9BZ95", "publication_year": 2025, "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. 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unit; heavy atoms with occupancy >0; alternate locations retained; no symmetry expansion", "instance": { "alternate_locations": "[]", "auth_asym_ids": "[\"C\"]", "auth_seq_id": "401", "ccd_id": "V01", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "component_context": "nonpolymer_component", "contacted_polymer_partners": "[{\"description\": \"Histone-lysine N-methyltransferase NSD2\", \"entity_id\": \"1\", \"is_PWWP_family_protein\": true, \"label_asym_id\": \"C\", \"sequence_length\": 141, \"uniprot_ids\": [\"O96028\"]}]", "covalent_connection_ids": "[]", "heavy_atom_row_count": 33, "ideal_CCD_SDF_is_source_pose": 0, "label_asym_id": "I", "label_seq_id": null, "ligand_instance_id": "PDB:6XCG:LIG:I:V01:401:.", "nearest_polypeptide_distance_angstrom": 2.794, "nearest_polypeptide_label_asym_id": "C", "occupancy_max": 1.0, "occupancy_min": 1.0, "pdb_id": "6XCG", "polypeptide_contact_residues_5A": "[{\"auth_asym_id\": \"C\", \"auth_seq_id\": \"230\", \"component\": \"VAL\", \"entity_position\": 21, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 3.7533, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"233\", \"component\": \"TYR\", \"entity_position\": 24, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 3.326, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"236\", \"component\": \"TRP\", \"entity_position\": 27, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 3.5912, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"266\", \"component\": \"PHE\", \"entity_position\": 57, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 3.1984, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"267\", \"component\": \"PHE\", \"entity_position\": 58, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 3.2908, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"268\", \"component\": \"GLY\", \"entity_position\": 59, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 3.1601, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"269\", \"component\": \"ASP\", \"entity_position\": 60, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 3.206, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"270\", \"component\": \"ALA\", \"entity_position\": 61, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 2.9688, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"271\", \"component\": \"PRO\", \"entity_position\": 62, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 4.4163, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"272\", \"component\": \"GLU\", \"entity_position\": 63, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 3.4199, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"273\", \"component\": \"ARG\", \"entity_position\": 64, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 2.886, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"274\", \"component\": \"ALA\", \"entity_position\": 65, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 3.7615, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"318\", \"component\": \"LEU\", \"entity_position\": 109, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 3.3244, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"321\", \"component\": \"GLN\", \"entity_position\": 112, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 2.794, \"uniprot_position\": null}]", "pose_kind": "deposited_source_coordinates", "reference_model": "1", "source_coordinate_file": "Structures/NSD2__HUMAN__O96028/Co-Crystals/6XCG/original.cif", "source_coordinate_sha256": "2c370701c9b83de7ae6137f91d2130519a48c261a93ec5bc480dfcc3bc982200", "unique_heavy_atom_names": 33 }, "ligand_instance_id": "PDB:6XCG:LIG:I:V01:401:.", "ligand_label_asym_id": "I", "minimum_Pfam_distance_angstrom": 2.794, "minimum_chain_distance_angstrom": 2.794, "minimum_core_distance_angstrom": 2.886, "multiple_contacting_mapped_chains": 0, "pdb_id": "6XCG", "protein_id": "UP:O96028", "protein_label_asym_id": "C", "rank_interpretation": "Distance rank among mapped chains only; crystal packing and biological site assignment require separate review.", "role": "experimentally studied ligand", "role_category": "functional", "site_id": "PDB:6XCG:LIG:I:V01:401:.:SITE:UP:O96028:PWWP1:C", "source_coordinate_sha256": "2c370701c9b83de7ae6137f91d2130519a48c261a93ec5bc480dfcc3bc982200" } ], "context_assay_count": 6, "context_measured_count": 6, "context_bound_count": 1, "context_pdb_count": 1, "context_negative_count": 1, "context_is_probe": true, "context_bioactivity_only": false, "context_kind": "Measured + bound structure", "science": { "studied_compound": true, "measured_count": 6, "structural_research_ligand": true, "research_pdb_count": 1, "other_component": false, "component_site_count": 0, "verification_queue": false, "positive_direct_binder": true, "reported_probe": true, "reported_control": false, "cellular_activity": true, "protein_degradation": false, "bioactivity_only": false, "research_site_count": 3, "unknown_site_count": 0, "annotation_roles": [ "studied", "structural" ] }, "science_label": "Studied + deposited research ligand", "science_profile": { "annotation_roles": [ "studied", "structural" ], "cellular_activity": true, "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "entity_kind": "chemical_identity", "identity_resolved": true, "measured_observation_count": 6, "name": "UNC6934", "other_pdb_component": false, "other_site_count": 0, "positive_direct_binder": true, "primary_view": "studied", "protein_degradation": false, "reported_control": false, "reported_probe": true, "rule": "Independent source observations + per-site coordinate role, not universal pharmacology", "source_observation_ids": [ "PWWP:ASSAY:0021", "PWWP:ASSAY:0014", "PWWP11:ASSAY:0001", "PWWP:ASSAY:0004", "PWWP:ASSAY:0005", "PWWP:ASSAY:0006" ], "source_site_ids": [ "PDB:6XCG:LIG:D:V01:401:.:SITE:UP:O96028:PWWP1:A", "PDB:6XCG:LIG:E:V01:401:.:SITE:UP:O96028:PWWP1:B", "PDB:6XCG:LIG:I:V01:401:.:SITE:UP:O96028:PWWP1:C" ], "structural_research_ligand": true, "structural_research_site_count": 3, "studied_compound": true, "total_observation_count": 6, "uncertain_site_count": 0, "uncertainty": "Classification is evidence- and experiment-scoped; missing assays do not prove nonbinding.", "verification_queue": false, "verification_status": "source_scoped_mixed" }, "science_site_roles": { "PDB:6XCG:LIG:D:V01:401:.:SITE:UP:O96028:PWWP1:A": { "ccd_url": "https://www.rcsb.org/ligand/V01", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "contact_class": "native_annotation_core_contact", "coordinate_sha256": "2c370701c9b83de7ae6137f91d2130519a48c261a93ec5bc480dfcc3bc982200", "domain_id": "UP:O96028:PWWP1", "exact_pwwp_contact": true, "ligand_instance_id": "PDB:6XCG:LIG:D:V01:401:.", "observed_other_component": false, "pdb_id": "6XCG", "protein_id": "UP:O96028", "role_code": "reported_studied_structural_ligand", "role_group": "research_ligand", "rule": "Phase5 exact deposited site role, measured heavy-atom contacts and native-domain scope", "site_id": "PDB:6XCG:LIG:D:V01:401:.:SITE:UP:O96028:PWWP1:A", "source_role": "experimentally studied ligand", "source_url": "https://www.rcsb.org/structure/6XCG", "structural_research_ligand": true, "uncertainty": "Role is source-annotated; deposited proximity alone does not establish solution binding or biological activity.", "verification_status": "phase5_derived_deposited_geometry" }, "PDB:6XCG:LIG:E:V01:401:.:SITE:UP:O96028:PWWP1:B": { "ccd_url": "https://www.rcsb.org/ligand/V01", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "contact_class": "native_annotation_core_contact", "coordinate_sha256": "2c370701c9b83de7ae6137f91d2130519a48c261a93ec5bc480dfcc3bc982200", "domain_id": "UP:O96028:PWWP1", "exact_pwwp_contact": true, "ligand_instance_id": "PDB:6XCG:LIG:E:V01:401:.", "observed_other_component": false, "pdb_id": "6XCG", "protein_id": "UP:O96028", "role_code": "reported_studied_structural_ligand", "role_group": "research_ligand", "rule": "Phase5 exact deposited site role, measured heavy-atom contacts and native-domain scope", "site_id": "PDB:6XCG:LIG:E:V01:401:.:SITE:UP:O96028:PWWP1:B", "source_role": "experimentally studied ligand", "source_url": "https://www.rcsb.org/structure/6XCG", "structural_research_ligand": true, "uncertainty": "Role is source-annotated; deposited proximity alone does not establish solution binding or biological activity.", "verification_status": "phase5_derived_deposited_geometry" }, "PDB:6XCG:LIG:I:V01:401:.:SITE:UP:O96028:PWWP1:C": { "ccd_url": "https://www.rcsb.org/ligand/V01", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "contact_class": "native_annotation_core_contact", "coordinate_sha256": "2c370701c9b83de7ae6137f91d2130519a48c261a93ec5bc480dfcc3bc982200", "domain_id": "UP:O96028:PWWP1", "exact_pwwp_contact": true, "ligand_instance_id": "PDB:6XCG:LIG:I:V01:401:.", "observed_other_component": false, "pdb_id": "6XCG", "protein_id": "UP:O96028", "role_code": "reported_studied_structural_ligand", "role_group": "research_ligand", "rule": "Phase5 exact deposited site role, measured heavy-atom contacts and native-domain scope", "site_id": "PDB:6XCG:LIG:I:V01:401:.:SITE:UP:O96028:PWWP1:C", "source_role": "experimentally studied ligand", "source_url": "https://www.rcsb.org/structure/6XCG", "structural_research_ligand": true, "uncertainty": "Role is source-annotated; deposited proximity alone does not establish solution binding or biological activity.", "verification_status": "phase5_derived_deposited_geometry" } }, "science_assay_roles": { "PWWP:ASSAY:0004": { "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_type": "direct_binding", "explicitly_negative": false, "measured": true, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP:ASSAY:0004", "operator": "=", "positive_direct_binder": true, "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "remaining_uncertainty": "SPR temperature and exact uncertainty definition are not specified in the inspected assay-specific source. Triplicate experiments reported. Preparation/assay construct differs from crystallization 211–350.", "reported_cellular": false, "reported_control": false, "reported_probe": true, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "S02", "source_location": "Results; Figures 1–2", "source_role": "reported_chemical_probe", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "studied_compound": true, "target_scope": "domain_specific", "target_variant": null, "units": "nM", "value": 91.0, "verification_status": "primary_full_text_sections_verified" }, "PWWP:ASSAY:0005": { "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "domain_id": "UP:O96028:PWWP1", "endpoint": "IC50", "evidence_type": "biochemical_function", "explicitly_negative": false, "measured": true, "method": "AlphaScreen", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP:ASSAY:0005", "operator": "=", "positive_direct_binder": false, "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "remaining_uncertainty": "23°C is the antagonist preincubation temperature, not a verified readout temperature. Final DMSO fraction and SD-versus-SEM definition for ±13 nM are not explicit in the inspected assay-specific text.", "reported_cellular": false, "reported_control": false, "reported_probe": true, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "S02", "source_location": "Discussion; biochemical characterization", "source_role": "reported_chemical_probe", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "studied_compound": true, "target_scope": "domain_specific", "target_variant": null, "units": "nM", "value": 104.0, "verification_status": "primary_full_text_sections_verified" }, "PWWP:ASSAY:0006": { "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "domain_id": "UP:O96028:PWWP1", "endpoint": "Unstandardized half-response concentration", "evidence_type": "cellular_activity", "explicitly_negative": false, "measured": true, "method": "NanoBRET PPI half-response", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP:ASSAY:0006", "operator": "=", "positive_direct_binder": false, "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "remaining_uncertainty": "NanoLuc construct boundaries, readout temperature and SD-versus-SEM are not explicit in the inspected source. Results say EC50 while Discussion says IC50; neutral half-response label retained.", "reported_cellular": true, "reported_control": false, "reported_probe": true, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "S02", "source_location": "Results: cellular target engagement; Figure 4d", "source_role": "reported_chemical_probe", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "studied_compound": true, "target_scope": "domain_specific", "target_variant": null, "units": "µM", "value": 1.23, "verification_status": "primary_full_text_sections_verified" }, "PWWP:ASSAY:0014": { "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_type": "direct_binding", "explicitly_negative": false, "measured": true, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP:ASSAY:0014", "operator": "=", "positive_direct_binder": true, "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "reported_cellular": false, "reported_control": false, "reported_probe": true, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "S05", "source_location": "Table 1", "source_role": "reported_chemical_probe", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "studied_compound": true, "target_scope": "domain_specific", "target_variant": null, "units": "µM", "value": 0.24, "verification_status": "primary_full_text_sections_verified" }, "PWWP:ASSAY:0021": { "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_type": "direct_binding", "explicitly_negative": false, "measured": true, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP:ASSAY:0021", "operator": "=", "positive_direct_binder": true, "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "reported_cellular": false, "reported_control": false, "reported_probe": true, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "S05", "source_location": "Table 1", "source_role": "reported_chemical_probe", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "studied_compound": true, "target_scope": "domain_specific", "target_variant": null, "units": "µM", "value": 1.33, "verification_status": "primary_full_text_sections_verified" }, "PWWP11:ASSAY:0001": { "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "domain_id": "UP:Q9BZ95:PWWP1", "endpoint": "Kd", "evidence_type": "censored_binding", "explicitly_negative": true, "measured": true, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP11:ASSAY:0001", "operator": ">", "positive_direct_binder": false, "preparation_id": "PREP:UNC6934", "protein_id": "UP:Q9BZ95", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "reported_cellular": false, "reported_control": false, "reported_probe": false, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "S05", "source_location": "Table 1 NSD3 (263–398) column", "source_role": "counter_target_assay", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "studied_compound": true, "target_scope": "domain_specific", "target_variant": null, "units": "µM", "value": 30.0, "verification_status": "source_scope_unresolved" } }, "example": { "DMSO_percent": 0.5, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0004", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.05% Tween-20; 0.5% DMSO", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_name": "UNC6934", "conditions": "{\"phase3_verification\": \"SV02A\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"AviTag/NSD2(208–368)/polyhistidine; biotinylated\", \"source_protocol_highest_concentration_uM\": 2}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Results; Figures 1–2", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": null, "is_measured": true, "is_negative": false, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 0.091, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": 7.4, "pdb_id": "6XCG", "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "publication_year": 2022, "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "SPR temperature and exact uncertainty definition are not specified in the inspected assay-specific source. Triplicate experiments reported. Preparation/assay construct differs from crystallization 211–350.", "replicates": "3 (triplicate experiments; independence level not specified)", "role": "reported_chemical_probe", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S02", "source_measurement_key": "7c16700328b32cfd3cd5e66dec0c4ccaa8b2dca48c21be5b56df68be8add7388", "source_original": { "DMSO_percent": 0.5, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0004", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.05% Tween-20; 0.5% DMSO", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "UNC6934", "conditions": "{\"phase3_verification\": \"SV02A\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"AviTag/NSD2(208–368)/polyhistidine; biotinylated\", \"source_protocol_highest_concentration_uM\": 2}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Results; Figures 1–2", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": null, "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": 7.4, "pdb_id": "6XCG", "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "SPR temperature and exact uncertainty definition are not specified in the inspected assay-specific source. Triplicate experiments reported. Preparation/assay construct differs from crystallization 211–350.", "replicates": "3 (triplicate experiments; independence level not specified)", "role": "reported_chemical_probe", "source_component_url": null, "source_id": "S02", "source_reported_uncertainty": "8", "source_reported_units": "nM", "source_reported_value": "91", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "temperature_C": null, "uncertainty": 8.0, "uncertainty_type": null, "uncertainty_uM": 0.008, "unit_conversion": null, "units": "nM", "value": 91.0, "value_operator": "=", "value_uM": 0.091, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "8", "source_reported_units": "nM", "source_reported_value": "91", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 8.0, "uncertainty_type": null, "uncertainty_uM": 0.008, "unit_conversion": null, "units": "nM", "value": 91.0, "value_operator": "=", "value_uM": 0.091, "verification_level": "primary_full_text_sections_verified" }, "matched_observations": [ { "DMSO_percent": 0.5, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0004", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.05% Tween-20; 0.5% DMSO", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_name": "UNC6934", "conditions": "{\"phase3_verification\": \"SV02A\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"AviTag/NSD2(208–368)/polyhistidine; biotinylated\", \"source_protocol_highest_concentration_uM\": 2}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Results; Figures 1–2", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": null, "is_measured": true, "is_negative": false, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 0.091, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": 7.4, "pdb_id": "6XCG", "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "publication_year": 2022, "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "SPR temperature and exact uncertainty definition are not specified in the inspected assay-specific source. Triplicate experiments reported. Preparation/assay construct differs from crystallization 211–350.", "replicates": "3 (triplicate experiments; independence level not specified)", "role": "reported_chemical_probe", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S02", "source_measurement_key": "7c16700328b32cfd3cd5e66dec0c4ccaa8b2dca48c21be5b56df68be8add7388", "source_original": { "DMSO_percent": 0.5, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0004", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.05% Tween-20; 0.5% DMSO", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "UNC6934", "conditions": "{\"phase3_verification\": \"SV02A\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"AviTag/NSD2(208–368)/polyhistidine; biotinylated\", \"source_protocol_highest_concentration_uM\": 2}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Results; Figures 1–2", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": null, "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": 7.4, "pdb_id": "6XCG", "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "SPR temperature and exact uncertainty definition are not specified in the inspected assay-specific source. Triplicate experiments reported. Preparation/assay construct differs from crystallization 211–350.", "replicates": "3 (triplicate experiments; independence level not specified)", "role": "reported_chemical_probe", "source_component_url": null, "source_id": "S02", "source_reported_uncertainty": "8", "source_reported_units": "nM", "source_reported_value": "91", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "temperature_C": null, "uncertainty": 8.0, "uncertainty_type": null, "uncertainty_uM": 0.008, "unit_conversion": null, "units": "nM", "value": 91.0, "value_operator": "=", "value_uM": 0.091, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "8", "source_reported_units": "nM", "source_reported_value": "91", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 8.0, "uncertainty_type": null, "uncertainty_uM": 0.008, "unit_conversion": null, "units": "nM", "value": 91.0, "value_operator": "=", "value_uM": 0.091, "verification_level": "primary_full_text_sections_verified" }, { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0005", "assay_type": "AlphaScreen IC50", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "150 mM NaCl; 20 mM Tris; 0.01% BSA; 0.01% NP-40; 1 mM DTT (DTT omitted from bead buffer)", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_name": "UNC6934", "conditions": "{\"phase3_verification\": \"SV02A\", \"protein_construct\": \"NSD2 208–368\", \"readout\": \"His-NSD2-PWWP1 binding to H3K36me2 designer nucleosome\", \"tag\": \"6His\", \"temperature_scope\": \"23°C compound/protein and nucleosome preincubation; bead incubation room temperature\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint": "IC50", "endpoint_label_status": null, "evidence_class": "biochemical_interaction_inhibition", "evidence_location": "Discussion; biochemical characterization", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": "Binding-interaction assay, not a direct catalytic SET-domain inhibition measurement.", "is_measured": true, "is_negative": false, "method": "AlphaScreen", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 0.10400000000000001, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": 7.5, "pdb_id": "6XCG", "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "publication_year": 2022, "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "23°C is the antagonist preincubation temperature, not a verified readout temperature. Final DMSO fraction and SD-versus-SEM definition for ±13 nM are not explicit in the inspected assay-specific text.", "replicates": "3 independent experiments; each 10-point curve in duplicate", "role": "reported_chemical_probe", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S02", "source_measurement_key": "ebb1bfa66d69be833d6a30c211d24a8fda7200d43b65ab3b9be6418909d92987", "source_original": { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0005", "assay_type": "AlphaScreen IC50", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "150 mM NaCl; 20 mM Tris; 0.01% BSA; 0.01% NP-40; 1 mM DTT (DTT omitted from bead buffer)", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "UNC6934", "conditions": "{\"phase3_verification\": \"SV02A\", \"protein_construct\": \"NSD2 208–368\", \"readout\": \"His-NSD2-PWWP1 binding to H3K36me2 designer nucleosome\", \"tag\": \"6His\", \"temperature_scope\": \"23°C compound/protein and nucleosome preincubation; bead incubation room temperature\"}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": null, "evidence_class": "biochemical_interaction_inhibition", "evidence_location": "Discussion; biochemical characterization", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": "Binding-interaction assay, not a direct catalytic SET-domain inhibition measurement.