data_9Q8 # _chem_comp.id 9Q8 _chem_comp.name "tris($l^{3}-oxidanyl)-tris(oxidaniumylidynemethyl)ruthenium" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C3 H6 O6 Ru" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge ? _chem_comp.pdbx_initial_date 2017-06-26 _chem_comp.pdbx_modified_date 2026-07-31 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 239.146 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ? _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details MetalCoord _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 5OB6 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y _chem_comp.pdbx_comp_type "metal-containing ligand" # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal 9Q8 O1 O1 O 1 1 N N N N N N 8.208 -8.112 -6.612 0.218 -0.907 -2.058 O1 9Q8 1 9Q8 C1 C1 C -1 1 N N N N N N 8.310 -8.825 -5.874 0.292 -0.608 -0.878 C1 9Q8 2 9Q8 RU RU1 RU ? 0 N N N N N N 8.442 -10.100 -4.583 0.406 -0.151 0.921 RU 9Q8 3 9Q8 C2 C2 C -1 1 N N N N N N 6.777 -10.485 -4.955 0.884 -1.901 1.335 C2 9Q8 4 9Q8 O2 O2 O 1 1 N N N N N N 5.829 -10.731 -5.129 1.197 -3.048 1.606 O2 9Q8 5 9Q8 C3 C3 C -1 1 N Y N N N N 8.833 -11.153 -5.899 -1.388 -0.588 1.146 C3 9Q8 6 9Q8 O3 O3 O 1 1 N Y N N N N 9.126 -11.783 -6.648 -2.565 -0.875 1.293 O3 9Q8 7 9Q8 O5 O4 O 0 1 N Y N N N N 7.938 -8.630 -2.851 2.441 0.345 0.667 O5 9Q8 8 9Q8 O4 O5 O 0 1 N N N N N N 10.613 -9.581 -4.069 -0.136 1.833 0.452 O4 9Q8 9 9Q8 O6 O6 O 0 1 N Y N N N N ? ? ? 0.535 0.367 2.963 O6 9Q8 10 9Q8 H1 H1 H 0 1 N N N N N N 7.584 -9.116 -2.115 2.522 0.901 0.012 H1 9Q8 11 9Q8 H2 H2 H 0 1 N Y N N N N ? ? ? -0.140 0.859 3.178 H2 9Q8 12 9Q8 H3 H3 H 0 1 N Y N N N N 10.630 -8.981 -3.333 -0.904 1.836 0.058 H3 9Q8 13 9Q8 H4 H4 H 0 1 N N N N N N 8.728 -8.177 -2.580 2.886 -0.365 0.459 H4 9Q8 14 9Q8 H5 H5 H 0 1 N Y N N N N ? ? ? 1.248 0.834 3.096 H5 9Q8 15 9Q8 H6 H6 H 0 1 N Y N N N N 11.083 -10.375 -3.841 0.438 2.166 -0.100 H6 9Q8 16 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_metal_coordination_flag _chem_comp_bond.pdbx_metal_pi_flag 9Q8 O3 C3 TRIP N N 1 N N 9Q8 O1 C1 TRIP N N 2 N N 9Q8 C3 RU SING N N 3 Y N 9Q8 C1 RU SING N N 4 Y N 9Q8 O2 C2 TRIP N N 5 N N 9Q8 C2 RU SING N N 6 Y N 9Q8 RU O4 SING N N 7 Y N 9Q8 RU O5 SING N N 8 Y N 9Q8 RU O6 SING N N 9 Y N 9Q8 O5 H1 SING N N 10 N N 9Q8 O6 H2 SING N N 11 N N 9Q8 O4 H3 SING N N 12 N N 9Q8 H4 O5 SING N N 13 N N 9Q8 H5 O6 SING N N 14 N N 9Q8 H6 O4 SING N N 15 N N # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor 9Q8 SMILES ACDLabs 14.52 "[O+]#C[Ru]([OH2])([OH2])([OH2])(C#[O+])C#[O+]" 9Q8 InChI InChI 1.06 InChI=1S/3CO.3H2O.Ru/c3*1-2;;;;/h;;;3*1H2;/q3*+1;;;; 9Q8 InChIKey InChI 1.06 UHCBCCBXGQEMOY-UHFFFAOYSA-N 9Q8 SMILES_CANONICAL CACTVS 3.385 "O.O.O.[O+]#C[Ru](C#[O+])C#[O+]" 9Q8 SMILES CACTVS 3.385 "O.O.O.