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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" } ], "context_structures": [], "context_assay_count": 1, "context_measured_count": 1, "context_bound_count": 0, "context_pdb_count": 0, "context_negative_count": 1, "context_is_probe": false, "context_bioactivity_only": true, "context_kind": "Bioactivity only", "science": { "studied_compound": true, "measured_count": 1, "structural_research_ligand": false, "research_pdb_count": 0, "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": true, "research_site_count": 0, "unknown_site_count": 0, "annotation_roles": [ "studied" ] }, "science_label": "Studied · no deposited PWWP research ligand", "science_profile": { "annotation_roles": [ "studied", "structural" ], "cellular_activity": false, "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "compound_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N", "entity_kind": "chemical_identity", "identity_resolved": true, "measured_observation_count": 8, "name": "BPP", "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:0011", "PWWP:ASSAY:0012", "PWWP:ASSAY:0013", "PWWP5:ASSAY:0028", "PWWP5:ASSAY:0032", "PWWP5:ASSAY:0029", "PWWP5:ASSAY:0030", "PWWP5:ASSAY:0031" ], "source_site_ids": [ "PDB:8Z6C:LIG:D:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:A", "PDB:9G94:LIG:D:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:A", "PDB:9G94:LIG:G:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:A", "PDB:8Z6C:LIG:G:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:B", "PDB:9G94:LIG:G:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:B", "PDB:8Z6C:LIG:J:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:C", "PDB:9G94:LIG:J:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:C", "PDB:8Z6C:LIG:D:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:C" ], "structural_research_ligand": true, "structural_research_site_count": 8, "studied_compound": true, "total_observation_count": 8, "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": {}, "science_assay_roles": { "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" } }, "example": null, "matched_observations": [ { "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 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\"266\", \"component\": \"ASP\", \"entity_position\": 52, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 2.3774, \"uniprot_position\": 266}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"297\", \"component\": \"SER\", \"entity_position\": 83, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.9926, \"uniprot_position\": 297}]", "chain_id": "PDB:6R3E:CHAIN:A:UP:Q9UBC3", "chemical_id": "INCHIKEY:SLINHMUFWFWBMU-CIUDSAMLSA-N", "contact_class": "native_annotation_core_contact", "contact_distance_rank": 1, "core_contacts_5A": "[{\"auth_asym_id\": \"A\", \"auth_seq_id\": \"233\", \"component\": \"ILE\", \"entity_position\": 19, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.9699, \"uniprot_position\": 233}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"236\", \"component\": \"PHE\", \"entity_position\": 22, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.4411, \"uniprot_position\": 236}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"237\", \"component\": \"SER\", \"entity_position\": 23, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.9513, \"uniprot_position\": 237}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"239\", \"component\": \"TRP\", \"entity_position\": 25, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.3189, \"uniprot_position\": 239}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"263\", \"component\": \"TRP\", \"entity_position\": 49, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.3547, \"uniprot_position\": 263}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"264\", \"component\": \"PHE\", \"entity_position\": 50, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.6152, \"uniprot_position\": 264}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"266\", \"component\": \"ASP\", \"entity_position\": 52, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 2.3774, \"uniprot_position\": 266}]", "covalent_connection_ids": "[]", "cutoff_angstrom": 5.0, "domain_id": "UP:Q9UBC3:PWWP1", "exact_pwwp_contact": true, "gene": "DNMT3B", "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": "501", "ccd_id": "96H", "chemical_id": "INCHIKEY:SLINHMUFWFWBMU-CIUDSAMLSA-N", "component_context": "nonpolymer_component", "contacted_polymer_partners": "[{\"description\": \"DNA (cytosine-5)-methyltransferase 3B,DNA (cytosine-5)-methyltransferase 3B\", \"entity_id\": \"1\", \"is_PWWP_family_protein\": true, \"label_asym_id\": \"A\", \"sequence_length\": 274, \"uniprot_ids\": [\"Q9UBC3\"]}]", "covalent_connection_ids": "[]", "heavy_atom_row_count": 