{ "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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"glycerol inchikey:pedcqbhivmgvhv-uhfffaoysa-n glycerol dnmt3b hdgfl2 nsd2 psip1 pwwp2b up:o75475:pwwp1 up:o96028:pwwp1 up:q6nuj5:pwwp1 up:q7z4v5:pwwp1 up:q9ubc3:pwwp1 4fu6 4ld6 5ciu 5y1z 9i7d 9kna {\"aliases\":[\"glycerol\"],\"ccd_ids\":[\"gol\"],\"ccd_names\":\"[\\\"glycerol\\\"]\",\"ccd_types\":\"[\\\"non-polymer\\\"]\",\"chemical_id\":\"inchikey:pedcqbhivmgvhv-uhfffaoysa-n\",\"connectivity_block\":\"pedcqbhivmgvhv\",\"curated_source_sha256\":null,\"curation_version\":\"frozen-v1.2\",\"external_identifiers\":{},\"formal_charge_by_ccd\":\"{\\\"gol\\\": 0}\",\"formulae\":\"[\\\"c3 h8 o3\\\"]\",\"geometry_note\":\"ccd ideal sdf is a reference chemical geometry, not a deposited bound pose.\",\"identity_status\":\"complete_deposited_inchikey\",\"inchikey\":\"pedcqbhivmgvhv-uhfffaoysa-n\",\"inventory_origin\":\"v1_ccd_inventory\",\"isomeric_smiles\":\"c(c(co)o)o\",\"primary_name\":\"glycerol\",\"retrieval_date\":\"2026-10-24\",\"smiles_stereo_by_ccd\":\"{\\\"gol\\\": 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"[{\"auth_asym_id\": \"A\", \"auth_seq_id\": \"498\", \"component\": \"ILE\", \"entity_position\": 25, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.6895, \"uniprot_position\": 498}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"501\", \"component\": \"PHE\", \"entity_position\": 28, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.0835, \"uniprot_position\": 501}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"502\", \"component\": \"PRO\", \"entity_position\": 29, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.1638, \"uniprot_position\": 502}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"504\", \"component\": \"TRP\", \"entity_position\": 31, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.6599, \"uniprot_position\": 504}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"530\", \"component\": \"TRP\", \"entity_position\": 57, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.4478, \"uniprot_position\": 530}, {\"auth_asym_id\": \"A\", 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\"THR\", \"entity_position\": 62, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.6908, \"uniprot_position\": 535}]", "covalent_connection_ids": "[]", "cutoff_angstrom": 5.0, "domain_id": "UP:Q6NUJ5:PWWP1", "exact_pwwp_contact": true, "gene": "PWWP2B", "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": "3001", "ccd_id": "GOL", "chemical_id": "INCHIKEY:PEDCQBHIVMGVHV-UHFFFAOYSA-N", "component_context": "nonpolymer_component", "contacted_polymer_partners": "[{\"description\": \"PWWP domain-containing protein 2B\", \"entity_id\": \"1\", \"is_PWWP_family_protein\": true, \"label_asym_id\": \"A\", \"sequence_length\": 117, \"uniprot_ids\": [\"Q6NUJ5\"]}]", "covalent_connection_ids": "[]", "heavy_atom_row_count": 6, "ideal_CCD_SDF_is_source_pose": 0, "label_asym_id": "B", "label_seq_id": null, 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\"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"530\", \"component\": \"TRP\", \"entity_position\": 57, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.4478, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"533\", \"component\": \"SER\", \"entity_position\": 60, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 2.6227, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"535\", \"component\": \"THR\", \"entity_position\": 62, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 