[O+]#C[Ru](C#[O+])C#[O+]" 9Q8 SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C(#[O+])[Ru](C#[O+])(C#[O+])([OH2])([OH2])[OH2]" 9Q8 SMILES "OpenEye OEToolkits" 3.1.0.0 "C(#[O+])[Ru](C#[O+])(C#[O+])([OH2])([OH2])[OH2]" # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier 9Q8 "SYSTEMATIC NAME" ACDLabs 14.52 "triaquatris(carbonyl-kappaC)ruthenium(3+)" 9Q8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "tris($l^{3}-oxidanyl)-tris(oxidaniumylidynemethyl)ruthenium" # loop_ _pdbx_chem_comp_atom_coordination.geometry_id _pdbx_chem_comp_atom_coordination.comp_id _pdbx_chem_comp_atom_coordination.atom_id _pdbx_chem_comp_atom_coordination.number _pdbx_chem_comp_atom_coordination.geometry_calculated _pdbx_chem_comp_atom_coordination.geometry_generic _pdbx_chem_comp_atom_coordination.geometry_abbr _pdbx_chem_comp_atom_coordination.provenance _pdbx_chem_comp_atom_coordination.representative_entry_id 1 9Q8 RU 6 octahedral octahedral OCT MetalCoord 5OB6 1 9Q8 RU 6 octahedron octahedral OCT FindGeo 5OB7 2 9Q8 RU 5 "square pyramid" "square pyramidal" SPY FindGeo 5OBE 2 9Q8 RU 5 square-pyramid "square pyramidal" SQP MetalCoord 5OBE # loop_ _pdbx_chem_comp_atom_coordination_sphere.id _pdbx_chem_comp_atom_coordination_sphere.geometry_id _pdbx_chem_comp_atom_coordination_sphere.comp_id _pdbx_chem_comp_atom_coordination_sphere.atom_id _pdbx_chem_comp_atom_coordination_sphere.descriptor _pdbx_chem_comp_atom_coordination_sphere.provenance _pdbx_chem_comp_atom_coordination_sphere.representative_entry_id 1 1 9Q8 RU "@OCT{Ru,C,C,N,O,C,O}" MetalCoord 5OB6 2 1 9Q8 RU "@OCT{Ru,C,C,O,O,O,O}" MetalCoord 5OB7 3 1 9Q8 RU "@OCT{Ru,C,C,O,O,C,O}" MetalCoord 5OB9 4 2 9Q8 RU "@SQP{Ru,C,C,N,O,C}" MetalCoord 5OBE 5 2 9Q8 RU "@SQP{Ru,C,N,O,O,C}" MetalCoord 5OB9 # loop_ _pdbx_chem_comp_pcm.pcm_id _pdbx_chem_comp_pcm.comp_id _pdbx_chem_comp_pcm.modified_residue_id _pdbx_chem_comp_pcm.type _pdbx_chem_comp_pcm.category _pdbx_chem_comp_pcm.polypeptide_position _pdbx_chem_comp_pcm.comp_id_linking_atom _pdbx_chem_comp_pcm.modified_residue_id_linking_atom _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession _pdbx_chem_comp_pcm.position 1 9Q8 ASP None "Metal coordination" "Any position" RU OD2 ? ? "Amino-acid side chain" 2 9Q8 GLN None "Metal coordination" "Any position" RU OE1 ? ? "Amino-acid side chain" 3 9Q8 HIS None "Metal coordination" "Any position" RU ND1 ? ? "Amino-acid side chain" 4 9Q8 HIS None "Metal coordination" "Any position" RU NE2 ? ? "Amino-acid side chain" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 9Q8 "Create component" 2017-06-26 RCSB 9Q8 "Other modification" 2017-06-26 EBI 9Q8 "Initial release" 2017-07-26 RCSB 9Q8 "Other modification" 2026-07-08 RCSB 9Q8 "Other modification" 2026-07-17 RCSB 9Q8 "Other modification" 2026-07-31 RCSB #