13, "ideal_CCD_SDF_is_source_pose": 0, "label_asym_id": "C", "label_seq_id": null, "ligand_instance_id": "PDB:6R3E:LIG:C:96H:501:.", "nearest_polypeptide_distance_angstrom": 2.3774, "nearest_polypeptide_label_asym_id": "A", "occupancy_max": 0.94, "occupancy_min": 0.94, "pdb_id": "6R3E", "polypeptide_contact_residues_5A": "[{\"auth_asym_id\": \"A\", \"auth_seq_id\": \"233\", \"component\": \"ILE\", \"entity_position\": 19, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.9699, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"236\", \"component\": \"PHE\", \"entity_position\": 22, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.4411, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"237\", \"component\": \"SER\", \"entity_position\": 23, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.9513, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"239\", \"component\": \"TRP\", \"entity_position\": 25, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.3189, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"263\", \"component\": \"TRP\", \"entity_position\": 49, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.3547, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"264\", \"component\": \"PHE\", \"entity_position\": 50, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.6152, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"266\", \"component\": \"ASP\", \"entity_position\": 52, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 2.3774, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"297\", \"component\": \"SER\", \"entity_position\": 83, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.9926, \"uniprot_position\": null}]", "pose_kind": "deposited_source_coordinates", "reference_model": "1", "source_coordinate_file": "Structures/DNMT3B__HUMAN__Q9UBC3/Co-Crystals/6R3E/original.cif", "source_coordinate_sha256": "f11f4e7bcd8a67152407442feee80117e2f1d3146e35bbce7e8eacb39e404552", "unique_heavy_atom_names": 13 }, "ligand_instance_id": "PDB:6R3E:LIG:C:96H:501:.", "ligand_label_asym_id": "C", "minimum_Pfam_distance_angstrom": null, "minimum_chain_distance_angstrom": 2.3774, "minimum_core_distance_angstrom": 2.3774, "multiple_contacting_mapped_chains": 0, "pdb_id": "6R3E", "protein_id": "UP:Q9UBC3", "protein_label_asym_id": "A", "rank_interpretation": "Distance rank among mapped chains only; crystal packing and biological site assignment require separate review.", "role": "experimentally deposited ligand", "role_category": "functional", "site_id": "PDB:6R3E:LIG:C:96H:501:.:SITE:UP:Q9UBC3:PWWP1:A", "source_coordinate_sha256": "f11f4e7bcd8a67152407442feee80117e2f1d3146e35bbce7e8eacb39e404552" } ], "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": 1, "unknown_site_count": 0, "annotation_roles": [ "structural" ] }, "science_label": "Deposited research ligand · no curated assay", "science_profile": { "annotation_roles": [ "structural" ], "cellular_activity": false, "chemical_id": "INCHIKEY:SLINHMUFWFWBMU-CIUDSAMLSA-N", "compound_id": "INCHIKEY:SLINHMUFWFWBMU-CIUDSAMLSA-N", "entity_kind": "chemical_identity", "identity_resolved": true, "measured_observation_count": 0, "name": "Triisopropanolamine", "other_pdb_component": false, "other_site_count": 0, "positive_direct_binder": false, "primary_view": "structural", "protein_degradation": false, "reported_control": false, "reported_probe": false, "rule": "Independent source observations + per-site coordinate role, not universal pharmacology", "source_observation_ids": [], "source_site_ids": [ "PDB:6R3E:LIG:C:96H:501:.:SITE:UP:Q9UBC3:PWWP1:A" ], "structural_research_ligand": true, "structural_research_site_count": 1, "studied_compound": false, "total_observation_count": 0, "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:6R3E:LIG:C:96H:501:.:SITE:UP:Q9UBC3:PWWP1:A": { "ccd_url": "https://www.rcsb.org/ligand/96H", "chemical_id": "INCHIKEY:SLINHMUFWFWBMU-CIUDSAMLSA-N", "compound_id": "INCHIKEY:SLINHMUFWFWBMU-CIUDSAMLSA-N", "contact_class": "native_annotation_core_contact", "coordinate_sha256": "f11f4e7bcd8a67152407442feee80117e2f1d3146e35bbce7e8eacb39e404552", "domain_id": "UP:Q9UBC3:PWWP1", "exact_pwwp_contact": true, "ligand_instance_id": "PDB:6R3E:LIG:C:96H:501:.", "observed_other_component": false, "pdb_id": "6R3E", "protein_id": "UP:Q9UBC3", "role_code": "deposited_research_ligand", "role_group": "research_ligand", "rule": "Phase5 exact deposited site role, measured heavy-atom contacts and native-domain scope", "site_id": "PDB:6R3E:LIG:C:96H:501:.:SITE:UP:Q9UBC3:PWWP1:A", "source_role": "experimentally deposited ligand", "source_url": "https://www.rcsb.org/structure/6R3E", "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": {}, "example": null, "matched_observations": [], "matched_assay_count": 0 } ] }