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\"uniprot_position\": 47}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"49\", \"component\": \"GLU\", \"entity_position\": 50, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 2.5973, \"uniprot_position\": 49}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"50\", \"component\": \"THR\", \"entity_position\": 51, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 4.238, \"uniprot_position\": 50}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"51\", \"component\": \"ALA\", \"entity_position\": 52, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 4.2169, \"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": "[\"C\"]", "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\": \"C\", \"sequence_length\": 94, \"uniprot_ids\": [\"Q7Z4V5\"]}]", "covalent_connection_ids": "[]", "heavy_atom_row_count": 12, "ideal_CCD_SDF_is_source_pose": 0, "label_asym_id": "J", "label_seq_id": null, "ligand_instance_id": "PDB:9G94:LIG:J:A1D73:101:.", "nearest_polypeptide_distance_angstrom": 2.5415, "nearest_polypeptide_label_asym_id": "C", "occupancy_max": 0.94, "occupancy_min": 0.94, "pdb_id": "9G94", "polypeptide_contact_residues_5A": "[{\"auth_asym_id\": \"C\", \"auth_seq_id\": \"13\", \"component\": \"ALA\", \"entity_position\": 14, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 4.7946, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"15\", \"component\": \"MET\", \"entity_position\": 16, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 3.4535, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"18\", \"component\": \"TYR\", \"entity_position\": 19, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 3.3784, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"19\", \"component\": \"PRO\", \"entity_position\": 20, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 4.7336, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"21\", \"component\": \"TRP\", \"entity_position\": 22, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 3.4555, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"44\", \"component\": \"PHE\", \"entity_position\": 45, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 3.4725, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"47\", \"component\": \"THR\", \"entity_position\": 48, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 2.5415, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"49\", \"component\": \"GLU\", \"entity_position\": 50, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 2.5973, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"50\", \"component\": \"THR\", \"entity_position\": 51, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 4.238, \"uniprot_position\": null}, {\"auth_asym_id\": \"C\", \"auth_seq_id\": \"51\", \"component\": \"ALA\", \"entity_position\": 52, \"label_asym_id\": \"C\", \"minimum_distance_angstrom\": 4.2169, \"uniprot_position\": null}]", "pose_kind": "deposited_source_coordinates", "reference_model": "1", "source_coordinate_file": "Structures/HDGFL2__HUMAN__Q7Z4V5/Co-Crystals/9G94/original.cif", "source_coordinate_sha256": "77cc947e76da8d5e49e56df359b3db472fe81dbdfabfc36f99d53b3c18200802", "unique_heavy_atom_names": 12 }, "ligand_instance_id": "PDB:9G94:LIG:J:A1D73:101:.", "ligand_label_asym_id": "J", "minimum_Pfam_distance_angstrom": 2.5415, "minimum_chain_distance_angstrom": 2.5415, "minimum_core_distance_angstrom": 2.5415, "multiple_contacting_mapped_chains": 0, "pdb_id": "9G94", "protein_id": "UP:Q7Z4V5", "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:9G94:LIG:J:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:C", "source_coordinate_sha256": "77cc947e76da8d5e49e56df359b3db472fe81dbdfabfc36f99d53b3c18200802" } ], "context_assay_count": 2, "context_measured_count": 2, "context_bound_count": 2, "context_pdb_count": 2, "context_negative_count": 0, "context_is_probe": false, "context_bioactivity_only": false, "context_kind": "Measured + bound structure", "science": { "studied_compound": true, "measured_count": 2, "structural_research_ligand": true, "research_pdb_count": 2, "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": 8, "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: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": { "PDB:8Z6C: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": "a52b0ce0d915a4ec6357f5dce14e0dbbacdb5fa856c24981a9187cf4168156c2", "domain_id": "UP:Q7Z4V5:PWWP1", "exact_pwwp_contact": true, "ligand_instance_id": "PDB:8Z6C:LIG:D: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:D:A1D73:101:.:SITE:UP:Q7Z4V5:PWWP1:A", "source_role": "experimentally studied ligand", "source_url": "https://www.rcsb.org/structure/8Z6C", 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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" }, "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", 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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" }, { "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. 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": "ffcc722dc4af4f80ffe47c5d374303804d84ce0ece347772ae8ec971c8c8d9c4", "source_original": { "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_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" }, "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_negative": false, "numeric_transcription_status": "source_preserved", "numeric_value_inferred_from_structure": false, "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. 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, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved", "target_scope": "domain_specific", "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" } ], "context_structures": [ { "Pfam_contacts_5A": "[{\"auth_asym_id\": \"B\", \"auth_seq_id\": \"15\", \"component\": \"MET\", \"entity_position\": 15, \"label_asym_id\": \"B\", \"minimum_distance_angstrom\": 3.579, \"uniprot_position\": 15}, {\"auth_asym_id\": \"B\", \"auth_seq_id\": \"18\", \"component\": \"TYR\", \"entity_position\": 18, \"label_asym_id\": \"B\", \"minimum_distance_angstrom\": 3.4485, \"uniprot_position\": 18}, {\"auth_asym_id\": \"B\", \"auth_seq_id\": \"21\", \"component\": \"TRP\", \"entity_position\": 21, \"label_asym_id\": \"B\", 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\"uniprot_position\": 51}]", "biochemical_activity_inferred": 0, "ccd_id": "QMR", "chain_contacts_5A": "[{\"auth_asym_id\": \"B\", \"auth_seq_id\": \"15\", \"component\": \"MET\", \"entity_position\": 15, \"label_asym_id\": \"B\", \"minimum_distance_angstrom\": 3.579, \"uniprot_position\": 15}, {\"auth_asym_id\": \"B\", \"auth_seq_id\": \"18\", \"component\": \"TYR\", \"entity_position\": 18, \"label_asym_id\": \"B\", \"minimum_distance_angstrom\": 3.4485, \"uniprot_position\": 18}, {\"auth_asym_id\": \"B\", \"auth_seq_id\": \"21\", \"component\": \"TRP\", \"entity_position\": 21, \"label_asym_id\": \"B\", \"minimum_distance_angstrom\": 3.6336, \"uniprot_position\": 21}, {\"auth_asym_id\": \"B\", \"auth_seq_id\": \"44\", \"component\": \"PHE\", \"entity_position\": 44, \"label_asym_id\": \"B\", \"minimum_distance_angstrom\": 3.5123, \"uniprot_position\": 44}, {\"auth_asym_id\": \"B\", \"auth_seq_id\": \"47\", \"component\": \"THR\", \"entity_position\": 47, \"label_asym_id\": \"B\", 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"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": 250.0, "verification_status": "primary_full_text_sections_verified" }, "PWWP5:ASSAY:0027": { "chemical_id": "INCHIKEY:JQSHBVHOMNKWFT-DTORHVGOSA-N", "compound_id": "INCHIKEY:JQSHBVHOMNKWFT-DTORHVGOSA-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:0027", "operator": "=", "positive_direct_binder": true, "preparation_id": "PREP:VARENICLINE", "protein_id": "UP:Q7Z4V5", "remaining_uncertainty": "Y18S mutant measurement; must not be pooled with wild-type affinity. 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