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": 7.5, "pdb_id": "6XCG", "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "23°C is the antagonist preincubation temperature, not a verified readout temperature. Final DMSO fraction and SD-versus-SEM definition for ±13 nM are not explicit in the inspected assay-specific text.", "replicates": "3 independent experiments; each 10-point curve in duplicate", "role": "reported_chemical_probe", "source_component_url": null, "source_id": "S02", "source_reported_uncertainty": "13", "source_reported_units": "nM", "source_reported_value": "104", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "temperature_C": 23, "uncertainty": 13.0, "uncertainty_type": null, "uncertainty_uM": 0.013, "unit_conversion": null, "units": "nM", "value": 104.0, "value_operator": "=", "value_uM": 0.104, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "13", "source_reported_units": "nM", "source_reported_value": "104", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "target_scope": "domain_specific", "temperature_C": 23, "uncertainty": 13.0, "uncertainty_type": null, "uncertainty_uM": 0.013, "unit_conversion": null, "units": "nM", "value": 104.0, "value_operator": "=", "value_uM": 0.104, "verification_level": "primary_full_text_sections_verified" }, { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP:ASSAY:0006", "assay_type": "NanoBRET PPI half-response", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "DMEM/F12 without phenol red; 4% FBS; 100 U/mL penicillin; 100 ug/mL streptomycin", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_name": "UNC6934", "conditions": "{\"cell_line\": \"U2OS\", \"readout\": \"NSD2 PWWP1–histone H3.3 interaction\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint": "Unstandardized half-response concentration", "endpoint_label_status": "Results/Figure use EC50, Discussion uses IC50; neutral half-response retained", "evidence_class": "cellular_interaction_response", "evidence_location": "Results: cellular target engagement; Figure 4d", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": "Main Results calls this EC50; Discussion calls it IC50. Original value retained without conflating it with Kd.", "is_measured": true, "is_negative": false, "method": "NanoBRET PPI half-response", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": null, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": null, "pdb_id": "6XCG", "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "publication_year": 2022, "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "NanoLuc construct boundaries, readout temperature and SD-versus-SEM are not explicit in the inspected source. Results say EC50 while Discussion says IC50; neutral half-response label retained.", "replicates": "3 independent replicates", "role": "reported_chemical_probe", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S02", "source_measurement_key": "73dd58f0b5956416fa5d2f849b2939bcaf1b614b24b1131628947441ac92994c", "source_original": { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP:ASSAY:0006", "assay_type": "NanoBRET PPI half-response", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "DMEM/F12 without phenol red; 4% FBS; 100 U/mL penicillin; 100 ug/mL streptomycin", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "UNC6934", "conditions": "{\"cell_line\": \"U2OS\", \"readout\": \"NSD2 PWWP1–histone H3.3 interaction\"}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": "Results/Figure use EC50, Discussion uses IC50; neutral half-response retained", "evidence_class": "cellular_interaction_response", "evidence_location": "Results: cellular target engagement; Figure 4d", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": "Main Results calls this EC50; Discussion calls it IC50. Original value retained without conflating it with Kd.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": null, "pdb_id": "6XCG", "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "NanoLuc construct boundaries, readout temperature and SD-versus-SEM are not explicit in the inspected source. Results say EC50 while Discussion says IC50; neutral half-response label retained.", "replicates": "3 independent replicates", "role": "reported_chemical_probe", "source_component_url": null, "source_id": "S02", "source_reported_uncertainty": "0.25", "source_reported_units": "µM", "source_reported_value": "1.23", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "temperature_C": null, "uncertainty": 0.25, "uncertainty_type": null, "uncertainty_uM": 0.25, "unit_conversion": null, "units": "µM", "value": 1.23, "value_operator": "=", "value_uM": 1.23, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "0.25", "source_reported_units": "µM", "source_reported_value": "1.23", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 0.25, "uncertainty_type": null, "uncertainty_uM": 0.25, "unit_conversion": null, "units": "µM", "value": 1.23, "value_operator": "=", "value_uM": 1.23, "verification_level": "primary_full_text_sections_verified" }, { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0014", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_name": "UNC6934", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Table 1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD2", "interpretation": "Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.", "is_measured": true, "is_negative": false, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 0.24, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": 7.5, "pdb_id": null, "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "publication_year": 2025, "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "role": "reported_chemical_probe", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S05", "source_measurement_key": "b6a422c24a429b6fecbccb8c4722557675fbd65bfeca995764913f27fe18a750", "source_original": { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0014", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "UNC6934", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Table 1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD2", "interpretation": "Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": 7.5, "pdb_id": null, "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "role": "reported_chemical_probe", "source_component_url": null, "source_id": "S05", "source_reported_uncertainty": "0.03", "source_reported_units": "µM", "source_reported_value": "0.24", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "temperature_C": 25, "uncertainty": 0.03, "uncertainty_type": "SD", "uncertainty_uM": 0.03, "unit_conversion": null, "units": "µM", "value": 0.24, "value_operator": "=", "value_uM": 0.24, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "0.03", "source_reported_units": "µM", "source_reported_value": "0.24", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.03, "uncertainty_type": "SD", "uncertainty_uM": 0.03, "unit_conversion": null, "units": "µM", "value": 0.24, "value_operator": "=", "value_uM": 0.24, "verification_level": "primary_full_text_sections_verified" }, { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 350, "assay_construct_start": 211, "assay_record_id": "PWWP:ASSAY:0021", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_name": "UNC6934", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 211–350\", \"purified_tags\": \"N-terminal GS remnant; C-terminal Avi; biotinylated after GST/6His removal\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Table 1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD2", "interpretation": "Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.", "is_measured": true, "is_negative": false, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 1.33, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": 7.5, "pdb_id": null, "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "publication_year": 2025, "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "role": "reported_chemical_probe", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S05", "source_measurement_key": "5c3b0577823f4dad06be18dce48cded60d31905a2adf864071aa56e64dcad6a9", "source_original": { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 350, "assay_construct_start": 211, "assay_record_id": "PWWP:ASSAY:0021", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "UNC6934", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 211–350\", \"purified_tags\": \"N-terminal GS remnant; C-terminal Avi; biotinylated after GST/6His removal\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Table 1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD2", "interpretation": "Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": 7.5, "pdb_id": null, "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "role": "reported_chemical_probe", "source_component_url": null, "source_id": "S05", "source_reported_uncertainty": "0.19", "source_reported_units": "µM", "source_reported_value": "1.33", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "temperature_C": 25, "uncertainty": 0.19, "uncertainty_type": "SD", "uncertainty_uM": 0.19, "unit_conversion": null, "units": "µM", "value": 1.33, "value_operator": "=", "value_uM": 1.33, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "0.19", "source_reported_units": "µM", "source_reported_value": "1.33", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.19, "uncertainty_type": "SD", "uncertainty_uM": 0.19, "unit_conversion": null, "units": "µM", "value": 1.33, "value_operator": "=", "value_uM": 1.33, "verification_level": "primary_full_text_sections_verified" }, { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 398, "assay_construct_start": 263, "assay_record_id": "PWWP11:ASSAY:0001", "assay_type": "SPR Kd counter-screen", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": null, "baseline_assay_record": 0, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "V01", "ccd_mapping_source": null, "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_name": "UNC6934", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD3 263–398\", \"purified_tags\": \"N-terminal 6His-TEV retained\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:Q9BZ95:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "censored_binding_limit", "evidence_location": "Table 1 NSD3 (263–398) column", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD3", "interpretation": "Single counter-target experiment; not evidence of proteome-wide selectivity. No-binding rows have no inferred numerical threshold.", "is_measured": true, "is_negative": true, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": null, "numeric_transcription_status": "matches_primary_table", "numeric_value_inferred_from_structure": null, "organism": "Homo sapiens", "pH": 7.5, "pdb_id": null, "preparation_id": "PREP:UNC6934", "protein_id": "UP:Q9BZ95", "publication_year": 2025, "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "role": "counter_target_assay", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S05", "source_measurement_key": "2d3d8be2eecdc71ef0bde5c1fc786cdfa6964ffc519e5f0b9249d5da8d89d31a", "source_original": { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 398, "assay_construct_start": 263, "assay_record_id": "PWWP11:ASSAY:0001", "assay_type": "SPR Kd counter-screen", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": null, "baseline_assay_record": 0, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "V01", "ccd_mapping_source": null, "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "UNC6934", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD3 263–398\", \"purified_tags\": \"N-terminal 6His-TEV retained\"}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:Q9BZ95:PWWP1", "endpoint_label_status": null, "evidence_class": "censored_binding_limit", "evidence_location": "Table 1 NSD3 (263–398) column", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD3", "interpretation": "Single counter-target experiment; not evidence of proteome-wide selectivity. No-binding rows have no inferred numerical threshold.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_table", "numeric_value_inferred_from_structure": null, "pH": 7.5, "pdb_id": null, "preparation_id": "PREP:UNC6934", "protein_id": "UP:Q9BZ95", "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. 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specific Figure S2 assay method remains unresolved.", "replicates": null, "role": "experimentally_studied_fragment_ligand", "source_component_url": null, "source_id": "S04", "source_reported_uncertainty": "2", "source_reported_units": "µM", "source_reported_value": "14", "source_verification_scope": "primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved", "temperature_C": null, "uncertainty": 2.0, "uncertainty_type": "fitting_error", "uncertainty_uM": 2.0, "unit_conversion": null, "units": "µM", "value": 14.0, "value_operator": "=", "value_uM": 14.0, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "2", "source_reported_units": "µM", "source_reported_value": "14", "source_verification_scope": "primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 2.0, "uncertainty_type": "fitting_error", "uncertainty_uM": 2.0, "unit_conversion": null, "units": "µM", "value": 14.0, "value_operator": "=", "value_uM": 14.0, "verification_level": "primary_full_text_sections_verified" }, { "assay_construct_end": 93, "assay_construct_start": 1, "assay_context": "purified_mutant_domain", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0028", "assay_type": "NMR chemical-shift perturbation Kd", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_name": "BPP", "conditions": { "binding_model": "1:1 global fit of perturbed residues", "buffer": "HEPES-buffered saline; CSP subsection does not separately give HEPES/NaCl concentrations", "ligand_protein_molar_ratio_range": [ 0, 6 ], "pH": 7.4, "protein_concentration_mM": 0.1, "target_variant": "Y18S" }, "curation_version": "phase5-1.0.0", "domain": "PWWP1", "domain_id": "UP:Q7Z4V5:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_location": "Results; Figure 3D", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "HDGFL2", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_measured": true, "is_negative": false, "method": "NMR chemical-shift perturbation", "normalized_exact_uM": 290.0, "numeric_transcription_status": "source_preserved", "numeric_value_inferred_from_structure": false, "organism": "Homo sapiens", "pH": 7.4, "pdb_id": null, "preparation_id": "PREP:BPP", "protein_id": "UP:Q7Z4V5", "publication_year": 2024, "reference_id": "PMID:39031937", "remaining_uncertainty": "Y18S mutant measurement; must not be pooled with wild-type affinity. Construct is the source HDGFRP2 PWWP expression fragment (1–93) carrying the stated mutation. Replicate number and titration-specific temperature are not independently specified.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_database": "Primary literature (Phase 5)", "source_id": "P5:S:WEI2024", "source_measurement_key": "9d30a9d0eb5e0c4aeafe0b022d48c9264242ab9e5b5210df4a0778575e81cdcd", "source_original": { "assay_construct_end": 93, "assay_construct_start": 1, "assay_context": "purified_mutant_domain", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0028", "assay_type": "NMR chemical-shift perturbation Kd", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_name": "BPP", "conditions": { "binding_model": "1:1 global fit of perturbed residues", "buffer": "HEPES-buffered saline; CSP subsection does not separately give HEPES/NaCl concentrations", "ligand_protein_molar_ratio_range": [ 0, 6 ], "pH": 7.4, "protein_concentration_mM": 0.1, "target_variant": "Y18S" }, "domain": "PWWP1", "domain_id": "UP:Q7Z4V5:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_location": "Results; Figure 3D", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "HDGFL2", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_negative": false, "numeric_transcription_status": "source_preserved", "numeric_value_inferred_from_structure": false, "pH": 7.4, "pdb_id": null, "preparation_id": "PREP:BPP", "protein_id": "UP:Q7Z4V5", "publication_year": 2024, "reference_id": "PMID:39031937", "remaining_uncertainty": "Y18S mutant measurement; must not be pooled with wild-type affinity. Construct is the source HDGFRP2 PWWP expression fragment (1–93) carrying the stated mutation. Replicate number and titration-specific temperature are not independently specified.