{ "science_site": { "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" }, "structure": { "pdb_id": "6XCG", "title": "Histone-lysine N-methyltransferase NSD2-PWWP1 with compound UNC6934", "method": "[\"X-RAY DIFFRACTION\"]", "resolution_angstrom": 1.64, "primary_classification": "Co-Crystals", "observed_PWWP": 1, "review_required": 1, "review_reasons": "[\"Unresolved chemical role: UNX\"]", "release_date": "2020-07-22T00:00:00.000+00:00", "source_url": "https://www.rcsb.org/structure/6XCG", "coordinate_url": "https://files.rcsb.org/download/6XCG.cif", "original_cif_sha256": "2c370701c9b83de7ae6137f91d2130519a48c261a93ec5bc480dfcc3bc982200", "classification_status": "v1 classification retained; independent coverage/contact evidence and sampled scientific audit are separate layers" }, "chains": [ { "auth_asym_ids_observed": "[\"A\"]", "broader_scope_basis": "source Pfam feature intersecting native core; entire chain reported separately", "chain_id": 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true, "within_broader_Pfam": true } }, { "auth_asym_id": "A", "auth_seq_id": "318", "component": "LEU", "entity_position": 109, "label_asym_id": "A", "minimum_distance_angstrom": 3.4573, "uniprot_position": 318, "scope": "broader Pfam PWWP", "quality": { "canonical_position": 318, "entity_position": 109, "component": "LEU", "observed_components": [ "LEU" ], "label_asym_id": "A", "auth_asym_id": "A", "auth_seq_id": "318", "insertion_code": null, "observed": true, "observed_atom_names": [ "C", "CA", "CB", "CD1", "CD2", "CG", "N", "O" ], "expected_standard_heavy_atoms": [ "C", "CA", "CB", "CD1", "CD2", "CG", "N", "O" ], "standard_template_available": true, "missing_standard_heavy_atoms": [], "missing_backbone_atoms": [], "missing_sidechain_atoms": [], "alternate_conformers": [], "alternate_completeness": [], "occupancy_min": 1.0, "occupancy_max": 1.0, "within_annotation_core": false, "within_broader_Pfam": true } }, { "auth_asym_id": "A", "auth_seq_id": "321", "component": "GLN", "entity_position": 112, "label_asym_id": "A", "minimum_distance_angstrom": 2.867, "uniprot_position": 321, "scope": "broader Pfam PWWP", "quality": { "canonical_position": 321, "entity_position": 112, "component": "GLN", "observed_components": [ "GLN" ], "label_asym_id": "A", "auth_asym_id": "A", "auth_seq_id": "321", "insertion_code": null, "observed": true, "observed_atom_names": [ "C", "CA", "CB", "CD", "CG", "N", "NE2", "O", "OE1" ], "expected_standard_heavy_atoms": [ "C", "CA", "CB", "CD", "CG", "N", "NE2", "O", "OE1" ], "standard_template_available": true, "missing_standard_heavy_atoms": [], "missing_backbone_atoms": [], "missing_sidechain_atoms": [], "alternate_conformers": [], "alternate_completeness": [], "occupancy_min": 1.0, "occupancy_max": 1.0, "within_annotation_core": false, "within_broader_Pfam": true } } ], "comparison": { "comparison_id": "6XCG:A:UP:O96028:PWWP1", "pdb_id": "6XCG", "protein_id": "UP:O96028", "gene": "NSD2", "taxonomy_id": "9606", "domain_id": "UP:O96028:PWWP1", "label_asym_id": "A", "auth_asym_ids": "[\"A\"]", "first_model": "1", "domain_start": 222, "domain_end": 286, "annotation_core_length": 65, "n_observed_CA": 65, "core_CA_coverage": 1.0, "v1_observed_any_atom_residues": 65, "CA_minus_v1_any_atom": 0, "n_common_AF_CA": 65, "core_observed_substitutions": 0, "substitutions": "[]", "duplicate_canonical_positions": "[]", "experimental_method": "X-RAY DIFFRACTION", "resolution_angstrom": 1.64, "primary_classification": "Co-Crystals", "classification_review_required": 1, "source_cif": "Structures/NSD2__HUMAN__O96028/Co-Crystals/6XCG/original.cif", "source_sha256": "2c370701c9b83de7ae6137f91d2130519a48c261a93ec5bc480dfcc3bc982200", "mapping_sha256": "418264be7a54411ac6af7554a221954f7604af5a64255f2ba78bb2ee873077a5", "comparison_status": "eligible", "AF_model_record_id": "AF-O96028-F1:v6", "rmsd_all_common_CA": 1.441063, "n_AF_CA_ge70": 60, "rmsd_AF_ge70_CA": 0.579492, "AF_core_mean_plddt": 87.1043 }, "assays": [ { "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", "link_semantics": "same exact chemical identity and native domain; construct equivalence not assumed", "site_id": "PDB:6XCG:LIG:D:V01:401:.:SITE:UP:O96028:PWWP1:A" }, { "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", "link_semantics": "same exact chemical identity and native domain; construct equivalence not assumed", "site_id": "PDB:6XCG:LIG:D:V01:401:.:SITE:UP:O96028:PWWP1:A" }, { "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", "link_semantics": "same exact chemical identity and native domain; construct equivalence not assumed", "site_id": "PDB:6XCG:LIG:D:V01:401:.:SITE:UP:O96028:PWWP1:A" }, { "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", "link_semantics": "same exact chemical identity and native domain; construct equivalence not assumed", "site_id": "PDB:6XCG:LIG:D:V01:401:.:SITE:UP:O96028:PWWP1:A" }, { "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", "link_semantics": "same exact chemical identity and native domain; construct equivalence not assumed", "site_id": "PDB:6XCG:LIG:D:V01:401:.:SITE:UP:O96028:PWWP1:A" } ], "local_coordinates": true, "coordinate_url": "/coordinates/6XCG.cif", "interpretation": "Heavy-atom distances use the first deposited model and asymmetric unit, occupancy >0 and retained alternate locations. No symmetry expansion or affinity inference.", "quality_scope": "Detailed atom completeness only for the three packaged original-coordinate files; quality uses observed atom-name union across positive-occupancy alternate conformers, with per-alt differences retained. Missing entire residues are separate. Nonstandard amino-acid templates are unassessed. No density reinterpretation, receptor repair, docking or MD.", "analysis_id": "PWWP_POCKET_QUALITY_1.0.0", "source_conflict": null }