4.6908, \"uniprot_position\": null}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": \"562\", \"component\": \"MET\", \"entity_position\": 89, \"label_asym_id\": \"A\", \"minimum_distance_angstrom\": 3.6199, \"uniprot_position\": null}]", "pose_kind": "deposited_source_coordinates", "reference_model": "1", "source_coordinate_file": "Structures/PWWP2B__HUMAN__Q6NUJ5/Unclassified_Review/4LD6/original.cif", "source_coordinate_sha256": "61a425f683439fa460d75deddfb94e2af770bfdf5882cf88af12c6ea78e30308", "unique_heavy_atom_names": 6 }, "ligand_instance_id": "PDB:4LD6:LIG:B:GOL:3001:.", "ligand_label_asym_id": "B", "minimum_Pfam_distance_angstrom": 2.6227, "minimum_chain_distance_angstrom": 2.6227, "minimum_core_distance_angstrom": 2.6227, "multiple_contacting_mapped_chains": 0, "pdb_id": "4LD6", "protein_id": "UP:Q6NUJ5", "protein_label_asym_id": "A", "rank_interpretation": "Distance rank among mapped chains only; crystal packing and biological site assignment require separate review.", "role": "cryoprotectant/additive", "role_category": "incidental", "site_id": "PDB:4LD6:LIG:B:GOL:3001:.:SITE:UP:Q6NUJ5:PWWP1:A", "source_coordinate_sha256": "61a425f683439fa460d75deddfb94e2af770bfdf5882cf88af12c6ea78e30308" } ], "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": false, "research_pdb_count": 0, "other_component": true, "component_site_count": 1, "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": 0, "unknown_site_count": 0, "annotation_roles": [ "components" ] }, "science_label": "Other PDB component ยท not a studied ligand", "science_profile": { "annotation_roles": [ "components" ], "cellular_activity": false, "chemical_id": "INCHIKEY:PEDCQBHIVMGVHV-UHFFFAOYSA-N", "compound_id": "INCHIKEY:PEDCQBHIVMGVHV-UHFFFAOYSA-N", "entity_kind": "chemical_identity", "identity_resolved": true, "measured_observation_count": 0, "name": "GLYCEROL", "other_pdb_component": true, "other_site_count": 11, "positive_direct_binder": false, "primary_view": "components", "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:5Y1Z:LIG:Q:GOL:506:.:SITE:UP:Q9ULU4:PWWP1:C", "PDB:5Y1Z:LIG:Q:GOL:506:.:SITE:UP:Q9ULU4:PWWP1:D", "PDB:9I7D:LIG:C:GOL:201:.:SITE:UP:Q7Z4V5:PWWP1:A", "PDB:4FU6:LIG:E:GOL:204:.:SITE:UP:O75475:PWWP1:A", "PDB:9KNA:LIG:F:GOL:404:.:SITE:UP:O96028:PWWP1:A", "PDB:9KNA:LIG:K:GOL:403:.:SITE:UP:O96028:PWWP1:A", "PDB:4LD6:LIG:B:GOL:3001:.:SITE:UP:Q6NUJ5:PWWP1:A", "PDB:9I7D:LIG:H:GOL:201:.:SITE:UP:Q7Z4V5:PWWP1:B", "PDB:9KNA:LIG:K:GOL:403:.:SITE:UP:O96028:PWWP1:B", "PDB:9KNA:LIG:F:GOL:404:.:SITE:UP:O96028:PWWP1:B", "PDB:5CIU:LIG:E:GOL:401:.:SITE:UP:Q9UBC3:PWWP1:B" ], "structural_research_ligand": false, "structural_research_site_count": 0, "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:4LD6:LIG:B:GOL:3001:.:SITE:UP:Q6NUJ5:PWWP1:A": { "ccd_url": "https://www.rcsb.org/ligand/GOL", "chemical_id": "INCHIKEY:PEDCQBHIVMGVHV-UHFFFAOYSA-N", "compound_id": "INCHIKEY:PEDCQBHIVMGVHV-UHFFFAOYSA-N", "contact_class": "native_annotation_core_contact", "coordinate_sha256": "61a425f683439fa460d75deddfb94e2af770bfdf5882cf88af12c6ea78e30308", "domain_id": "UP:Q6NUJ5:PWWP1", "exact_pwwp_contact": true, "ligand_instance_id": "PDB:4LD6:LIG:B:GOL:3001:.", "observed_other_component": true, "pdb_id": "4LD6", "protein_id": "UP:Q6NUJ5", "role_code": "cryoprotectant", "role_group": "other_component", "rule": "Phase5 exact deposited site role, measured heavy-atom contacts and native-domain scope", "site_id": "PDB:4LD6:LIG:B:GOL:3001:.:SITE:UP:Q6NUJ5:PWWP1:A", "source_role": "cryoprotectant/additive", "source_url": "https://www.rcsb.org/structure/4LD6", "structural_research_ligand": false, "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 } ] }