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_id": "P5:S:WEI2024", "source_reported_uncertainty": "0.02", "source_reported_units": "mM", "source_reported_value": "0.29", "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "target_variant": "Y18S", "uncertainty": 0.02, "uncertainty_type": "fitting error", "uncertainty_uM": 20.0, "unit_conversion": "mM × 1000 = µM", "units": "mM", "value": 0.29, "value_operator": "=", "value_uM": 290.0, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" }, "source_reported_uncertainty": "0.02", "source_reported_units": "mM", "source_reported_value": "0.29", "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "target_scope": "domain_specific", "target_variant": "Y18S", "uncertainty": 0.02, "uncertainty_type": "fitting error", "uncertainty_uM": 20.0, "unit_conversion": "mM × 1000 = µM", "units": "mM", "value": 0.29, "value_operator": "=", "value_uM": 290.0, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" }, { "assay_construct_end": null, "assay_construct_start": null, "assay_context": "purified_domain", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0029", "assay_type": "Binding selectivity; assay method not verified in Figure S2", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_name": "BPP", "conditions": {}, "curation_version": "phase5-1.0.0", "domain": "PWWP1", "domain_id": "UP:Q49A26:PWWP1", "endpoint": "qualitative", "evidence_class": "qualitative_binding", "evidence_location": "Results: selectivity paragraph referring to Figure S2", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "GLYR1", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_measured": true, "is_negative": true, "method": "Binding selectivity; assay method not verified in Figure S2", "negative_evidence_scope": "Non-detectable binding in the source experimental comparison; assay limits not recovered.", "normalized_exact_uM": null, "numeric_transcription_status": "qualitative_or_not_reported", "numeric_value_inferred_from_structure": false, "organism": "Homo sapiens", "pdb_id": null, "preparation_id": "PREP:BPP", "protein_id": "UP:Q49A26", "publication_year": 2024, "qualitative_result": "Source reports non-detectable affinity in the tested selectivity comparison.", "reference_id": "PMID:39031937", "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_database": "Primary literature (Phase 5)", "source_id": "P5:S:WEI2024", "source_measurement_key": "1bb84a49b8cfa231e7556fd293906f4c077290f112c8295d63faa44bcc59ca3e", "source_original": { "assay_construct_end": null, "assay_construct_start": null, "assay_context": "purified_domain", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0029", "assay_type": "Binding selectivity; assay method not verified in Figure S2", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_name": "BPP", "conditions": {}, "domain": "PWWP1", "domain_id": "UP:Q49A26:PWWP1", "endpoint": "qualitative", "evidence_class": "qualitative_binding", "evidence_location": "Results: selectivity paragraph referring to Figure S2", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "GLYR1", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_negative": true, "negative_evidence_scope": "Non-detectable binding in the source experimental comparison; assay limits not recovered.", "numeric_transcription_status": "qualitative_or_not_reported", "numeric_value_inferred_from_structure": false, "pdb_id": null, "preparation_id": "PREP:BPP", "protein_id": "UP:Q49A26", "publication_year": 2024, "qualitative_result": "Source reports non-detectable affinity in the tested selectivity comparison.", "reference_id": "PMID:39031937", "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_id": "P5:S:WEI2024", "source_reported_uncertainty": null, "source_reported_units": null, "source_reported_value": null, "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "uncertainty": null, "uncertainty_type": null, "uncertainty_uM": null, "units": null, "value": null, "value_operator": null, "value_uM": null, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" }, "source_reported_uncertainty": null, "source_reported_units": null, "source_reported_value": null, "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "target_scope": "domain_specific", "uncertainty": null, "uncertainty_type": null, "uncertainty_uM": null, "units": null, "value": null, "value_operator": null, "value_uM": null, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" }, { "assay_construct_end": null, "assay_construct_start": null, "assay_context": "purified_domain", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0030", "assay_type": "Binding selectivity; assay method not verified in Figure S2", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_name": "BPP", "conditions": {}, "curation_version": "phase5-1.0.0", "domain": "PWWP1", "domain_id": "UP:P55201:PWWP1", "endpoint": "qualitative", "evidence_class": "qualitative_binding", "evidence_location": "Results: selectivity paragraph referring to Figure S2", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "BRPF1", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_measured": true, "is_negative": true, "method": "Binding selectivity; assay method not verified in Figure S2", "negative_evidence_scope": "Non-detectable binding in the source experimental comparison; assay limits not recovered.", "normalized_exact_uM": null, "numeric_transcription_status": "qualitative_or_not_reported", "numeric_value_inferred_from_structure": false, "organism": "Homo sapiens", "pdb_id": null, "preparation_id": "PREP:BPP", "protein_id": "UP:P55201", "publication_year": 2024, "qualitative_result": "Source reports non-detectable affinity in the tested selectivity comparison.", "reference_id": "PMID:39031937", "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_database": "Primary literature (Phase 5)", "source_id": "P5:S:WEI2024", "source_measurement_key": "8b0073aae5fc1c92500107f909e335ed9da0b5cd65e6267735d56dfaa9bcf493", "source_original": { "assay_construct_end": null, "assay_construct_start": null, "assay_context": "purified_domain", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0030", "assay_type": "Binding selectivity; assay method not verified in Figure S2", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_name": "BPP", "conditions": {}, "domain": "PWWP1", "domain_id": "UP:P55201:PWWP1", "endpoint": "qualitative", "evidence_class": "qualitative_binding", "evidence_location": "Results: selectivity paragraph referring to Figure S2", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "BRPF1", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_negative": true, "negative_evidence_scope": "Non-detectable binding in the source experimental comparison; assay limits not recovered.", "numeric_transcription_status": "qualitative_or_not_reported", "numeric_value_inferred_from_structure": false, "pdb_id": null, "preparation_id": "PREP:BPP", "protein_id": "UP:P55201", "publication_year": 2024, "qualitative_result": "Source reports non-detectable affinity in the tested selectivity comparison.", "reference_id": "PMID:39031937", "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_id": "P5:S:WEI2024", "source_reported_uncertainty": null, "source_reported_units": null, "source_reported_value": null, "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "uncertainty": null, "uncertainty_type": null, "uncertainty_uM": null, "units": null, "value": null, "value_operator": null, "value_uM": null, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" }, "source_reported_uncertainty": null, "source_reported_units": null, "source_reported_value": null, "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "target_scope": "domain_specific", "uncertainty": null, "uncertainty_type": null, "uncertainty_uM": null, "units": null, "value": null, "value_operator": null, "value_uM": null, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" }, { "assay_construct_end": null, "assay_construct_start": null, "assay_context": "purified_domain", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0031", "assay_type": "Binding selectivity; assay method not verified in Figure S2", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_name": "BPP", "conditions": {}, "curation_version": "phase5-1.0.0", "domain": "PWWP1", "domain_id": "UP:Q9UBC3:PWWP1", "endpoint": "qualitative", "evidence_class": "qualitative_binding", "evidence_location": "Results: selectivity paragraph referring to Figure S2", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "DNMT3B", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_measured": true, "is_negative": true, "method": "Binding selectivity; assay method not verified in Figure S2", "negative_evidence_scope": "Non-detectable binding in the source experimental comparison; assay limits not recovered.", "normalized_exact_uM": null, "numeric_transcription_status": "qualitative_or_not_reported", "numeric_value_inferred_from_structure": false, "organism": "Homo sapiens", "pdb_id": null, "preparation_id": "PREP:BPP", "protein_id": "UP:Q9UBC3", "publication_year": 2024, "qualitative_result": "Source reports non-detectable affinity in the tested selectivity comparison.", "reference_id": "PMID:39031937", "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_database": "Primary literature (Phase 5)", "source_id": "P5:S:WEI2024", "source_measurement_key": "acc240f8b47f7ec0bf4cba699326f80d34b983774139f69e6474e0dbda1a9fa9", "source_original": { "assay_construct_end": null, "assay_construct_start": null, "assay_context": "purified_domain", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0031", "assay_type": "Binding selectivity; assay method not verified in Figure S2", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_name": "BPP", "conditions": {}, "domain": "PWWP1", "domain_id": "UP:Q9UBC3:PWWP1", "endpoint": "qualitative", "evidence_class": "qualitative_binding", "evidence_location": "Results: selectivity paragraph referring to Figure S2", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "DNMT3B", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_negative": true, "negative_evidence_scope": "Non-detectable binding in the source experimental comparison; assay limits not recovered.", "numeric_transcription_status": "qualitative_or_not_reported", "numeric_value_inferred_from_structure": false, "pdb_id": null, "preparation_id": "PREP:BPP", "protein_id": "UP:Q9UBC3", "publication_year": 2024, "qualitative_result": "Source reports non-detectable affinity in the tested selectivity comparison.", "reference_id": "PMID:39031937", "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_id": "P5:S:WEI2024", "source_reported_uncertainty": null, "source_reported_units": null, "source_reported_value": null, "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "uncertainty": null, "uncertainty_type": null, "uncertainty_uM": null, "units": null, "value": null, "value_operator": null, "value_uM": null, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" }, "source_reported_uncertainty": null, "source_reported_units": null, "source_reported_value": null, "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "target_scope": "domain_specific", "uncertainty": null, "uncertainty_type": null, "uncertainty_uM": null, "units": null, "value": null, "value_operator": null, "value_uM": null, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" }, { "assay_construct_end": null, "assay_construct_start": null, "assay_context": "purified_PWWP_domain_unspecified_instance", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0032", "assay_type": "Binding selectivity; assay method not verified in Figure S2", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_name": "BPP", "conditions": {}, "curation_version": "phase5-1.0.0", "domain": null, "domain_id": null, "endpoint": "qualitative", "evidence_class": "qualitative_binding", "evidence_location": "Results: selectivity paragraph referring to Figure S2", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "NSD2", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_measured": true, "is_negative": true, "method": "Binding selectivity; assay method not verified in Figure S2", "negative_evidence_scope": "Non-detectable binding in the source experimental comparison; assay limits not recovered.", "normalized_exact_uM": null, "numeric_transcription_status": "qualitative_or_not_reported", "numeric_value_inferred_from_structure": false, "organism": "Homo sapiens", "pdb_id": null, "preparation_id": "PREP:BPP", "protein_id": "UP:O96028", "publication_year": 2024, "qualitative_result": "Source reports non-detectable affinity in the tested selectivity comparison.", "reference_id": "PMID:39031937", "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Source says NSD2 PWWP but does not specify PWWP1 versus PWWP2 in the inspected passage; domain_id remains null.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_database": "Primary literature (Phase 5)", "source_id": "P5:S:WEI2024", "source_measurement_key": "547aaaaad799d3248757429cbab8a53de50effe040eaddcef5fb1e1884e970cd", "source_original": { "assay_construct_end": null, "assay_construct_start": null, "assay_context": "purified_PWWP_domain_unspecified_instance", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0032", "assay_type": "Binding selectivity; assay method not verified in Figure S2", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_name": "BPP", "conditions": {}, "domain": null, "domain_id": null, "endpoint": "qualitative", "evidence_class": "qualitative_binding", "evidence_location": "Results: selectivity paragraph referring to Figure S2", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "NSD2", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_negative": true, "negative_evidence_scope": "Non-detectable binding in the source experimental comparison; assay limits not recovered.", "numeric_transcription_status": "qualitative_or_not_reported", "numeric_value_inferred_from_structure": false, "pdb_id": null, "preparation_id": "PREP:BPP", "protein_id": "UP:O96028", "publication_year": 2024, "qualitative_result": "Source reports non-detectable affinity in the tested selectivity comparison.", "reference_id": "PMID:39031937", "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Source says NSD2 PWWP but does not specify PWWP1 versus PWWP2 in the inspected passage; domain_id remains null.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_id": "P5:S:WEI2024", "source_reported_uncertainty": null, "source_reported_units": null, "source_reported_value": null, "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "uncertainty": null, "uncertainty_type": null, "uncertainty_uM": null, "units": null, "value": null, "value_operator": null, "value_uM": null, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" }, "source_reported_uncertainty": null, "source_reported_units": null, "source_reported_value": null, "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "target_scope": "domain_unresolved", "uncertainty": null, "uncertainty_type": null, "uncertainty_uM": null, "units": null, "value": null, "value_operator": null, "value_uM": null, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" } ], "context_structures": [ { "Pfam_contacts_5A": "[{\"auth_asym_id\": \"A\", \"auth_seq_id\": \"15\", \"component\": \"MET\", \"entity_position\": 15, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.2305, \"uniprot_position\": 15}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"18\", \"component\": \"TYR\", \"entity_position\": 18, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.4757, \"uniprot_position\": 18}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"21\", \"component\": \"TRP\", \"entity_position\": 21, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.3231, \"uniprot_position\": 21}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"44\", \"component\": \"PHE\", \"entity_position\": 44, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.3686, \"uniprot_position\": 44}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"45\", \"component\": \"PHE\", \"entity_position\": 45, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.9751, \"uniprot_position\": 45}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"47\", \"component\": \"THR\", \"entity_position\": 47, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 2.488, \"uniprot_position\": 47}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"49\", \"component\": \"GLU\", \"entity_position\": 49, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.306, \"uniprot_position\": 49}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"50\", \"component\": \"THR\", \"entity_position\": 50, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.3798, \"uniprot_position\": 50}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"51\", \"component\": \"ALA\", \"entity_position\": 51, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.9037, \"uniprot_position\": 51}]", "biochemical_activity_inferred": 0, "ccd_id": "A1D73", "chain_contacts_5A": "[{\"auth_asym_id\": \"A\", \"auth_seq_id\": \"15\", \"component\": \"MET\", \"entity_position\": 15, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.2305, \"uniprot_position\": 15}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"18\", \"component\": \"TYR\", \"entity_position\": 18, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.4757, \"uniprot_position\": 18}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"21\", \"component\": \"TRP\", \"entity_position\": 21, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.3231, \"uniprot_position\": 21}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"44\", \"component\": \"PHE\", \"entity_position\": 44, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.3686, \"uniprot_position\": 44}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"45\", \"component\": \"PHE\", \"entity_position\": 45, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.9751, \"uniprot_position\": 45}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"47\", \"component\": \"THR\", \"entity_position\": 47, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 2.488, \"uniprot_position\": 47}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"49\", \"component\": \"GLU\", \"entity_position\": 49, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.306, \"uniprot_position\": 49}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"50\", \"component\": \"THR\", \"entity_position\": 50, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.3798, \"uniprot_position\": 50}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"51\", \"component\": \"ALA\", \"entity_position\": 51, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.9037, \"uniprot_position\": 51}]", "chain_id": "PDB:8Z6C:CHAIN:A:UP:Q7Z4V5", "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "contact_class": "native_annotation_core_contact", "contact_distance_rank": 1, "core_contacts_5A": "[{\"auth_asym_id\": \"A\", \"auth_seq_id\": \"15\", \"component\": \"MET\", \"entity_position\": 15, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.2305, \"uniprot_position\": 15}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"18\", \"component\": \"TYR\", \"entity_position\": 18, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.4757, \"uniprot_position\": 18}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"21\", \"component\": \"TRP\", \"entity_position\": 21, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.3231, \"uniprot_position\": 21}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"44\", \"component\": \"PHE\", \"entity_position\": 44, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.3686, \"uniprot_position\": 44}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"45\", \"component\": \"PHE\", \"entity_position\": 45, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.9751, \"uniprot_position\": 45}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"47\", \"component\": \"THR\", \"entity_position\": 47, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 2.488, \"uniprot_position\": 47}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"49\", \"component\": \"GLU\", \"entity_position\": 49, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.306, \"uniprot_position\": 49}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"50\", \"component\": \"THR\", \"entity_position\": 50, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.3798, \"uniprot_position\": 50}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"51\", \"component\": \"ALA\", \"entity_position\": 51, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.9037, \"uniprot_position\": 51}]", "covalent_connection_ids": "[]", "cutoff_angstrom": 5.0, "domain_id": "UP:Q7Z4V5:PWWP1", "exact_pwwp_contact": true, "gene": "HDGFL2", "geometry_scope": "first deposited model; asymmetric unit; heavy atoms with occupancy >0; alternate locations retained; no symmetry expansion", "instance": { "alternate_locations": "[]", "auth_asym_ids": "[\"A\"]", "auth_seq_id": "101", "ccd_id": "A1D73", "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "component_context": "nonpolymer_component", "contacted_polymer_partners": "[{\"description\": \"Hepatoma-derived growth factor-related protein 2\", \"entity_id\": \"1\", \"is_PWWP_family_protein\": true, \"label_asym_id\": \"A\", \"sequence_length\": 93, \"uniprot_ids\": [\"Q7Z4V5\"]}, {\"description\": \"Hepatoma-derived growth factor-related protein 2\", \"entity_id\": \"1\", \"is_PWWP_family_protein\": true, \"label_asym_id\": \"C\", \"sequence_length\": 93, \"uniprot_ids\": [\"Q7Z4V5\"]}]", "covalent_connection_ids": "[]", "heavy_atom_row_count": 12, "ideal_CCD_SDF_is_source_pose": 0, "label_asym_id": "D", "label_seq_id": null, "ligand_instance_id": "PDB:8Z6C:LIG:D:A1D73:101:.", "nearest_polypeptide_distance_angstrom": 2.488, "nearest_polypeptide_label_asym_id": "A", "occupancy_max": 0.59, "occupancy_min": 0.59, "pdb_id": "8Z6C", "polypeptide_contact_residues_5A": "[{\"auth_asym_id\": \"A\", \"auth_seq_id\": \"15\", \"component\": \"MET\", \"entity_position\": 15, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.2305, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"18\", \"component\": \"TYR\", \"entity_position\": 18, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.4757, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"21\", \"component\": \"TRP\", \"entity_position\": 21, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.3231, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"44\", \"component\": \"PHE\", \"entity_position\": 44, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.3686, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"45\", \"component\": \"PHE\", \"entity_position\": 45, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.9751, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"47\", \"component\": \"THR\", \"entity_position\": 47, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 2.488, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"49\", \"component\": \"GLU\", \"entity_position\": 49, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.306, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"50\", \"component\": \"THR\", \"entity_position\": 50, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.3798, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"51\", \"component\": \"ALA\", \"entity_position\": 51, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.9037, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"17\", \"component\": \"GLY\", \"entity_position\": 17, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 4.8102, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"19\", \"component\": \"PRO\", \"entity_position\": 19, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 4.9993, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"74\", \"component\": \"ARG\", \"entity_position\": 74, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 2.9842, \"uniprot_position\": null}]", "pose_kind": "deposited_source_coordinates", "reference_model": "1", "source_coordinate_file": "Structures/HDGFL2__HUMAN__Q7Z4V5/Co-Crystals/8Z6C/original.cif", "source_coordinate_sha256": "a52b0ce0d915a4ec6357f5dce14e0dbbacdb5fa856c24981a9187cf4168156c2", "unique_heavy_atom_names": 12 }, "ligand_instance_id": "PDB:8Z6C:LIG:D:A1D73:101:.", "ligand_label_asym_id": "D", "minimum_Pfam_distance_angstrom": 2.488, "minimum_chain_distance_angstrom": 2.488, "minimum_core_distance_angstrom": 2.488, "multiple_contacting_mapped_chains": 1, "pdb_id": "8Z6C", "protein_id": "UP:Q7Z4V5", "protein_label_asym_id": "A", "rank_interpretation": "Distance rank among mapped chains only; crystal packing and biological site assignment require separate review.", "role": "experimentally studied ligand", "role_category": "functional", "site_id": "PDB:8Z6C:LIG:D:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:A", "source_coordinate_sha256": "a52b0ce0d915a4ec6357f5dce14e0dbbacdb5fa856c24981a9187cf4168156c2" }, { "Pfam_contacts_5A": "[{\"auth_asym_id\": \"C\", \"auth_seq_id\": \"17\", \"component\": \"GLY\", \"entity_position\": 17, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 4.8102, \"uniprot_position\": 17}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"19\", \"component\": \"PRO\", \"entity_position\": 19, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 4.9993, \"uniprot_position\": 19}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"74\", \"component\": \"ARG\", \"entity_position\": 74, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 2.9842, \"uniprot_position\": 74}]", "biochemical_activity_inferred": 0, "ccd_id": "A1D73", "chain_contacts_5A": "[{\"auth_asym_id\": \"C\", \"auth_seq_id\": \"17\", \"component\": \"GLY\", \"entity_position\": 17, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 4.8102, \"uniprot_position\": 17}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"19\", \"component\": \"PRO\", \"entity_position\": 19, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 4.9993, \"uniprot_position\": 19}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"74\", \"component\": \"ARG\", \"entity_position\": 74, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 2.9842, \"uniprot_position\": 74}]", "chain_id": "PDB:8Z6C:CHAIN:C:UP:Q7Z4V5", "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "contact_class": "native_annotation_core_contact", "contact_distance_rank": 2, "core_contacts_5A": "[{\"auth_asym_id\": \"C\", \"auth_seq_id\": \"17\", \"component\": \"GLY\", \"entity_position\": 17, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 4.8102, \"uniprot_position\": 17}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"19\", \"component\": \"PRO\", \"entity_position\": 19, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 4.9993, \"uniprot_position\": 19}]", "covalent_connection_ids": "[]", "cutoff_angstrom": 5.0, "domain_id": "UP:Q7Z4V5:PWWP1", "exact_pwwp_contact": true, "gene": "HDGFL2", "geometry_scope": "first deposited model; asymmetric unit; heavy atoms with occupancy >0; alternate locations retained; no symmetry expansion", "instance": { "alternate_locations": "[]", "auth_asym_ids": "[\"A\"]", "auth_seq_id": "101", "ccd_id": "A1D73", "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "component_context": "nonpolymer_component", "contacted_polymer_partners": "[{\"description\": \"Hepatoma-derived 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\"auth_seq_id\": \"18\", \"component\": \"TYR\", \"entity_position\": 18, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.4757, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"21\", \"component\": \"TRP\", \"entity_position\": 21, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.3231, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"44\", \"component\": \"PHE\", \"entity_position\": 44, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.3686, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"45\", \"component\": \"PHE\", \"entity_position\": 45, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.9751, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"47\", \"component\": \"THR\", \"entity_position\": 47, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 2.488, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"49\", 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"PDB:8Z6C:LIG:D:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:C", "source_role": "experimentally studied ligand", "source_url": "https://www.rcsb.org/structure/8Z6C", "structural_research_ligand": true, "uncertainty": "Role is source-annotated; deposited proximity alone does not establish solution binding or biological activity.", "verification_status": "phase5_derived_deposited_geometry" }, "PDB:8Z6C:LIG:G:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:B": { "ccd_url": "https://www.rcsb.org/ligand/A1D73", "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "contact_class": "native_annotation_core_contact", "coordinate_sha256": "a52b0ce0d915a4ec6357f5dce14e0dbbacdb5fa856c24981a9187cf4168156c2", "domain_id": "UP:Q7Z4V5:PWWP1", "exact_pwwp_contact": true, "ligand_instance_id": "PDB:8Z6C:LIG:G:A1D73:101:.", "observed_other_component": false, "pdb_id": "8Z6C", "protein_id": "UP:Q7Z4V5", "role_code": "reported_studied_structural_ligand", "role_group": "research_ligand", "rule": "Phase5 exact deposited site role, measured heavy-atom contacts and native-domain scope", "site_id": "PDB:8Z6C:LIG:G:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:B", "source_role": "experimentally studied ligand", "source_url": "https://www.rcsb.org/structure/8Z6C", "structural_research_ligand": true, "uncertainty": "Role is source-annotated; deposited proximity alone does not establish solution binding or biological activity.", "verification_status": "phase5_derived_deposited_geometry" }, "PDB:8Z6C:LIG:J:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:C": { "ccd_url": "https://www.rcsb.org/ligand/A1D73", "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "contact_class": "native_annotation_core_contact", "coordinate_sha256": "a52b0ce0d915a4ec6357f5dce14e0dbbacdb5fa856c24981a9187cf4168156c2", "domain_id": "UP:Q7Z4V5:PWWP1", "exact_pwwp_contact": true, "ligand_instance_id": "PDB:8Z6C:LIG:J:A1D73:101:.", "observed_other_component": false, "pdb_id": "8Z6C", "protein_id": "UP:Q7Z4V5", "role_code": "reported_studied_structural_ligand", "role_group": "research_ligand", "rule": "Phase5 exact deposited site role, measured heavy-atom contacts and native-domain scope", "site_id": "PDB:8Z6C:LIG:J:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:C", "source_role": "experimentally studied ligand", "source_url": "https://www.rcsb.org/structure/8Z6C", "structural_research_ligand": true, "uncertainty": "Role is source-annotated; deposited proximity alone does not establish solution binding or biological activity.", "verification_status": "phase5_derived_deposited_geometry" }, "PDB:9G94:LIG:D:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:A": { "ccd_url": "https://www.rcsb.org/ligand/A1D73", "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "contact_class": "native_annotation_core_contact", "coordinate_sha256": "77cc947e76da8d5e49e56df359b3db472fe81dbdfabfc36f99d53b3c18200802", "domain_id": "UP:Q7Z4V5:PWWP1", "exact_pwwp_contact": true, "ligand_instance_id": "PDB:9G94:LIG:D:A1D73:101:.", "observed_other_component": false, "pdb_id": "9G94", "protein_id": "UP:Q7Z4V5", "role_code": "reported_studied_structural_ligand", "role_group": "research_ligand", "rule": "Phase5 exact deposited site role, measured heavy-atom contacts and native-domain scope", "site_id": "PDB:9G94:LIG:D:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:A", "source_role": "experimentally studied ligand", "source_url": "https://www.rcsb.org/structure/9G94", "structural_research_ligand": true, "uncertainty": "Role is source-annotated; deposited proximity alone does not establish solution binding or biological activity.", "verification_status": "phase5_derived_deposited_geometry" }, "PDB:9G94:LIG:G:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:A": { "ccd_url": "https://www.rcsb.org/ligand/A1D73", "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "contact_class": "native_annotation_core_contact", "coordinate_sha256": "77cc947e76da8d5e49e56df359b3db472fe81dbdfabfc36f99d53b3c18200802", "domain_id": "UP:Q7Z4V5:PWWP1", "exact_pwwp_contact": true, "ligand_instance_id": "PDB:9G94:LIG:G:A1D73:101:.", "observed_other_component": false, "pdb_id": "9G94", "protein_id": "UP:Q7Z4V5", "role_code": "reported_studied_structural_ligand", "role_group": "research_ligand", "rule": "Phase5 exact deposited site role, measured heavy-atom contacts and native-domain scope", "site_id": "PDB:9G94:LIG:G:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:A", "source_role": "experimentally studied ligand", "source_url": "https://www.rcsb.org/structure/9G94", "structural_research_ligand": true, "uncertainty": "Role is source-annotated; deposited proximity alone does not establish solution binding or biological activity.", "verification_status": "phase5_derived_deposited_geometry" }, "PDB:9G94:LIG:G:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:B": { "ccd_url": "https://www.rcsb.org/ligand/A1D73", "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "contact_class": "native_annotation_core_contact", "coordinate_sha256": "77cc947e76da8d5e49e56df359b3db472fe81dbdfabfc36f99d53b3c18200802", "domain_id": "UP:Q7Z4V5:PWWP1", "exact_pwwp_contact": true, "ligand_instance_id": "PDB:9G94:LIG:G:A1D73:101:.", "observed_other_component": false, "pdb_id": "9G94", "protein_id": "UP:Q7Z4V5", "role_code": "reported_studied_structural_ligand", "role_group": "research_ligand", "rule": "Phase5 exact deposited site role, measured heavy-atom contacts and native-domain scope", "site_id": "PDB:9G94:LIG:G:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:B", "source_role": "experimentally studied ligand", "source_url": "https://www.rcsb.org/structure/9G94", "structural_research_ligand": true, "uncertainty": "Role is source-annotated; deposited proximity alone does not establish solution binding or biological activity.", "verification_status": "phase5_derived_deposited_geometry" }, "PDB:9G94:LIG:J:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:C": { "ccd_url": "https://www.rcsb.org/ligand/A1D73", "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "contact_class": "native_annotation_core_contact", "coordinate_sha256": "77cc947e76da8d5e49e56df359b3db472fe81dbdfabfc36f99d53b3c18200802", "domain_id": "UP:Q7Z4V5:PWWP1", "exact_pwwp_contact": true, "ligand_instance_id": "PDB:9G94:LIG:J:A1D73:101:.", "observed_other_component": false, "pdb_id": "9G94", "protein_id": "UP:Q7Z4V5", "role_code": "reported_studied_structural_ligand", "role_group": "research_ligand", "rule": "Phase5 exact deposited site role, measured heavy-atom contacts and native-domain scope", "site_id": "PDB:9G94:LIG:J:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:C", "source_role": "experimentally studied ligand", "source_url": "https://www.rcsb.org/structure/9G94", "structural_research_ligand": true, "uncertainty": "Role is source-annotated; deposited proximity alone does not establish solution binding or biological activity.", "verification_status": "phase5_derived_deposited_geometry" } }, "science_assay_roles": { "PWWP:ASSAY:0011": { "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "domain_id": "UP:Q7Z4V5:PWWP1", "endpoint": "Kd", "evidence_type": "direct_binding", "explicitly_negative": false, "measured": true, "method": "NMR chemical-shift perturbation", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP:ASSAY:0011", "operator": "=", "positive_direct_binder": true, "preparation_id": "PREP:BPP", "protein_id": "UP:Q7Z4V5", "remaining_uncertainty": "Intermediate-exchange NMR fit has large fitting error; ITC cross-validation reported, exact separate ITC number not extracted.", "reported_cellular": false, "reported_control": false, "reported_probe": false, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "S04", "source_location": "Results; Figure 1E", "source_role": "experimentally_studied_fragment_ligand", "source_url": "https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981", "source_verification_scope": "primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved", "studied_compound": true, "target_scope": "domain_specific", "target_variant": null, "units": "µM", "value": 7.0, "verification_status": "primary_full_text_sections_verified" }, "PWWP:ASSAY:0012": { "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "domain_id": "UP:O75475:PWWP1", "endpoint": "Kd", "evidence_type": "direct_binding", "explicitly_negative": false, "measured": true, "method": "ITC", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP:ASSAY:0012", "operator": "=", "positive_direct_binder": true, "preparation_id": "PREP:BPP", "protein_id": "UP:O75475", "remaining_uncertainty": "Full assay buffer, temperature and incubation metadata not transcribed; null means uncurated, not absent.", "reported_cellular": false, "reported_control": false, "reported_probe": false, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "S04", "source_location": "Results; Figure 4B", "source_role": "experimentally_studied_fragment_ligand", "source_url": "https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981", "source_verification_scope": "primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved", "studied_compound": true, "target_scope": "domain_specific", "target_variant": null, "units": "µM", "value": 27.0, "verification_status": "primary_full_text_sections_verified" }, "PWWP:ASSAY:0013": { "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "domain_id": "UP:Q9Y3E1:PWWP1", "endpoint": "Kd", "evidence_type": "direct_binding", "explicitly_negative": false, "measured": true, "method": "Binding", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP:ASSAY:0013", "operator": "=", "positive_direct_binder": true, "preparation_id": "PREP:BPP", "protein_id": "UP:Q9Y3E1", "remaining_uncertainty": "14 ± 2 µM confirmed in primary Results; specific Figure S2 assay method remains unresolved.", "reported_cellular": false, "reported_control": false, "reported_probe": false, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "S04", "source_location": "Results: selectivity paragraph", "source_role": "experimentally_studied_fragment_ligand", "source_url": "https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981", "source_verification_scope": "primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved", "studied_compound": true, "target_scope": "domain_specific", "target_variant": null, "units": "µM", "value": 14.0, "verification_status": "primary_full_text_sections_verified" }, "PWWP5:ASSAY:0028": { "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "domain_id": "UP:Q7Z4V5:PWWP1", "endpoint": "Kd", "evidence_type": "direct_binding", "explicitly_negative": false, "measured": true, "method": "NMR chemical-shift perturbation", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP5:ASSAY:0028", "operator": "=", "positive_direct_binder": true, "preparation_id": "PREP:BPP", "protein_id": "UP:Q7Z4V5", "remaining_uncertainty": "Y18S mutant measurement; must not be pooled with wild-type affinity. Construct is the source HDGFRP2 PWWP expression fragment (1–93) carrying the stated mutation. Replicate number and titration-specific temperature are not independently specified.", "reported_cellular": false, "reported_control": false, "reported_probe": false, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "P5:S:WEI2024", "source_location": "Results; Figure 3D", "source_role": "experimentally_studied_ligand", "source_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "studied_compound": true, "target_scope": "domain_specific", "target_variant": "Y18S", "units": "mM", "value": 0.29, "verification_status": "primary_source_verified" }, "PWWP5:ASSAY:0029": { "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "domain_id": "UP:Q49A26:PWWP1", "endpoint": "qualitative", "evidence_type": "qualitative_binding", "explicitly_negative": true, "measured": true, "method": "Binding selectivity; assay method not verified in Figure S2", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP5:ASSAY:0029", "operator": null, "positive_direct_binder": false, "preparation_id": "PREP:BPP", "protein_id": "UP:Q49A26", "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.", "reported_cellular": false, "reported_control": false, "reported_probe": false, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "P5:S:WEI2024", "source_location": "Results: selectivity paragraph referring to Figure S2", "source_role": "experimentally_studied_ligand", "source_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "studied_compound": true, "target_scope": "domain_specific", "target_variant": null, "units": null, "value": null, "verification_status": "primary_source_verified" }, "PWWP5:ASSAY:0030": { "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "domain_id": "UP:P55201:PWWP1", "endpoint": "qualitative", "evidence_type": "qualitative_binding", "explicitly_negative": true, "measured": true, "method": "Binding selectivity; assay method not verified in Figure S2", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP5:ASSAY:0030", "operator": null, "positive_direct_binder": false, "preparation_id": "PREP:BPP", "protein_id": "UP:P55201", "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.", "reported_cellular": false, "reported_control": false, "reported_probe": false, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "P5:S:WEI2024", "source_location": "Results: selectivity paragraph referring to Figure S2", "source_role": "experimentally_studied_ligand", "source_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "studied_compound": true, "target_scope": "domain_specific", "target_variant": null, "units": null, "value": null, "verification_status": "primary_source_verified" }, "PWWP5:ASSAY:0031": { "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "domain_id": "UP:Q9UBC3:PWWP1", "endpoint": "qualitative", "evidence_type": "qualitative_binding", "explicitly_negative": true, "measured": true, "method": "Binding selectivity; assay method not verified in Figure S2", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP5:ASSAY:0031", "operator": null, "positive_direct_binder": false, "preparation_id": "PREP:BPP", "protein_id": "UP:Q9UBC3", "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.", "reported_cellular": false, "reported_control": false, "reported_probe": false, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "P5:S:WEI2024", "source_location": "Results: selectivity paragraph referring to Figure S2", "source_role": "experimentally_studied_ligand", "source_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "studied_compound": true, "target_scope": "domain_specific", "target_variant": null, "units": null, "value": null, "verification_status": "primary_source_verified" }, "PWWP5:ASSAY:0032": { "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "domain_id": null, "endpoint": "qualitative", "evidence_type": "qualitative_binding", "explicitly_negative": true, "measured": true, "method": "Binding selectivity; assay method not verified in Figure S2", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP5:ASSAY:0032", "operator": null, "positive_direct_binder": false, "preparation_id": "PREP:BPP", "protein_id": "UP:O96028", "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Source says NSD2 PWWP but does not specify PWWP1 versus PWWP2 in the inspected passage; domain_id remains null.", "reported_cellular": false, "reported_control": false, "reported_probe": false, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "P5:S:WEI2024", "source_location": "Results: selectivity paragraph referring to Figure S2", "source_role": "experimentally_studied_ligand", "source_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "studied_compound": true, "target_scope": "domain_unresolved", "target_variant": null, "units": null, "value": null, "verification_status": "primary_source_verified" } }, "example": { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 93, "assay_construct_start": 1, "assay_record_id": "PWWP:ASSAY:0011", "assay_type": "NMR chemical-shift perturbation Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "HEPES-buffered saline; exact buffer/salt concentrations not restated in CSP subsection", "ccd_id": "A1D73", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_name": "BPP", "conditions": "{\"fit_model\": \"1:1 binding; global fit with shared Kd\", \"ligand_to_protein_molar_ratio_range\": [0, 6], \"protein_concentration_uM\": 100, \"protein_construct\": \"HDGFL2 1–93\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP", "domain_id": "UP:Q7Z4V5:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Results; Figure 1E", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981", "gene": "HDGFL2", "interpretation": "Authors report intermediate-exchange limitations and additional ITC validation. This record preserves the NMR value and fitting error.", "is_measured": true, "is_negative": false, "method": "NMR chemical-shift perturbation", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 7.0, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": 7.4, "pdb_id": "8Z6C", "preparation_id": "PREP:BPP", "protein_id": "UP:Q7Z4V5", "publication_year": 2024, "qualitative_result": null, "reference_id": "PMID:39031937", "remaining_uncertainty": "Intermediate-exchange NMR fit has large fitting error; ITC cross-validation reported, exact separate ITC number not extracted.", "replicates": null, "role": "experimentally_studied_fragment_ligand", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S04", "source_measurement_key": "d4c00922e7b4cb60789dae0c9cd6d4d76f72574cab8eead4c9a2552558cfebcc", "source_original": { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 93, "assay_construct_start": 1, "assay_record_id": "PWWP:ASSAY:0011", "assay_type": "NMR chemical-shift perturbation Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "HEPES-buffered saline; exact buffer/salt concentrations not restated in CSP subsection", "ccd_id": "A1D73", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "BPP", "conditions": "{\"fit_model\": \"1:1 binding; global fit with shared Kd\", \"ligand_to_protein_molar_ratio_range\": [0, 6], \"protein_concentration_uM\": 100, \"protein_construct\": \"HDGFL2 1–93\"}", "crystallographic_component_ids": null, "domain": "PWWP", "domain_id": "UP:Q7Z4V5:PWWP1", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Results; Figure 1E", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981", "gene": "HDGFL2", "interpretation": "Authors report intermediate-exchange limitations and additional ITC validation. 