{ "version": { "version": "phase5-1.0.0", "date": "2026-10-26", "frozen_database_sha256": "0c53107a39e222b48611302b21fda5fb4ed50b190b6b39d41423ccc5ca5958f6", "chemical_identities": 148, "profiles": 163, "relevant_profiles": 132, "preparations": 30, "observations": 80, "frozen_observations": 46, "new_observations": 34, "bioactivity_only_profiles": 21, "exact_PWWP_structural_profiles": 130, "verified_depictions": 139, "reconciled_duplicate_rows": 0, "candidate_records": 150, "curated_scope": "Documented targeted snapshot; not an exhaustive inventory of all literature compounds. 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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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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. 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