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CSP subsection does not separately give HEPES/NaCl concentrations", "ligand_protein_molar_ratio_range": [ 0, 6 ], "pH": 7.4, "protein_concentration_mM": 0.1, "target_variant": "Y18S" }, "curation_version": "phase5-1.0.0", "domain": "PWWP1", "domain_id": "UP:Q7Z4V5:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_location": "Results; Figure 3D", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "HDGFL2", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_measured": true, "is_negative": false, "method": "NMR chemical-shift perturbation", "normalized_exact_uM": 290.0, "numeric_transcription_status": "source_preserved", "numeric_value_inferred_from_structure": false, "organism": "Homo sapiens", "pH": 7.4, "pdb_id": null, "preparation_id": "PREP:BPP", "protein_id": "UP:Q7Z4V5", "publication_year": 2024, "reference_id": "PMID:39031937", "remaining_uncertainty": "Y18S mutant measurement; must not be pooled with wild-type affinity. Construct is the source HDGFRP2 PWWP expression fragment (1–93) carrying the stated mutation. Replicate number and titration-specific temperature are not independently specified.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_database": "Primary literature (Phase 5)", "source_id": "P5:S:WEI2024", "source_measurement_key": "9d30a9d0eb5e0c4aeafe0b022d48c9264242ab9e5b5210df4a0778575e81cdcd", "source_original": { "assay_construct_end": 93, "assay_construct_start": 1, "assay_context": "purified_mutant_domain", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0028", "assay_type": "NMR chemical-shift perturbation Kd", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_name": "BPP", "conditions": { "binding_model": "1:1 global fit of perturbed residues", "buffer": "HEPES-buffered saline; CSP subsection does not separately give HEPES/NaCl concentrations", "ligand_protein_molar_ratio_range": [ 0, 6 ], "pH": 7.4, "protein_concentration_mM": 0.1, "target_variant": "Y18S" }, "domain": "PWWP1", "domain_id": "UP:Q7Z4V5:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_location": "Results; Figure 3D", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "HDGFL2", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_negative": false, "numeric_transcription_status": "source_preserved", "numeric_value_inferred_from_structure": false, "pH": 7.4, "pdb_id": null, "preparation_id": "PREP:BPP", "protein_id": "UP:Q7Z4V5", "publication_year": 2024, "reference_id": "PMID:39031937", "remaining_uncertainty": "Y18S mutant measurement; must not be pooled with wild-type affinity. Construct is the source HDGFRP2 PWWP expression fragment (1–93) carrying the stated mutation. Replicate number and titration-specific temperature are not independently specified.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_id": "P5:S:WEI2024", "source_reported_uncertainty": "0.02", "source_reported_units": "mM", "source_reported_value": "0.29", "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "target_variant": "Y18S", "uncertainty": 0.02, "uncertainty_type": "fitting error", "uncertainty_uM": 20.0, "unit_conversion": "mM × 1000 = µM", "units": "mM", "value": 0.29, "value_operator": "=", "value_uM": 290.0, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" }, "source_reported_uncertainty": "0.02", "source_reported_units": "mM", "source_reported_value": "0.29", "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "target_scope": "domain_specific", "target_variant": "Y18S", "uncertainty": 0.02, "uncertainty_type": "fitting error", "uncertainty_uM": 20.0, "unit_conversion": "mM × 1000 = µM", "units": "mM", "value": 0.29, "value_operator": "=", "value_uM": 290.0, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" }, { "assay_construct_end": null, "assay_construct_start": null, "assay_context": "purified_domain", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0029", "assay_type": "Binding selectivity; assay method not verified in Figure S2", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_name": "BPP", "conditions": {}, "curation_version": "phase5-1.0.0", "domain": "PWWP1", "domain_id": "UP:Q49A26:PWWP1", "endpoint": "qualitative", "evidence_class": "qualitative_binding", "evidence_location": "Results: selectivity paragraph referring to Figure S2", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "GLYR1", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_measured": true, "is_negative": true, "method": "Binding selectivity; assay method not verified in Figure S2", "negative_evidence_scope": "Non-detectable binding in the source experimental comparison; assay limits not recovered.", "normalized_exact_uM": null, "numeric_transcription_status": "qualitative_or_not_reported", "numeric_value_inferred_from_structure": false, "organism": "Homo sapiens", "pdb_id": null, "preparation_id": "PREP:BPP", "protein_id": "UP:Q49A26", "publication_year": 2024, "qualitative_result": "Source reports non-detectable affinity in the tested selectivity comparison.", "reference_id": "PMID:39031937", "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_database": "Primary literature (Phase 5)", "source_id": "P5:S:WEI2024", "source_measurement_key": "1bb84a49b8cfa231e7556fd293906f4c077290f112c8295d63faa44bcc59ca3e", "source_original": { "assay_construct_end": null, "assay_construct_start": null, "assay_context": "purified_domain", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0029", "assay_type": "Binding selectivity; assay method not verified in Figure S2", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_name": "BPP", "conditions": {}, "domain": "PWWP1", "domain_id": "UP:Q49A26:PWWP1", "endpoint": "qualitative", "evidence_class": "qualitative_binding", "evidence_location": "Results: selectivity paragraph referring to Figure S2", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "GLYR1", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_negative": true, "negative_evidence_scope": "Non-detectable binding in the source experimental comparison; assay limits not recovered.", "numeric_transcription_status": "qualitative_or_not_reported", "numeric_value_inferred_from_structure": false, "pdb_id": null, "preparation_id": "PREP:BPP", "protein_id": "UP:Q49A26", "publication_year": 2024, "qualitative_result": "Source reports non-detectable affinity in the tested selectivity comparison.", "reference_id": "PMID:39031937", "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_id": "P5:S:WEI2024", "source_reported_uncertainty": null, "source_reported_units": null, "source_reported_value": null, "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "uncertainty": null, "uncertainty_type": null, "uncertainty_uM": null, "units": null, "value": null, "value_operator": null, "value_uM": null, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" }, "source_reported_uncertainty": null, "source_reported_units": null, "source_reported_value": null, "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "target_scope": "domain_specific", "uncertainty": null, "uncertainty_type": null, "uncertainty_uM": null, "units": null, "value": null, "value_operator": null, "value_uM": null, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" }, { "assay_construct_end": null, "assay_construct_start": null, "assay_context": "purified_domain", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0030", "assay_type": "Binding selectivity; assay method not verified in Figure S2", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_name": "BPP", "conditions": {}, "curation_version": "phase5-1.0.0", "domain": "PWWP1", "domain_id": "UP:P55201:PWWP1", "endpoint": "qualitative", "evidence_class": "qualitative_binding", "evidence_location": "Results: selectivity paragraph referring to Figure S2", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "BRPF1", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_measured": true, "is_negative": true, "method": "Binding selectivity; assay method not verified in Figure S2", "negative_evidence_scope": "Non-detectable binding in the source experimental comparison; assay limits not recovered.", "normalized_exact_uM": null, "numeric_transcription_status": "qualitative_or_not_reported", "numeric_value_inferred_from_structure": false, "organism": "Homo sapiens", "pdb_id": null, "preparation_id": "PREP:BPP", "protein_id": "UP:P55201", "publication_year": 2024, "qualitative_result": "Source reports non-detectable affinity in the tested selectivity comparison.", "reference_id": "PMID:39031937", "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_database": "Primary literature (Phase 5)", "source_id": "P5:S:WEI2024", "source_measurement_key": "8b0073aae5fc1c92500107f909e335ed9da0b5cd65e6267735d56dfaa9bcf493", "source_original": { "assay_construct_end": null, "assay_construct_start": null, "assay_context": "purified_domain", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0030", "assay_type": "Binding selectivity; assay method not verified in Figure S2", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_name": "BPP", "conditions": {}, "domain": "PWWP1", "domain_id": "UP:P55201:PWWP1", "endpoint": "qualitative", "evidence_class": "qualitative_binding", "evidence_location": "Results: selectivity paragraph referring to Figure S2", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "BRPF1", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_negative": true, "negative_evidence_scope": "Non-detectable binding in the source experimental comparison; assay limits not recovered.", "numeric_transcription_status": "qualitative_or_not_reported", "numeric_value_inferred_from_structure": false, "pdb_id": null, "preparation_id": "PREP:BPP", "protein_id": "UP:P55201", "publication_year": 2024, "qualitative_result": "Source reports non-detectable affinity in the tested selectivity comparison.", "reference_id": "PMID:39031937", "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_id": "P5:S:WEI2024", "source_reported_uncertainty": null, "source_reported_units": null, "source_reported_value": null, "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "uncertainty": null, "uncertainty_type": null, "uncertainty_uM": null, "units": null, "value": null, "value_operator": null, "value_uM": null, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" }, "source_reported_uncertainty": null, "source_reported_units": null, "source_reported_value": null, "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "target_scope": "domain_specific", "uncertainty": null, "uncertainty_type": null, "uncertainty_uM": null, "units": null, "value": null, "value_operator": null, "value_uM": null, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" }, { "assay_construct_end": null, "assay_construct_start": null, "assay_context": "purified_domain", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0031", "assay_type": "Binding selectivity; assay method not verified in Figure S2", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_name": "BPP", "conditions": {}, "curation_version": "phase5-1.0.0", "domain": "PWWP1", "domain_id": "UP:Q9UBC3:PWWP1", "endpoint": "qualitative", "evidence_class": "qualitative_binding", "evidence_location": "Results: selectivity paragraph referring to Figure S2", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "DNMT3B", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_measured": true, "is_negative": true, "method": "Binding selectivity; assay method not verified in Figure S2", "negative_evidence_scope": "Non-detectable binding in the source experimental comparison; assay limits not recovered.", "normalized_exact_uM": null, "numeric_transcription_status": "qualitative_or_not_reported", "numeric_value_inferred_from_structure": false, "organism": "Homo sapiens", "pdb_id": null, "preparation_id": "PREP:BPP", "protein_id": "UP:Q9UBC3", "publication_year": 2024, "qualitative_result": "Source reports non-detectable affinity in the tested selectivity comparison.", "reference_id": "PMID:39031937", "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_database": "Primary literature (Phase 5)", "source_id": "P5:S:WEI2024", "source_measurement_key": "acc240f8b47f7ec0bf4cba699326f80d34b983774139f69e6474e0dbda1a9fa9", "source_original": { "assay_construct_end": null, "assay_construct_start": null, "assay_context": "purified_domain", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0031", "assay_type": "Binding selectivity; assay method not verified in Figure S2", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_name": "BPP", "conditions": {}, "domain": "PWWP1", "domain_id": "UP:Q9UBC3:PWWP1", "endpoint": "qualitative", "evidence_class": "qualitative_binding", "evidence_location": "Results: selectivity paragraph referring to Figure S2", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "DNMT3B", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_negative": true, "negative_evidence_scope": "Non-detectable binding in the source experimental comparison; assay limits not recovered.", "numeric_transcription_status": "qualitative_or_not_reported", "numeric_value_inferred_from_structure": false, "pdb_id": null, "preparation_id": "PREP:BPP", "protein_id": "UP:Q9UBC3", "publication_year": 2024, "qualitative_result": "Source reports non-detectable affinity in the tested selectivity comparison.", "reference_id": "PMID:39031937", "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_id": "P5:S:WEI2024", "source_reported_uncertainty": null, "source_reported_units": null, "source_reported_value": null, "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "uncertainty": null, "uncertainty_type": null, "uncertainty_uM": null, "units": null, "value": null, "value_operator": null, "value_uM": null, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" }, "source_reported_uncertainty": null, "source_reported_units": null, "source_reported_value": null, "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "target_scope": "domain_specific", "uncertainty": null, "uncertainty_type": null, "uncertainty_uM": null, "units": null, "value": null, "value_operator": null, "value_uM": null, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" }, { "assay_construct_end": null, "assay_construct_start": null, "assay_context": "purified_PWWP_domain_unspecified_instance", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0032", "assay_type": "Binding selectivity; assay method not verified in Figure S2", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_name": "BPP", "conditions": {}, "curation_version": "phase5-1.0.0", "domain": null, "domain_id": null, "endpoint": "qualitative", "evidence_class": "qualitative_binding", "evidence_location": "Results: selectivity paragraph referring to Figure S2", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "NSD2", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_measured": true, "is_negative": true, "method": "Binding selectivity; assay method not verified in Figure S2", "negative_evidence_scope": "Non-detectable binding in the source experimental comparison; assay limits not recovered.", "normalized_exact_uM": null, "numeric_transcription_status": "qualitative_or_not_reported", "numeric_value_inferred_from_structure": false, "organism": "Homo sapiens", "pdb_id": null, "preparation_id": "PREP:BPP", "protein_id": "UP:O96028", "publication_year": 2024, "qualitative_result": "Source reports non-detectable affinity in the tested selectivity comparison.", "reference_id": "PMID:39031937", "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Source says NSD2 PWWP but does not specify PWWP1 versus PWWP2 in the inspected passage; domain_id remains null.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_database": "Primary literature (Phase 5)", "source_id": "P5:S:WEI2024", "source_measurement_key": "547aaaaad799d3248757429cbab8a53de50effe040eaddcef5fb1e1884e970cd", "source_original": { "assay_construct_end": null, "assay_construct_start": null, "assay_context": "purified_PWWP_domain_unspecified_instance", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0032", "assay_type": "Binding selectivity; assay method not verified in Figure S2", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_name": "BPP", "conditions": {}, "domain": null, "domain_id": null, "endpoint": "qualitative", "evidence_class": "qualitative_binding", "evidence_location": "Results: selectivity paragraph referring to Figure S2", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "NSD2", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_negative": true, "negative_evidence_scope": "Non-detectable binding in the source experimental comparison; assay limits not recovered.", "numeric_transcription_status": "qualitative_or_not_reported", "numeric_value_inferred_from_structure": false, "pdb_id": null, "preparation_id": "PREP:BPP", "protein_id": "UP:O96028", "publication_year": 2024, "qualitative_result": "Source reports non-detectable affinity in the tested selectivity comparison.", "reference_id": "PMID:39031937", "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Source says NSD2 PWWP but does not specify PWWP1 versus PWWP2 in the inspected passage; domain_id remains null.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_id": "P5:S:WEI2024", "source_reported_uncertainty": null, "source_reported_units": null, "source_reported_value": null, "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "uncertainty": null, "uncertainty_type": null, "uncertainty_uM": null, "units": null, "value": null, "value_operator": null, "value_uM": null, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" }, "source_reported_uncertainty": null, "source_reported_units": null, "source_reported_value": null, "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "target_scope": "domain_unresolved", "uncertainty": null, "uncertainty_type": null, "uncertainty_uM": null, "units": null, "value": null, "value_operator": null, "value_uM": null, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" } ], "matched_assay_count": 8 }, { "aliases": [ "1-[[(2~{S})-1-[4-[ethyl(pyridin-4-ylmethyl)amino]-6-methyl-pyrimidin-2-yl]pyrrolidin-2-yl]methyl]urea", "compound 7 (Collie 2025)" ], "assay_count": 4, "associated_pdb_ids": [ "9FOE" ], "bound_structure_count": 1, "category": "Bioactivity + bound structure", "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "classifications": [ "Negative / censored observations" ], "compound_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "curation_version": "phase5-1.0.0", "depiction": { "calculated_HBA": 6, "calculated_HBD": 2, "calculated_TPSA": 100.27, "calculated_formula": "C19H27N7O", "calculated_logP": 1.8436, "calculated_molecular_weight": 369.473, "computed_inchikey": "HHACEXLLNHJLFT-INIZCTEOSA-N", "descriptor_scope": "RDKit calculation for the source identity; not an experimental measurement", "files": { "dark": "34b3883f2e3f003ea1c8-dark.svg", "light": "34b3883f2e3f003ea1c8-light.svg" }, "rdkit_version": "2025.09.3", "status": "verified_smiles_full_inchikey_match" }, "development_status": "Not independently curated", "domain_ids": [ "UP:O96028:PWWP1", "UP:Q9BZ95:PWWP1" ], "entity_kind": "chemical_identity", "genes": [ "NSD2", "NSD3" ], "has_bioactivity_only": false, "has_source_conflict": false, "identity": { "aliases": [ "1-[[(2~{S})-1-[4-[ethyl(pyridin-4-ylmethyl)amino]-6-methyl-pyrimidin-2-yl]pyrrolidin-2-yl]methyl]urea" ], "ccd_ids": [ "A1IEF" ], "ccd_names": "[\"1-[[(2~{S})-1-[4-[ethyl(pyridin-4-ylmethyl)amino]-6-methyl-pyrimidin-2-yl]pyrrolidin-2-yl]methyl]urea\"]", "ccd_types": "[\"non-polymer\"]", "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "connectivity_block": "HHACEXLLNHJLFT", "curated_source_sha256": null, "curation_version": "frozen-v1.2", "external_identifiers": {}, "formal_charge_by_ccd": "{\"A1IEF\": 0}", "formulae": "[\"C19 H27 N7 O\"]", "geometry_note": "CCD ideal SDF is a reference chemical geometry, not a deposited bound pose.", "identity_status": "complete_deposited_InChIKey", "inchikey": "HHACEXLLNHJLFT-INIZCTEOSA-N", "inventory_origin": "v1_CCD_inventory", "isomeric_smiles": "CCN(Cc1ccncc1)c2cc(nc(n2)N3CCC[C@H]3CNC(=O)N)C", "primary_name": "1-[[(2~{S})-1-[4-[ethyl(pyridin-4-ylmethyl)amino]-6-methyl-pyrimidin-2-yl]pyrrolidin-2-yl]methyl]urea", "retrieval_date": "2026-10-24", "smiles_stereo_by_ccd": "{\"A1IEF\": \"CCN(Cc1ccncc1)c2cc(nc(n2)N3CCC[C@H]3CNC(=O)N)C\"}", "source_metadata_sha256": "{\"A1IEF\": \"4a823beea94f9176b22d2c2cf26400c5afa4f9e6ae4c31a6a18a969d957e008f\"}", "source_urls": [ "https://www.rcsb.org/ligand/A1IEF" ] }, "identity_note": "Complete deposited identity retained; no connectivity-only or name-only merge.", "identity_resolved": true, "is_control": false, "is_probe": false, "measured_observation_count": 4, "name": "compound 7 (Collie 2025)", "negative_count": 1, "observation_ids": [ "PWWP:ASSAY:0017", "PWWP:ASSAY:0024", "PWWP:ASSAY:0029", "PWWP11:ASSAY:0004" ], "pdb_structure_count": 1, "preparation_count": 1, "preparation_ids": [ "PREP:COLLIE2025_7" ], "protein_ids": [ "UP:O96028", "UP:Q9BZ95" ], "relationships": [], "relevant": true, "search_text": "compound 7 (collie 2025) inchikey:hhacexllnhjlft-inizcteosa-n 1-[[(2~{s})-1-[4-[ethyl(pyridin-4-ylmethyl)amino]-6-methyl-pyrimidin-2-yl]pyrrolidin-2-yl]methyl]urea compound 7 (collie 2025) nsd2 nsd3 up:o96028:pwwp1 up:q9bz95:pwwp1 9foe {\"aliases\":[\"1-[[(2~{s})-1-[4-[ethyl(pyridin-4-ylmethyl)amino]-6-methyl-pyrimidin-2-yl]pyrrolidin-2-yl]methyl]urea\"],\"ccd_ids\":[\"a1ief\"],\"ccd_names\":\"[\\\"1-[[(2~{s})-1-[4-[ethyl(pyridin-4-ylmethyl)amino]-6-methyl-pyrimidin-2-yl]pyrrolidin-2-yl]methyl]urea\\\"]\",\"ccd_types\":\"[\\\"non-polymer\\\"]\",\"chemical_id\":\"inchikey:hhacexllnhjlft-inizcteosa-n\",\"connectivity_block\":\"hhacexllnhjlft\",\"curated_source_sha256\":null,\"curation_version\":\"frozen-v1.2\",\"external_identifiers\":{},\"formal_charge_by_ccd\":\"{\\\"a1ief\\\": 0}\",\"formulae\":\"[\\\"c19 h27 n7 o\\\"]\",\"geometry_note\":\"ccd ideal sdf is a reference chemical geometry, not a deposited bound pose.\",\"identity_status\":\"complete_deposited_inchikey\",\"inchikey\":\"hhacexllnhjlft-inizcteosa-n\",\"inventory_origin\":\"v1_ccd_inventory\",\"isomeric_smiles\":\"ccn(cc1ccncc1)c2cc(nc(n2)n3ccc[c@h]3cnc(=o)n)c\",\"primary_name\":\"1-[[(2~{s})-1-[4-[ethyl(pyridin-4-ylmethyl)amino]-6-methyl-pyrimidin-2-yl]pyrrolidin-2-yl]methyl]urea\",\"retrieval_date\":\"2026-10-24\",\"smiles_stereo_by_ccd\":\"{\\\"a1ief\\\": \\\"ccn(cc1ccncc1)c2cc(nc(n2)n3ccc[c@h]3cnc(=o)n)c\\\"}\",\"source_metadata_sha256\":\"{\\\"a1ief\\\": \\\"4a823beea94f9176b22d2c2cf26400c5afa4f9e6ae4c31a6a18a969d957e008f\\\"}\",\"source_urls\":[\"https://www.rcsb.org/ligand/a1ief\"]} pmid:40959233 2025 https://pmc.ncbi.nlm.nih.gov/articles/pmc12434523/ pmid:40959233 2025 https://pmc.ncbi.nlm.nih.gov/articles/pmc12434523/ pmid:40959233 2025 https://pmc.ncbi.nlm.nih.gov/articles/pmc12434523/ pmid:40959233 2025 https://pmc.ncbi.nlm.nih.gov/articles/pmc12434523/", "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "https://www.rcsb.org/ligand/A1IEF" ], "verification_pending": false, "context_observations": [ { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0017", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "A1IEF", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "compound_name": "compound 7 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Table 1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD2", "interpretation": "Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.", "is_measured": true, "is_negative": false, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 0.15, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": 7.5, "pdb_id": "9FOE", "preparation_id": "PREP:COLLIE2025_7", "protein_id": "UP:O96028", "publication_year": 2025, "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "role": "experimentally_studied_ligand", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S05", "source_measurement_key": "aad07c81cb428bb6e480af2d79e30d7415101720070de31ebcc123870d7a89c7", "source_original": { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0017", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "A1IEF", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "compound 7 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Table 1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD2", "interpretation": "Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": 7.5, "pdb_id": "9FOE", "preparation_id": "PREP:COLLIE2025_7", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "role": "experimentally_studied_ligand", "source_component_url": null, "source_id": "S05", "source_reported_uncertainty": "0.02", "source_reported_units": "µM", "source_reported_value": "0.15", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "temperature_C": 25, "uncertainty": 0.02, "uncertainty_type": "SD", "uncertainty_uM": 0.02, "unit_conversion": null, "units": "µM", "value": 0.15, "value_operator": "=", "value_uM": 0.15, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "0.02", "source_reported_units": "µM", "source_reported_value": "0.15", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.02, "uncertainty_type": "SD", "uncertainty_uM": 0.02, "unit_conversion": null, "units": "µM", "value": 0.15, "value_operator": "=", "value_uM": 0.15, "verification_level": "primary_full_text_sections_verified" }, { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 350, "assay_construct_start": 211, "assay_record_id": "PWWP:ASSAY:0024", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "A1IEF", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "compound_name": "compound 7 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 211–350\", \"purified_tags\": \"N-terminal GS remnant; C-terminal Avi; biotinylated after GST/6His removal\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Table 1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD2", "interpretation": "Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.", "is_measured": true, "is_negative": false, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 0.76, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": 7.5, "pdb_id": "9FOE", "preparation_id": "PREP:COLLIE2025_7", "protein_id": "UP:O96028", "publication_year": 2025, "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "role": "experimentally_studied_ligand", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S05", "source_measurement_key": "5f0286174b709de1049d65de0d5b3b1079b2fc658f0c37bede4acd893299d803", "source_original": { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 350, "assay_construct_start": 211, "assay_record_id": "PWWP:ASSAY:0024", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "A1IEF", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "compound 7 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 211–350\", \"purified_tags\": \"N-terminal GS remnant; C-terminal Avi; biotinylated after GST/6His removal\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Table 1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD2", "interpretation": "Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": 7.5, "pdb_id": "9FOE", "preparation_id": "PREP:COLLIE2025_7", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "role": "experimentally_studied_ligand", "source_component_url": null, "source_id": "S05", "source_reported_uncertainty": "0.01", "source_reported_units": "µM", "source_reported_value": "0.76", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "temperature_C": 25, "uncertainty": 0.01, "uncertainty_type": "SD", "uncertainty_uM": 0.01, "unit_conversion": null, "units": "µM", "value": 0.76, "value_operator": "=", "value_uM": 0.76, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "0.01", "source_reported_units": "µM", "source_reported_value": "0.76", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.01, "uncertainty_type": "SD", "uncertainty_uM": 0.01, "unit_conversion": null, "units": "µM", "value": 0.76, "value_operator": "=", "value_uM": 0.76, "verification_level": "primary_full_text_sections_verified" }, { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0029", "assay_type": "HTRF displacement IC50", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": null, "ccd_id": "A1IEF", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "compound_name": "compound 7 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SEM\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint": "IC50", "endpoint_label_status": null, "evidence_class": "biochemical_interaction_inhibition", "evidence_location": "Table 1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD2", "interpretation": "Probe displacement from the H3K36me2 binding site; not catalytic SET-domain inhibition.", "is_measured": true, "is_negative": false, "method": "HTRF displacement", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 0.21, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": null, "pdb_id": "9FOE", "preparation_id": "PREP:COLLIE2025_7", "protein_id": "UP:O96028", "publication_year": 2025, "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "HTRF full conditions are referenced to Carlino et al. 2024 DOI 10.1021/acs.jmedchem.4c00215. Its main protocol remains inaccessible after official repository checks. The actual supplement was inspected but contains no HTRF protocol. 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\"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.7262, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"236\", \"component\": \"TRP\", \"entity_position\": 33, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.3973, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"266\", \"component\": \"PHE\", \"entity_position\": 63, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.4717, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"267\", \"component\": \"PHE\", \"entity_position\": 64, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.7848, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"268\", \"component\": \"GLY\", \"entity_position\": 65, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.6954, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"269\", \"component\": \"ASP\", \"entity_position\": 66, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.4123, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"270\", \"component\": \"ALA\", \"entity_position\": 67, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.2268, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"272\", \"component\": \"GLU\", \"entity_position\": 69, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.1245, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"273\", \"component\": \"ARG\", \"entity_position\": 70, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.3528, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"274\", \"component\": \"ALA\", \"entity_position\": 71, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.8749, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"318\", \"component\": \"LEU\", \"entity_position\": 115, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.9402, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"321\", \"component\": \"GLN\", \"entity_position\": 118, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.4515, \"uniprot_position\": null}]", "pose_kind": "deposited_source_coordinates", "reference_model": "1", "source_coordinate_file": "Structures/NSD2__HUMAN__O96028/Co-Crystals/9FOE/original.cif", "source_coordinate_sha256": "f2b013ad297bf526cad83328b7e95e1b56e2e8ecd819ac082835ffadc0108034", "unique_heavy_atom_names": 27 }, "ligand_instance_id": "PDB:9FOE:LIG:B:A1IEF:401:.", "ligand_label_asym_id": "B", "minimum_Pfam_distance_angstrom": 3.1245, "minimum_chain_distance_angstrom": 3.1245, "minimum_core_distance_angstrom": 3.1245, "multiple_contacting_mapped_chains": 0, "pdb_id": "9FOE", "protein_id": "UP:O96028", "protein_label_asym_id": "A", "rank_interpretation": "Distance rank among mapped chains only; crystal packing and biological site assignment require separate review.", "role": "experimentally studied ligand", "role_category": "functional", "site_id": "PDB:9FOE:LIG:B:A1IEF:401:.:SITE:UP:O96028:PWWP1:A", "source_coordinate_sha256": "f2b013ad297bf526cad83328b7e95e1b56e2e8ecd819ac082835ffadc0108034" } ], "context_assay_count": 4, "context_measured_count": 4, "context_bound_count": 1, "context_pdb_count": 1, "context_negative_count": 1, "context_is_probe": false, "context_bioactivity_only": false, "context_kind": "Measured + bound structure", "science": { "studied_compound": true, "measured_count": 4, "structural_research_ligand": true, "research_pdb_count": 1, "other_component": false, "component_site_count": 0, "verification_queue": false, "positive_direct_binder": true, "reported_probe": false, "reported_control": false, "cellular_activity": false, "protein_degradation": false, "bioactivity_only": false, "research_site_count": 1, "unknown_site_count": 0, "annotation_roles": [ "studied", "structural" ] }, "science_label": "Studied + deposited research ligand", "science_profile": { "annotation_roles": [ "studied", "structural" ], "cellular_activity": false, "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "compound_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "entity_kind": "chemical_identity", "identity_resolved": true, "measured_observation_count": 4, "name": "compound 7 (Collie 2025)", "other_pdb_component": false, "other_site_count": 0, "positive_direct_binder": true, "primary_view": "studied", "protein_degradation": false, "reported_control": false, "reported_probe": false, "rule": "Independent source observations + per-site coordinate role, not universal pharmacology", "source_observation_ids": [ "PWWP:ASSAY:0024", "PWWP:ASSAY:0017", "PWWP11:ASSAY:0004", "PWWP:ASSAY:0029" ], "source_site_ids": [ "PDB:9FOE:LIG:B:A1IEF:401:.:SITE:UP:O96028:PWWP1:A" ], "structural_research_ligand": true, "structural_research_site_count": 1, "studied_compound": true, "total_observation_count": 4, "uncertain_site_count": 0, "uncertainty": "Classification is evidence- and experiment-scoped; missing assays do not prove nonbinding.", "verification_queue": false, "verification_status": "source_scoped_mixed" }, "science_site_roles": { "PDB:9FOE:LIG:B:A1IEF:401:.:SITE:UP:O96028:PWWP1:A": { "ccd_url": "https://www.rcsb.org/ligand/A1IEF", "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "compound_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "contact_class": "native_annotation_core_contact", "coordinate_sha256": "f2b013ad297bf526cad83328b7e95e1b56e2e8ecd819ac082835ffadc0108034", "domain_id": "UP:O96028:PWWP1", "exact_pwwp_contact": true, "ligand_instance_id": "PDB:9FOE:LIG:B:A1IEF:401:.", "observed_other_component": false, "pdb_id": "9FOE", "protein_id": "UP:O96028", "role_code": "reported_studied_structural_ligand", "role_group": "research_ligand", "rule": "Phase5 exact deposited site role, measured heavy-atom contacts and native-domain scope", "site_id": "PDB:9FOE:LIG:B:A1IEF:401:.:SITE:UP:O96028:PWWP1:A", "source_role": "experimentally studied ligand", "source_url": "https://www.rcsb.org/structure/9FOE", "structural_research_ligand": true, "uncertainty": "Role is source-annotated; deposited proximity alone does not establish solution binding or biological activity.", "verification_status": "phase5_derived_deposited_geometry" } }, "science_assay_roles": { "PWWP:ASSAY:0017": { "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "compound_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_type": "direct_binding", "explicitly_negative": false, "measured": true, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP:ASSAY:0017", "operator": "=", "positive_direct_binder": true, "preparation_id": "PREP:COLLIE2025_7", "protein_id": "UP:O96028", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "reported_cellular": false, "reported_control": false, "reported_probe": false, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "S05", "source_location": "Table 1", "source_role": "experimentally_studied_ligand", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "studied_compound": true, "target_scope": "domain_specific", "target_variant": null, "units": "µM", "value": 0.15, "verification_status": "primary_full_text_sections_verified" }, "PWWP:ASSAY:0024": { "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "compound_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_type": "direct_binding", "explicitly_negative": false, "measured": true, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP:ASSAY:0024", "operator": "=", "positive_direct_binder": true, "preparation_id": "PREP:COLLIE2025_7", "protein_id": "UP:O96028", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "reported_cellular": false, "reported_control": false, "reported_probe": false, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "S05", "source_location": "Table 1", "source_role": "experimentally_studied_ligand", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "studied_compound": true, "target_scope": "domain_specific", "target_variant": null, "units": "µM", "value": 0.76, "verification_status": "primary_full_text_sections_verified" }, "PWWP:ASSAY:0029": { "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "compound_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "domain_id": "UP:O96028:PWWP1", "endpoint": "IC50", "evidence_type": "biochemical_function", "explicitly_negative": false, "measured": true, "method": "HTRF displacement", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP:ASSAY:0029", "operator": "=", "positive_direct_binder": false, "preparation_id": "PREP:COLLIE2025_7", "protein_id": "UP:O96028", "remaining_uncertainty": "HTRF full conditions are referenced to Carlino et al. 2024 DOI 10.1021/acs.jmedchem.4c00215. Its main protocol remains inaccessible after official repository checks. The actual supplement was inspected but contains no HTRF protocol. Table 1 reports SEM; independence level of HTRF replicates is not specified.", "reported_cellular": false, "reported_control": false, "reported_probe": false, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "S05", "source_location": "Table 1", "source_role": "experimentally_studied_ligand", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "source_verification_scope": "Phase 3 primary Table 1 and actual Collie supporting PDF pages 7, 9 and 14; Carlino supporting PDF contents inspected, but the inherited main-article HTRF method remains not inspected after documented access attempts.", "studied_compound": true, "target_scope": "domain_specific", "target_variant": null, "units": "µM", "value": 0.21, "verification_status": "primary_full_text_sections_verified" }, "PWWP11:ASSAY:0004": { "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "compound_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "domain_id": "UP:Q9BZ95:PWWP1", "endpoint": "Kd", "evidence_type": "censored_binding", "explicitly_negative": true, "measured": true, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "observation_id": "PWWP11:ASSAY:0004", "operator": ">", "positive_direct_binder": false, "preparation_id": "PREP:COLLIE2025_7", "protein_id": "UP:Q9BZ95", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "reported_cellular": false, "reported_control": false, "reported_probe": false, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "S05", "source_location": "Table 1 NSD3 (263–398) column", "source_role": "counter_target_assay", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "studied_compound": true, "target_scope": "domain_specific", "target_variant": null, "units": "µM", "value": 30.0, "verification_status": "source_scope_unresolved" } }, "example": { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0017", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "A1IEF", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "compound_name": "compound 7 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Table 1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD2", "interpretation": "Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.", "is_measured": true, "is_negative": false, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 0.15, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": 7.5, "pdb_id": "9FOE", "preparation_id": "PREP:COLLIE2025_7", "protein_id": "UP:O96028", "publication_year": 2025, "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "role": "experimentally_studied_ligand", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S05", "source_measurement_key": "aad07c81cb428bb6e480af2d79e30d7415101720070de31ebcc123870d7a89c7", "source_original": { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0017", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "A1IEF", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "compound 7 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Table 1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD2", "interpretation": "Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": 7.5, "pdb_id": "9FOE", "preparation_id": "PREP:COLLIE2025_7", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "role": "experimentally_studied_ligand", "source_component_url": null, "source_id": "S05", "source_reported_uncertainty": "0.02", "source_reported_units": "µM", "source_reported_value": "0.15", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "temperature_C": 25, "uncertainty": 0.02, "uncertainty_type": "SD", "uncertainty_uM": 0.02, "unit_conversion": null, "units": "µM", "value": 0.15, "value_operator": "=", "value_uM": 0.15, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "0.02", "source_reported_units": "µM", "source_reported_value": "0.15", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.02, "uncertainty_type": "SD", "uncertainty_uM": 0.02, "unit_conversion": null, "units": "µM", "value": 0.15, "value_operator": "=", "value_uM": 0.15, "verification_level": "primary_full_text_sections_verified" }, "matched_observations": [ { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0017", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "A1IEF", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "compound_name": "compound 7 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Table 1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD2", "interpretation": "Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.", "is_measured": true, "is_negative": false, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 0.15, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": 7.5, "pdb_id": "9FOE", "preparation_id": "PREP:COLLIE2025_7", "protein_id": "UP:O96028", "publication_year": 2025, "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. 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Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "role": "experimentally_studied_ligand", "source_component_url": null, "source_id": "S05", "source_reported_uncertainty": "0.02", "source_reported_units": "µM", "source_reported_value": "0.15", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "temperature_C": 25, "uncertainty": 0.02, "uncertainty_type": "SD", "uncertainty_uM": 0.02, "unit_conversion": null, "units": "µM", "value": 0.15, "value_operator": "=", "value_uM": 0.15, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "0.02", "source_reported_units": "µM", "source_reported_value": "0.15", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.02, "uncertainty_type": "SD", "uncertainty_uM": 0.02, "unit_conversion": null, "units": "µM", "value": 0.15, "value_operator": "=", "value_uM": 0.15, "verification_level": "primary_full_text_sections_verified" }, { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 350, "assay_construct_start": 211, "assay_record_id": "PWWP:ASSAY:0024", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "A1IEF", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "compound_name": "compound 7 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 211–350\", \"purified_tags\": \"N-terminal GS remnant; C-terminal Avi; biotinylated after GST/6His removal\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Table 1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD2", "interpretation": "Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.", "is_measured": true, "is_negative": false, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 0.76, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": 7.5, "pdb_id": "9FOE", "preparation_id": "PREP:COLLIE2025_7", "protein_id": "UP:O96028", "publication_year": 2025, "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "role": "experimentally_studied_ligand", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S05", "source_measurement_key": "5f0286174b709de1049d65de0d5b3b1079b2fc658f0c37bede4acd893299d803", "source_original": { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 350, "assay_construct_start": 211, "assay_record_id": "PWWP:ASSAY:0024", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "A1IEF", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "compound 7 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 211–350\", \"purified_tags\": \"N-terminal GS remnant; C-terminal Avi; biotinylated after GST/6His removal\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Table 1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD2", "interpretation": "Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": 7.5, "pdb_id": "9FOE", "preparation_id": "PREP:COLLIE2025_7", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "role": "experimentally_studied_ligand", "source_component_url": null, "source_id": "S05", "source_reported_uncertainty": "0.01", "source_reported_units": "µM", "source_reported_value": "0.76", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "temperature_C": 25, "uncertainty": 0.01, "uncertainty_type": "SD", "uncertainty_uM": 0.01, "unit_conversion": null, "units": "µM", "value": 0.76, "value_operator": "=", "value_uM": 0.76, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "0.01", "source_reported_units": "µM", "source_reported_value": "0.76", "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.01, "uncertainty_type": "SD", "uncertainty_uM": 0.01, "unit_conversion": null, "units": "µM", "value": 0.76, "value_operator": "=", "value_uM": 0.76, "verification_level": "primary_full_text_sections_verified" }, { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0029", "assay_type": "HTRF displacement IC50", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": null, "ccd_id": "A1IEF", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "compound_name": "compound 7 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SEM\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint": "IC50", "endpoint_label_status": null, "evidence_class": "biochemical_interaction_inhibition", "evidence_location": "Table 1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD2", "interpretation": "Probe displacement from the H3K36me2 binding site; not catalytic SET-domain inhibition.", "is_measured": true, "is_negative": false, "method": "HTRF displacement", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 0.21, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": null, "pdb_id": "9FOE", "preparation_id": "PREP:COLLIE2025_7", "protein_id": "UP:O96028", "publication_year": 2025, "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "HTRF full conditions are referenced to Carlino et al. 2024 DOI 10.1021/acs.jmedchem.4c00215. Its main protocol remains inaccessible after official repository checks. The actual supplement was inspected but contains no HTRF protocol. Table 1 reports SEM; independence level of HTRF replicates is not specified.", "replicates": "at least 3", "role": "experimentally_studied_ligand", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S05", "source_measurement_key": "a35b96a8a0ecd79abf838e025cc07186635d60b69a1e38f19def0cc2cf8704ce", "source_original": { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0029", "assay_type": "HTRF displacement IC50", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": null, "ccd_id": "A1IEF", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "compound 7 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SEM\"}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": null, "evidence_class": "biochemical_interaction_inhibition", "evidence_location": "Table 1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD2", "interpretation": "Probe displacement from the H3K36me2 binding site; not catalytic SET-domain inhibition.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": null, "pdb_id": "9FOE", "preparation_id": "PREP:COLLIE2025_7", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "HTRF full conditions are referenced to Carlino et al. 2024 DOI 10.1021/acs.jmedchem.4c00215. Its main protocol remains inaccessible after official repository checks. The actual supplement was inspected but contains no HTRF protocol. Table 1 reports SEM; independence level of HTRF replicates is not specified.", "replicates": "at least 3", "role": "experimentally_studied_ligand", "source_component_url": null, "source_id": "S05", "source_reported_uncertainty": "0.01", "source_reported_units": "µM", "source_reported_value": "0.21", "source_verification_scope": "Phase 3 primary Table 1 and actual Collie supporting PDF pages 7, 9 and 14; Carlino supporting PDF contents inspected, but the inherited main-article HTRF method remains not inspected after documented access attempts.", "temperature_C": null, "uncertainty": 0.01, "uncertainty_type": "SEM", "uncertainty_uM": 0.01, "unit_conversion": null, "units": "µM", "value": 0.21, "value_operator": "=", "value_uM": 0.21, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "0.01", "source_reported_units": "µM", "source_reported_value": "0.21", "source_verification_scope": "Phase 3 primary Table 1 and actual Collie supporting PDF pages 7, 9 and 14; Carlino supporting PDF contents inspected, but the inherited main-article HTRF method remains not inspected after documented access attempts.", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 0.01, "uncertainty_type": "SEM", "uncertainty_uM": 0.01, "unit_conversion": null, "units": "µM", "value": 0.21, "value_operator": "=", "value_uM": 0.21, "verification_level": "primary_full_text_sections_verified" }, { "DMSO_percent": 0.3, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 398, "assay_construct_start": 263, "assay_record_id": "PWWP11:ASSAY:0004", "assay_type": "SPR Kd counter-screen", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": null, "baseline_assay_record": 0, "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "ccd_id": "A1IEF", "ccd_mapping_source": null, "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "compound_name": "compound 7 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD3 263–398\", \"purified_tags\": \"N-terminal 6His-TEV retained\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:Q9BZ95:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "censored_binding_limit", "evidence_location": "Table 1 NSD3 (263–398) column", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "gene": "NSD3", "interpretation": "Single counter-target experiment; not evidence of proteome-wide selectivity. No-binding rows have no inferred numerical threshold.", "is_measured": true, "is_negative": true, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": null, "numeric_transcription_status": "matches_primary_table", "numeric_value_inferred_from_structure": null, "organism": "Homo sapiens", "pH": 7.5, "pdb_id": null, "preparation_id": "PREP:COLLIE2025_7", "protein_id": "UP:Q9BZ95", "publication_year": 2025, "qualitative_result": null, "reference_id": "PMID:40959233", "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. 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inchikey:xphopapmjbslfn-uhfffaoysa-n mrt866 ~{n}-cyclopropyl-3-oxidanylidene-~{n}-(thiophen-2-ylmethyl)-4~{h}-1,4-benzoxazine-7-carboxamide nsd2 up:o96028:pwwp1 7lmt 7mdn {\"aliases\":[\"~{n}-cyclopropyl-3-oxidanylidene-~{n}-(thiophen-2-ylmethyl)-4~{h}-1,4-benzoxazine-7-carboxamide\"],\"ccd_ids\":[\"y6v\"],\"ccd_names\":\"[\\\"~{n}-cyclopropyl-3-oxidanylidene-~{n}-(thiophen-2-ylmethyl)-4~{h}-1,4-benzoxazine-7-carboxamide\\\"]\",\"ccd_types\":\"[\\\"non-polymer\\\"]\",\"chemical_id\":\"inchikey:xphopapmjbslfn-uhfffaoysa-n\",\"connectivity_block\":\"xphopapmjbslfn\",\"curated_source_sha256\":null,\"curation_version\":\"frozen-v1.2\",\"external_identifiers\":{},\"formal_charge_by_ccd\":\"{\\\"y6v\\\": 0}\",\"formulae\":\"[\\\"c17 h16 n2 o3 s\\\"]\",\"geometry_note\":\"ccd ideal sdf is a reference chemical geometry, not a deposited bound 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Crystallography 211–350 is not assigned as the binding-assay construct.", "reported_cellular": false, "reported_control": false, "reported_probe": false, "rule": "Phase5 source-curated evidence_class, material, target_scope, source role; no inferred affinities", "source_id": "S02", "source_location": "Results: Discovery of a potent ligand targeting NSD2-PWWP1", "source_role": "experimentally_studied_ligand", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "studied_compound": true, "target_scope": "domain_specific", "target_variant": null, "units": "nM", "value": 349.0, "verification_status": "primary_full_text_sections_verified" } }, "example": { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP:ASSAY:0003", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": null, "ccd_id": "Y6V", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:XPHOPAPMJBSLFN-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:XPHOPAPMJBSLFN-UHFFFAOYSA-N", "compound_name": "MRT866", "conditions": "{}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Results: Discovery of a potent ligand targeting NSD2-PWWP1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": null, "is_measured": true, "is_negative": false, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 0.34900000000000003, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": null, "pdb_id": "7MDN", "preparation_id": "PREP:MRT866", "protein_id": "UP:O96028", "publication_year": 2022, "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "349 ± 19 nM verified in Results; MRT866-specific SPR construct/protocol, replicate definition and uncertainty statistic remain unresolved. Crystallography 211–350 is not assigned as the binding-assay construct.", "replicates": null, "role": "experimentally_studied_ligand", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S02", "source_measurement_key": "aafd897bf3e781764d2d98e461b4ffe68e7f46cb4d921caafedd85f098c70d23", "source_original": { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP:ASSAY:0003", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": null, "ccd_id": "Y6V", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:XPHOPAPMJBSLFN-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "MRT866", "conditions": "{}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Results: Discovery of a potent ligand targeting NSD2-PWWP1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": null, "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": null, "pdb_id": "7MDN", "preparation_id": "PREP:MRT866", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "349 ± 19 nM verified in Results; MRT866-specific SPR construct/protocol, replicate definition and uncertainty statistic remain unresolved. Crystallography 211–350 is not assigned as the binding-assay construct.", "replicates": null, "role": "experimentally_studied_ligand", "source_component_url": null, "source_id": "S02", "source_reported_uncertainty": "19", "source_reported_units": "nM", "source_reported_value": "349", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "temperature_C": null, "uncertainty": 19.0, "uncertainty_type": null, "uncertainty_uM": 0.019, "unit_conversion": null, "units": "nM", "value": 349.0, "value_operator": "=", "value_uM": 0.349, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "19", "source_reported_units": "nM", "source_reported_value": "349", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 19.0, "uncertainty_type": null, "uncertainty_uM": 0.019, "unit_conversion": null, "units": "nM", "value": 349.0, "value_operator": "=", "value_uM": 0.349, "verification_level": "primary_full_text_sections_verified" }, "matched_observations": [ { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP:ASSAY:0003", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": null, "ccd_id": "Y6V", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:XPHOPAPMJBSLFN-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:XPHOPAPMJBSLFN-UHFFFAOYSA-N", "compound_name": "MRT866", "conditions": "{}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Results: Discovery of a potent ligand targeting NSD2-PWWP1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": null, "is_measured": true, "is_negative": false, "method": "SPR", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 0.34900000000000003, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": null, "pdb_id": "7MDN", "preparation_id": "PREP:MRT866", "protein_id": "UP:O96028", "publication_year": 2022, "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "349 ± 19 nM verified in Results; MRT866-specific SPR construct/protocol, replicate definition and uncertainty statistic remain unresolved. Crystallography 211–350 is not assigned as the binding-assay construct.", "replicates": null, "role": "experimentally_studied_ligand", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S02", "source_measurement_key": "aafd897bf3e781764d2d98e461b4ffe68e7f46cb4d921caafedd85f098c70d23", "source_original": { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP:ASSAY:0003", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": null, "ccd_id": "Y6V", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:XPHOPAPMJBSLFN-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "MRT866", "conditions": "{}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Results: Discovery of a potent ligand targeting NSD2-PWWP1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": null, "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": null, "pdb_id": "7MDN", "preparation_id": "PREP:MRT866", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "349 ± 19 nM verified in Results; MRT866-specific SPR construct/protocol, replicate definition and uncertainty statistic remain unresolved. Crystallography 211–350 is not assigned as the binding-assay construct.", "replicates": null, "role": "experimentally_studied_ligand", "source_component_url": null, "source_id": "S02", "source_reported_uncertainty": "19", "source_reported_units": "nM", "source_reported_value": "349", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "temperature_C": null, "uncertainty": 19.0, "uncertainty_type": null, "uncertainty_uM": 0.019, "unit_conversion": null, "units": "nM", "value": 349.0, "value_operator": "=", "value_uM": 0.349, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "19", "source_reported_units": "nM", "source_reported_value": "349", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 19.0, "uncertainty_type": null, "uncertainty_uM": 0.019, "unit_conversion": null, "units": "nM", "value": 349.0, "value_operator": "=", "value_uM": 0.349, "verification_level": "primary_full_text_sections_verified" } ], "matched_assay_count": 1 }, { "aliases": [ "VARENICLINE", "varenicline" ], "assay_count": 2, "associated_pdb_ids": [ "8Z6O" ], "bound_structure_count": 1, "category": "Bioactivity + bound structure", "chemical_id": "INCHIKEY:JQSHBVHOMNKWFT-DTORHVGOSA-N", "classifications": [], "compound_id": "INCHIKEY:JQSHBVHOMNKWFT-DTORHVGOSA-N", "curation_version": "phase5-1.0.0", "depiction": { "calculated_HBA": 3, "calculated_HBD": 1, "calculated_TPSA": 37.81, "calculated_formula": "C13H13N3", "calculated_logP": 1.8039, "calculated_molecular_weight": 211.268, "computed_inchikey": "JQSHBVHOMNKWFT-DTORHVGOSA-N", "descriptor_scope": "RDKit calculation for the source identity; not an experimental measurement", "files": { "dark": "9cae4a78dcd33a27aa30-dark.svg", "light": "9cae4a78dcd33a27aa30-light.svg" }, "rdkit_version": "2025.09.3", "status": "verified_smiles_full_inchikey_match" }, "development_status": "Not independently curated", "domain_ids": [ "UP:Q7Z4V5:PWWP1" ], "entity_kind": "chemical_identity", "genes": [ "HDGFL2" ], "has_bioactivity_only": false, "has_source_conflict": false, "identity": { "aliases": [ "VARENICLINE" ], "ccd_ids": [ "QMR" ], "ccd_names": "[\"VARENICLINE\"]", "ccd_types": "[\"non-polymer\"]", "chemical_id": "INCHIKEY:JQSHBVHOMNKWFT-DTORHVGOSA-N", "connectivity_block": "JQSHBVHOMNKWFT", "curated_source_sha256": null, "curation_version": "frozen-v1.2", "external_identifiers": {}, "formal_charge_by_ccd": "{\"QMR\": 0}", "formulae": "[\"C13 H13 N3\"]", "geometry_note": "CCD ideal SDF is a reference chemical geometry, not a deposited bound pose.", "identity_status": "complete_deposited_InChIKey", "inchikey": "JQSHBVHOMNKWFT-DTORHVGOSA-N", "inventory_origin": "v1_CCD_inventory", "isomeric_smiles": "c1cnc2cc3c(cc2n1)[C@@H]4C[C@H]3CNC4", "primary_name": "VARENICLINE", "retrieval_date": "2026-10-24", "smiles_stereo_by_ccd": "{\"QMR\": \"c1cnc2cc3c(cc2n1)[C@@H]4C[C@H]3CNC4\"}", "source_metadata_sha256": "{\"QMR\": \"0439a1f642c76ab4c22ef3c5263fd2b3dec2301d7a686de21385d3defd3e9814\"}", "source_urls": [ "https://www.rcsb.org/ligand/QMR" ] }, "identity_note": "Complete deposited identity retained; no connectivity-only or name-only merge.", "identity_resolved": true, "is_control": false, "is_probe": false, "measured_observation_count": 2, "name": "varenicline", "negative_count": 0, "observation_ids": [ "PWWP:ASSAY:0010", "PWWP5:ASSAY:0027" ], "pdb_structure_count": 1, "preparation_count": 1, "preparation_ids": [ "PREP:VARENICLINE" ], "protein_ids": [ "UP:Q7Z4V5" ], "relationships": [], "relevant": true, "search_text": "varenicline inchikey:jqshbvhomnkwft-dtorhvgosa-n varenicline varenicline hdgfl2 up:q7z4v5:pwwp1 8z6o {\"aliases\":[\"varenicline\"],\"ccd_ids\":[\"qmr\"],\"ccd_names\":\"[\\\"varenicline\\\"]\",\"ccd_types\":\"[\\\"non-polymer\\\"]\",\"chemical_id\":\"inchikey:jqshbvhomnkwft-dtorhvgosa-n\",\"connectivity_block\":\"jqshbvhomnkwft\",\"curated_source_sha256\":null,\"curation_version\":\"frozen-v1.2\",\"external_identifiers\":{},\"formal_charge_by_ccd\":\"{\\\"qmr\\\": 0}\",\"formulae\":\"[\\\"c13 h13 n3\\\"]\",\"geometry_note\":\"ccd ideal sdf is a reference chemical geometry, not a deposited bound pose.\",\"identity_status\":\"complete_deposited_inchikey\",\"inchikey\":\"jqshbvhomnkwft-dtorhvgosa-n\",\"inventory_origin\":\"v1_ccd_inventory\",\"isomeric_smiles\":\"c1cnc2cc3c(cc2n1)[c@@h]4c[c@h]3cnc4\",\"primary_name\":\"varenicline\",\"retrieval_date\":\"2026-10-24\",\"smiles_stereo_by_ccd\":\"{\\\"qmr\\\": \\\"c1cnc2cc3c(cc2n1)[c@@h]4c[c@h]3cnc4\\\"}\",\"source_metadata_sha256\":\"{\\\"qmr\\\": \\\"0439a1f642c76ab4c22ef3c5263fd2b3dec2301d7a686de21385d3defd3e9814\\\"}\",\"source_urls\":[\"https://www.rcsb.org/ligand/qmr\"]} pmid:39031937 2024 https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981 pmid:39031937 2024 https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "source_urls": [ "https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981", "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "https://www.rcsb.org/ligand/QMR" ], "verification_pending": false, "context_observations": [ { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 93, "assay_construct_start": 1, "assay_record_id": "PWWP:ASSAY:0010", "assay_type": "NMR chemical-shift perturbation Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "HEPES-buffered saline; exact buffer/salt concentrations not restated in CSP subsection", "ccd_id": "QMR", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:JQSHBVHOMNKWFT-DTORHVGOSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:JQSHBVHOMNKWFT-DTORHVGOSA-N", "compound_name": "varenicline", "conditions": "{\"fit_model\": \"1:1 binding; global fit with shared Kd\", \"ligand_to_protein_molar_ratio_range\": [0, 6], \"protein_concentration_uM\": 100, \"protein_construct\": \"HDGFL2 1–93\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP", "domain_id": "UP:Q7Z4V5:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Results; Figure 1E", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981", "gene": "HDGFL2", "interpretation": "Converted from 0.25 ± 0.04 mM. Receptor pharmacology in other systems is not evidence of PWWP potency.", "is_measured": true, "is_negative": false, "method": "NMR chemical-shift perturbation", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 250.0, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": 7.4, "pdb_id": "8Z6O", "preparation_id": "PREP:VARENICLINE", "protein_id": "UP:Q7Z4V5", "publication_year": 2024, "qualitative_result": null, "reference_id": "PMID:39031937", "remaining_uncertainty": "Full assay buffer, temperature and incubation metadata not transcribed; null means uncurated, not absent.", "replicates": null, "role": "experimentally_studied_fragment_ligand", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S04", "source_measurement_key": "2b9c01d4150ca3f35a87bce9ed5d4dde79bfafc9ecb109e3891ecdca18c484f1", "source_original": { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 93, "assay_construct_start": 1, "assay_record_id": "PWWP:ASSAY:0010", "assay_type": "NMR chemical-shift perturbation Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "HEPES-buffered saline; exact buffer/salt concentrations not restated in CSP subsection", "ccd_id": "QMR", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:JQSHBVHOMNKWFT-DTORHVGOSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "varenicline", "conditions": "{\"fit_model\": \"1:1 binding; global fit with shared Kd\", \"ligand_to_protein_molar_ratio_range\": [0, 6], \"protein_concentration_uM\": 100, \"protein_construct\": \"HDGFL2 1–93\"}", "crystallographic_component_ids": null, "domain": "PWWP", "domain_id": "UP:Q7Z4V5:PWWP1", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Results; Figure 1E", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981", "gene": "HDGFL2", "interpretation": "Converted from 0.25 ± 0.04 mM. Receptor pharmacology in other systems is not evidence of PWWP potency.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": 7.4, "pdb_id": "8Z6O", "preparation_id": "PREP:VARENICLINE", "protein_id": "UP:Q7Z4V5", "qualitative_result": null, "reference_id": "PMID:39031937", "remaining_uncertainty": "Full assay buffer, temperature and incubation metadata not transcribed; null means uncurated, not absent.", "replicates": null, "role": "experimentally_studied_fragment_ligand", "source_component_url": null, "source_id": "S04", "source_reported_uncertainty": "0.04", "source_reported_units": "mM", "source_reported_value": "0.25", "source_verification_scope": "primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved", "temperature_C": null, "uncertainty": 40.0, "uncertainty_type": "fitting_error", "uncertainty_uM": 40.0, "unit_conversion": "0.25 mM × 1000 = 250 µM; 0.04 mM × 1000 = 40 µM", "units": "µM", "value": 250.0, "value_operator": "=", "value_uM": 250.0, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "0.04", "source_reported_units": "mM", "source_reported_value": "0.25", "source_verification_scope": "primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 40.0, "uncertainty_type": "fitting_error", "uncertainty_uM": 40.0, "unit_conversion": "0.25 mM × 1000 = 250 µM; 0.04 mM × 1000 = 40 µM", "units": "µM", "value": 250.0, "value_operator": "=", "value_uM": 250.0, "verification_level": "primary_full_text_sections_verified" }, { "assay_construct_end": 93, "assay_construct_start": 1, "assay_context": "purified_mutant_domain", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0027", "assay_type": "NMR chemical-shift perturbation Kd", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:JQSHBVHOMNKWFT-DTORHVGOSA-N", "compound_id": "INCHIKEY:JQSHBVHOMNKWFT-DTORHVGOSA-N", "compound_name": "varenicline", "conditions": { "binding_model": "1:1 global fit of perturbed residues", "buffer": "HEPES-buffered saline; CSP subsection does not separately give HEPES/NaCl concentrations", "ligand_protein_molar_ratio_range": [ 0, 6 ], "pH": 7.4, "protein_concentration_mM": 0.1, "target_variant": "Y18S" }, "curation_version": "phase5-1.0.0", "domain": "PWWP1", "domain_id": "UP:Q7Z4V5:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_location": "Results; Figure 2E", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "HDGFL2", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_measured": true, "is_negative": false, "method": "NMR chemical-shift perturbation", "normalized_exact_uM": 780.0, "numeric_transcription_status": "source_preserved", "numeric_value_inferred_from_structure": false, "organism": "Homo sapiens", "pH": 7.4, "pdb_id": null, "preparation_id": "PREP:VARENICLINE", "protein_id": "UP:Q7Z4V5", "publication_year": 2024, "reference_id": "PMID:39031937", "remaining_uncertainty": "Y18S mutant measurement; must not be pooled with wild-type affinity. Construct is the source HDGFRP2 PWWP expression fragment (1–93) carrying the stated mutation. 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Receptor pharmacology in other systems is not evidence of PWWP potency.", "is_measured": true, "is_negative": false, "method": "NMR chemical-shift perturbation", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 250.0, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": 7.4, "pdb_id": "8Z6O", "preparation_id": "PREP:VARENICLINE", "protein_id": "UP:Q7Z4V5", "publication_year": 2024, "qualitative_result": null, "reference_id": "PMID:39031937", "remaining_uncertainty": "Full assay buffer, temperature and incubation metadata not transcribed; null means uncurated, not absent.", "replicates": null, "role": "experimentally_studied_fragment_ligand", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S04", "source_measurement_key": "2b9c01d4150ca3f35a87bce9ed5d4dde79bfafc9ecb109e3891ecdca18c484f1", "source_original": { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 93, "assay_construct_start": 1, "assay_record_id": "PWWP:ASSAY:0010", "assay_type": "NMR chemical-shift perturbation Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "HEPES-buffered saline; exact buffer/salt concentrations not restated in CSP subsection", "ccd_id": "QMR", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:JQSHBVHOMNKWFT-DTORHVGOSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "varenicline", "conditions": "{\"fit_model\": \"1:1 binding; global fit with shared Kd\", \"ligand_to_protein_molar_ratio_range\": [0, 6], \"protein_concentration_uM\": 100, \"protein_construct\": \"HDGFL2 1–93\"}", "crystallographic_component_ids": null, "domain": "PWWP", "domain_id": "UP:Q7Z4V5:PWWP1", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Results; Figure 1E", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981", "gene": "HDGFL2", "interpretation": "Converted from 0.25 ± 0.04 mM. Receptor pharmacology in other systems is not evidence of PWWP potency.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": 7.4, "pdb_id": "8Z6O", "preparation_id": "PREP:VARENICLINE", "protein_id": "UP:Q7Z4V5", "qualitative_result": null, "reference_id": "PMID:39031937", "remaining_uncertainty": "Full assay buffer, temperature and incubation metadata not transcribed; null means uncurated, not absent.", "replicates": null, "role": "experimentally_studied_fragment_ligand", "source_component_url": null, "source_id": "S04", "source_reported_uncertainty": "0.04", "source_reported_units": "mM", "source_reported_value": "0.25", "source_verification_scope": "primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved", "temperature_C": null, "uncertainty": 40.0, "uncertainty_type": "fitting_error", "uncertainty_uM": 40.0, "unit_conversion": "0.25 mM × 1000 = 250 µM; 0.04 mM × 1000 = 40 µM", "units": "µM", "value": 250.0, "value_operator": "=", "value_uM": 250.0, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "0.04", "source_reported_units": "mM", "source_reported_value": "0.25", "source_verification_scope": "primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 40.0, "uncertainty_type": "fitting_error", "uncertainty_uM": 40.0, "unit_conversion": "0.25 mM × 1000 = 250 µM; 0.04 mM × 1000 = 40 µM", "units": "µM", "value": 250.0, "value_operator": "=", "value_uM": 250.0, "verification_level": "primary_full_text_sections_verified" }, "matched_observations": [ { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 93, "assay_construct_start": 1, "assay_record_id": "PWWP:ASSAY:0010", "assay_type": "NMR chemical-shift perturbation Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "HEPES-buffered saline; exact buffer/salt concentrations not restated in CSP subsection", "ccd_id": "QMR", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:JQSHBVHOMNKWFT-DTORHVGOSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_id": "INCHIKEY:JQSHBVHOMNKWFT-DTORHVGOSA-N", "compound_name": "varenicline", "conditions": "{\"fit_model\": \"1:1 binding; global fit with shared Kd\", \"ligand_to_protein_molar_ratio_range\": [0, 6], \"protein_concentration_uM\": 100, \"protein_construct\": \"HDGFL2 1–93\"}", "crystallographic_component_ids": null, "curation_version": "frozen-v1.2", "domain": "PWWP", "domain_id": "UP:Q7Z4V5:PWWP1", "endpoint": "Kd", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Results; Figure 1E", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981", "gene": "HDGFL2", "interpretation": "Converted from 0.25 ± 0.04 mM. Receptor pharmacology in other systems is not evidence of PWWP potency.", "is_measured": true, "is_negative": false, "method": "NMR chemical-shift perturbation", "molecular_entity_type": "small_molecule_preparation", "normalized_exact_uM": 250.0, "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "organism": "Homo sapiens", "pH": 7.4, "pdb_id": "8Z6O", "preparation_id": "PREP:VARENICLINE", "protein_id": "UP:Q7Z4V5", "publication_year": 2024, "qualitative_result": null, "reference_id": "PMID:39031937", "remaining_uncertainty": "Full assay buffer, temperature and incubation metadata not transcribed; null means uncurated, not absent.", "replicates": null, "role": "experimentally_studied_fragment_ligand", "source_component_url": null, "source_database": "Primary literature (frozen Atlas)", "source_id": "S04", "source_measurement_key": "2b9c01d4150ca3f35a87bce9ed5d4dde79bfafc9ecb109e3891ecdca18c484f1", "source_original": { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": 93, "assay_construct_start": 1, "assay_record_id": "PWWP:ASSAY:0010", "assay_type": "NMR chemical-shift perturbation Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "buffer": "HEPES-buffered saline; exact buffer/salt concentrations not restated in CSP subsection", "ccd_id": "QMR", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:JQSHBVHOMNKWFT-DTORHVGOSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "varenicline", "conditions": "{\"fit_model\": \"1:1 binding; global fit with shared Kd\", \"ligand_to_protein_molar_ratio_range\": [0, 6], \"protein_concentration_uM\": 100, \"protein_construct\": \"HDGFL2 1–93\"}", "crystallographic_component_ids": null, "domain": "PWWP", "domain_id": "UP:Q7Z4V5:PWWP1", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Results; Figure 1E", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981", "gene": "HDGFL2", "interpretation": "Converted from 0.25 ± 0.04 mM. Receptor pharmacology in other systems is not evidence of PWWP potency.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": 7.4, "pdb_id": "8Z6O", "preparation_id": "PREP:VARENICLINE", "protein_id": "UP:Q7Z4V5", "qualitative_result": null, "reference_id": "PMID:39031937", "remaining_uncertainty": "Full assay buffer, temperature and incubation metadata not transcribed; null means uncurated, not absent.", "replicates": null, "role": "experimentally_studied_fragment_ligand", "source_component_url": null, "source_id": "S04", "source_reported_uncertainty": "0.04", "source_reported_units": "mM", "source_reported_value": "0.25", "source_verification_scope": "primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved", "temperature_C": null, "uncertainty": 40.0, "uncertainty_type": "fitting_error", "uncertainty_uM": 40.0, "unit_conversion": "0.25 mM × 1000 = 250 µM; 0.04 mM × 1000 = 40 µM", "units": "µM", "value": 250.0, "value_operator": "=", "value_uM": 250.0, "verification_level": "primary_full_text_sections_verified" }, "source_reported_uncertainty": "0.04", "source_reported_units": "mM", "source_reported_value": "0.25", "source_verification_scope": "primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 40.0, "uncertainty_type": "fitting_error", "uncertainty_uM": 40.0, "unit_conversion": "0.25 mM × 1000 = 250 µM; 0.04 mM × 1000 = 40 µM", "units": "µM", "value": 250.0, "value_operator": "=", "value_uM": 250.0, "verification_level": "primary_full_text_sections_verified" }, { "assay_construct_end": 93, "assay_construct_start": 1, "assay_context": "purified_mutant_domain", "assay_organism": "Homo sapiens", "assay_record_id": "PWWP5:ASSAY:0027", "assay_type": "NMR chemical-shift perturbation Kd", "assay_value_transferred_to_modeled_stereoisomers": false, "ccd_id": null, "chemical_id": "INCHIKEY:JQSHBVHOMNKWFT-DTORHVGOSA-N", "compound_id": "INCHIKEY:JQSHBVHOMNKWFT-DTORHVGOSA-N", "compound_name": "varenicline", "conditions": { "binding_model": "1:1 global fit of perturbed residues", "buffer": "HEPES-buffered saline; CSP subsection does not separately give HEPES/NaCl concentrations", "ligand_protein_molar_ratio_range": [ 0, 6 ], "pH": 7.4, "protein_concentration_mM": 0.1, "target_variant": "Y18S" }, "curation_version": "phase5-1.0.0", "domain": "PWWP1", "domain_id": "UP:Q7Z4V5:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_location": "Results; Figure 2E", "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981", "gene": "HDGFL2", "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.", "is_measured": true, "is_negative": false, "method": "NMR chemical-shift perturbation", "normalized_exact_uM": 780.0, "numeric_transcription_status": "source_preserved", "numeric_value_inferred_from_structure": false, "organism": "Homo sapiens", "pH": 7.4, "pdb_id": null, "preparation_id": "PREP:VARENICLINE", "protein_id": "UP:Q7Z4V5", "publication_year": 2024, "reference_id": "PMID:39031937", "remaining_uncertainty": "Y18S mutant measurement; must not be pooled with wild-type affinity. 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Construct is the source HDGFRP2 PWWP expression fragment (1–93) carrying the stated mutation. Replicate number and titration-specific temperature are not independently specified.", "replicates": null, "retrieval_date": "2026-10-26", "role": "experimentally_studied_ligand", "source_id": "P5:S:WEI2024", "source_reported_uncertainty": "0.05", "source_reported_units": "mM", "source_reported_value": "0.78", "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "target_variant": "Y18S", "uncertainty": 0.05, "uncertainty_type": "fitting error", "uncertainty_uM": 50.0, "unit_conversion": "mM × 1000 = µM", "units": "mM", "value": 0.78, "value_operator": "=", "value_uM": 780.0, "verification_level": "primary_source_verified", "version": "phase5.chemical_curation.1.1.0" }, "source_reported_uncertainty": "0.05", "source_reported_units": "mM", "source_reported_value": "0.78", "source_verification_scope": "Official publisher full HTML independently inspected: Methods, 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"measured_observation_count": 0, "name": "(2S)-1-[4-[[(3R)-1,1-bis(oxidanylidene)thiolan-3-yl]methyl-methyl-amino]-6-methyl-pyrimidin-2-yl]-N-methyl-pyrrolidine-2-carboxamide", "negative_count": 0, "observation_ids": [], "pdb_structure_count": 1, "preparation_count": 0, "preparation_ids": [], "protein_ids": [ "UP:O96028" ], "relationships": [ { "direction": "inverse", "object_id": "PREP:COLLIE2025_11", "original_object_id": "INCHIKEY:FPDVOQXTUVFQHW-KGLIPLIRSA-N", "original_subject_id": "PREP:COLLIE2025_11", "relationship": "has modeled candidate not exact identity", "scope": "Assayed diastereomeric preparation: pyrrolidine 2S fixed and sulfolane center racemic in the SI name. A1IEG/A1IFS are modeled candidates in 9FOC; mixture affinity is not assigned to either pure stereoisomer. Composition ratio and fraction-to-CCD assignment remain unresolved.", "source_url": "https://www.rcsb.org/structure/9FOC", "subject_id": "PREP:COLLIE2025_11" } ], "relevant": true, "search_text": "(2s)-1-[4-[[(3r)-1,1-bis(oxidanylidene)thiolan-3-yl]methyl-methyl-amino]-6-methyl-pyrimidin-2-yl]-n-methyl-pyrrolidine-2-carboxamide inchikey:fpdvoqxtuvfqhw-kgliplirsa-n (2s)-1-[4-[[(3r)-1,1-bis(oxidanylidene)thiolan-3-yl]methyl-methyl-amino]-6-methyl-pyrimidin-2-yl]-n-methyl-pyrrolidine-2-carboxamide nsd2 up:o96028:pwwp1 9foc {\"aliases\":[\"(2s)-1-[4-[[(3r)-1,1-bis(oxidanylidene)thiolan-3-yl]methyl-methyl-amino]-6-methyl-pyrimidin-2-yl]-n-methyl-pyrrolidine-2-carboxamide\"],\"ccd_ids\":[\"a1ifs\"],\"ccd_names\":\"[\\\"(2s)-1-[4-[[(3r)-1,1-bis(oxidanylidene)thiolan-3-yl]methyl-methyl-amino]-6-methyl-pyrimidin-2-yl]-n-methyl-pyrrolidine-2-carboxamide\\\"]\",\"ccd_types\":\"[\\\"non-polymer\\\"]\",\"chemical_id\":\"inchikey:fpdvoqxtuvfqhw-kgliplirsa-n\",\"connectivity_block\":\"fpdvoqxtuvfqhw\",\"curated_source_sha256\":null,\"curation_version\":\"frozen-v1.2\",\"external_identifiers\":{},\"formal_charge_by_ccd\":\"{\\\"a1ifs\\\": 0}\",\"formulae\":\"[\\\"c17 h27 n5 o3 s\\\"]\",\"geometry_note\":\"ccd ideal sdf is a reference chemical geometry, not a deposited bound pose.\",\"identity_status\":\"complete_deposited_inchikey\",\"inchikey\":\"fpdvoqxtuvfqhw-kgliplirsa-n\",\"inventory_origin\":\"v1_ccd_inventory\",\"isomeric_smiles\":\"cc1cc(nc(n1)n2ccc[c@h]2c(=o)nc)n(c)c[c@h]3ccs(=o)(=o)c3\",\"primary_name\":\"(2s)-1-[4-[[(3r)-1,1-bis(oxidanylidene)thiolan-3-yl]methyl-methyl-amino]-6-methyl-pyrimidin-2-yl]-n-methyl-pyrrolidine-2-carboxamide\",\"retrieval_date\":\"2026-10-24\",\"smiles_stereo_by_ccd\":\"{\\\"a1ifs\\\": \\\"cc1cc(nc(n1)n2ccc[c@h]2c(=o)nc)n(c)c[c@h]3ccs(=o)(=o)c3\\\"}\",\"source_metadata_sha256\":\"{\\\"a1ifs\\\": \\\"285d1afe197f252c26f800f7b7feae6d8c378fe339adecfdc2b4848567f04379\\\"}\",\"source_urls\":[\"https://www.rcsb.org/ligand/a1ifs\"]}", "source_urls": [ "https://www.rcsb.org/ligand/A1IFS" ], "verification_pending": false, "context_observations": [], "context_structures": [ { "Pfam_contacts_5A": "[{\"auth_asym_id\": \"A\", \"auth_seq_id\": \"230\", \"component\": \"VAL\", \"entity_position\": 27, \"label_asym_id\": \"A\", 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3.4254, \"uniprot_position\": 268}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"269\", \"component\": \"ASP\", \"entity_position\": 66, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.0724, \"uniprot_position\": 269}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"270\", \"component\": \"ALA\", \"entity_position\": 67, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 2.9375, \"uniprot_position\": 270}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"271\", \"component\": \"PRO\", \"entity_position\": 68, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.8733, \"uniprot_position\": 271}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"272\", \"component\": \"GLU\", \"entity_position\": 69, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 2.9054, \"uniprot_position\": 272}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"273\", \"component\": \"ARG\", \"entity_position\": 70, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.2474, \"uniprot_position\": 273}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"274\", \"component\": \"ALA\", \"entity_position\": 71, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.0475, \"uniprot_position\": 274}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"318\", \"component\": \"LEU\", \"entity_position\": 115, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.5523, \"uniprot_position\": 318}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"321\", \"component\": \"GLN\", \"entity_position\": 118, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.4813, \"uniprot_position\": 321}]", "biochemical_activity_inferred": 0, "ccd_id": "A1IFS", "chain_contacts_5A": "[{\"auth_asym_id\": \"A\", \"auth_seq_id\": \"230\", \"component\": \"VAL\", \"entity_position\": 27, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.2575, \"uniprot_position\": 230}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"233\", \"component\": \"TYR\", \"entity_position\": 30, \"label_asym_id\": \"A\", 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{\"auth_asym_id\": \"A\", \"auth_seq_id\": \"236\", \"component\": \"TRP\", \"entity_position\": 33, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.4814, \"uniprot_position\": 236}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"266\", \"component\": \"PHE\", \"entity_position\": 63, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.6163, \"uniprot_position\": 266}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"267\", \"component\": \"PHE\", \"entity_position\": 64, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.7477, \"uniprot_position\": 267}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"268\", \"component\": \"GLY\", \"entity_position\": 65, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.4254, \"uniprot_position\": 268}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"269\", \"component\": \"ASP\", \"entity_position\": 66, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.0724, \"uniprot_position\": 269}, {\"auth_asym_id\": \"A\", 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"INCHIKEY:FPDVOQXTUVFQHW-KBPBESRZSA-N", "original_subject_id": "PREP:COLLIE2025_11", "relationship": "has modeled candidate not exact identity", "scope": "Assayed diastereomeric preparation: pyrrolidine 2S fixed and sulfolane center racemic in the SI name. 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"experimentally deposited fragment", "role_category": "functional", "site_id": "PDB:7HH0:LIG:J:RYP:103:.:SITE:UP:Q7Z4V5:PWWP1:B", "source_coordinate_sha256": "0c18dba4b9a8f66eff6ddcb52e8b131a65291eb9b3438c1530299b3d273ee994" } ], "context_assay_count": 0, "context_measured_count": 0, "context_bound_count": 1, "context_pdb_count": 1, "context_negative_count": 0, "context_is_probe": false, "context_bioactivity_only": false, "context_kind": "PWWP-proximal structure", "science": { "studied_compound": false, "measured_count": 0, "structural_research_ligand": true, "research_pdb_count": 1, "other_component": false, "component_site_count": 0, "verification_queue": false, "positive_direct_binder": false, "reported_probe": false, "reported_control": false, "cellular_activity": false, "protein_degradation": false, "bioactivity_only": false, "research_site_count": 2, "unknown_site_count": 0, "annotation_roles": [ "structural" ] }, "science_label": "Deposited research ligand · no curated assay", 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experiment-scoped; missing assays do not prove nonbinding.", "verification_queue": false, "verification_status": "source_scoped_mixed" }, "science_site_roles": { "PDB:7HH0:LIG:J:RYP:103:.:SITE:UP:Q7Z4V5:PWWP1:A": { "ccd_url": "https://www.rcsb.org/ligand/RYP", "chemical_id": "INCHIKEY:DNBWGFKLIBQQSL-UHFFFAOYSA-N", "compound_id": "INCHIKEY:DNBWGFKLIBQQSL-UHFFFAOYSA-N", "contact_class": "native_annotation_core_contact", "coordinate_sha256": "0c18dba4b9a8f66eff6ddcb52e8b131a65291eb9b3438c1530299b3d273ee994", "domain_id": "UP:Q7Z4V5:PWWP1", "exact_pwwp_contact": true, "ligand_instance_id": "PDB:7HH0:LIG:J:RYP:103:.", "observed_other_component": false, "pdb_id": "7HH0", "protein_id": "UP:Q7Z4V5", "role_code": "screened_fragment_structure", "role_group": "research_ligand", "rule": "Phase5 exact deposited site role, measured heavy-atom contacts and native-domain scope", "site_id": "PDB:7HH0:LIG:J:RYP:103:.:SITE:UP:Q7Z4V5:PWWP1:A", "source_role": "experimentally deposited fragment", 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