data_A1JKO # _chem_comp.id A1JKO _chem_comp.name "Ruthenium[II]-benzene-phosphaadamantane" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H18 N3 P Ru" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge ? _chem_comp.pdbx_initial_date 2025-07-16 _chem_comp.pdbx_modified_date 2026-09-01 _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 336.335 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ? _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 9RY3 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _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 A1JKO C10 C1 C 0 1 Y N N N N N -30.802 -49.453 38.213 -30.802 -49.453 38.213 C10 A1JKO 1 A1JKO C16 C2 C 0 1 N N N N N N -30.277 -47.391 34.420 -30.277 -47.391 34.420 C16 A1JKO 2 A1JKO C17 C3 C 0 1 N N N N N N -31.212 -49.076 32.909 -31.212 -49.076 32.909 C17 A1JKO 3 A1JKO C18 C4 C 0 1 N N N N N N -32.249 -49.433 35.089 -32.249 -49.433 35.089 C18 A1JKO 4 A1JKO C19 C5 C 0 1 N N N N N N -31.926 -46.780 32.697 -31.926 -46.780 32.697 C19 A1JKO 5 A1JKO C2 C6 C 0 1 Y N N N N N -29.618 -48.755 37.744 -29.618 -48.755 37.744 C2 A1JKO 6 A1JKO C20 C7 C 0 1 N N N N N N -33.079 -46.724 34.841 -33.079 -46.724 34.841 C20 A1JKO 7 A1JKO C21 C8 C 0 1 N N N N N N -33.577 -48.502 33.257 -33.577 -48.502 33.257 C21 A1JKO 8 A1JKO C3 C9 C 0 1 Y N N N N N -29.244 -47.574 38.496 -29.244 -47.574 38.496 C3 A1JKO 9 A1JKO C4 C10 C 0 1 Y N R N N N -30.028 -47.091 39.603 -30.028 -47.091 39.603 C4 A1JKO 10 A1JKO C5 C11 C 0 1 Y N R N N N -31.243 -47.756 40.027 -31.243 -47.756 40.027 C5 A1JKO 11 A1JKO C9 C12 C 0 1 Y N N N N N -31.592 -48.967 39.310 -31.592 -48.967 39.310 C9 A1JKO 12 A1JKO N1 N1 N 0 1 N N N N N N -30.794 -47.667 33.059 -30.794 -47.667 33.059 N1 A1JKO 13 A1JKO N2 N2 N 0 1 N N N N N N -33.193 -47.084 33.414 -33.193 -47.084 33.414 N2 A1JKO 14 A1JKO N3 N3 N 0 1 N N N N N N -32.470 -49.415 33.627 -32.470 -49.415 33.627 N3 A1JKO 15 A1JKO RU RU1 RU ? 0 N N N N N N -31.369 -47.380 37.816 -31.369 -47.380 37.816 RU A1JKO 16 A1JKO P1 P1 P 0 1 N N N N N N -31.699 -47.734 35.533 -31.699 -47.734 35.533 P1 A1JKO 17 A1JKO H16A H1 H 0 0 N N N N N N -29.958 -46.342 34.509 -29.958 -46.342 34.509 H16A A1JKO 18 A1JKO H16B H2 H 0 0 N N N N N N -29.431 -48.053 34.656 -29.431 -48.053 34.656 H16B A1JKO 19 A1JKO H17A H3 H 0 0 N N N N N N -31.359 -49.281 31.838 -31.359 -49.281 31.838 H17A A1JKO 20 A1JKO H17B H4 H 0 0 N N N N N N -30.408 -49.718 33.298 -30.408 -49.718 33.298 H17B A1JKO 21 A1JKO H18A H5 H 0 0 N N N N N N -31.473 -50.167 35.350 -31.473 -50.167 35.350 H18A A1JKO 22 A1JKO H18B H6 H 0 0 N N N N N N -33.182 -49.683 35.615 -33.182 -49.683 35.615 H18B A1JKO 23 A1JKO H19A H7 H 0 0 N N N N N N -31.639 -45.743 32.928 -31.639 -45.743 32.928 H19A A1JKO 24 A1JKO H19B H8 H 0 0 N N N N N N -32.109 -46.878 31.617 -32.109 -46.878 31.617 H19B A1JKO 25 A1JKO H20A H9 H 0 0 N N N N N N -34.018 -46.954 35.366 -34.018 -46.954 35.366 H20A A1JKO 26 A1JKO H20B H10 H 0 0 N N N N N N -32.854 -45.652 34.945 -32.854 -45.652 34.945 H20B A1JKO 27 A1JKO H21A H11 H 0 0 N N N N N N -34.442 -48.711 33.904 -34.442 -48.710 33.904 H21A A1JKO 28 A1JKO H21B H12 H 0 0 N N N N N N -33.852 -48.683 32.207 -33.852 -48.682 32.207 H21B A1JKO 29 A1JKO H1 H13 H 0 1 N N N N N N -28.671 -46.815 37.943 -28.671 -46.815 37.943 H1 A1JKO 30 A1JKO H5 H14 H 0 1 N N N N N N -32.654 -49.255 39.321 -32.653 -49.255 39.321 H5 A1JKO 31 A1JKO H2 H2 H 0 1 N N N N N N -29.294 -48.866 36.699 -29.294 -48.867 36.699 H2 A1JKO 32 A1JKO H3 H3 H 0 1 N N N N N N -29.987 -46.007 39.785 -29.987 -46.007 39.785 H3 A1JKO 33 A1JKO H4 H4 H 0 1 N N N N N N -32.033 -47.175 40.526 -32.033 -47.175 40.526 H4 A1JKO 34 A1JKO H6 H6 H 0 1 N N N N N N -31.323 -50.077 37.472 -31.323 -50.077 37.472 H6 A1JKO 35 # 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 A1JKO P1 C16 SING N N 1 N N A1JKO C18 P1 SING N N 2 N N A1JKO C20 P1 SING N N 3 N N A1JKO P1 RU SING N N 4 Y N A1JKO C16 N1 SING N N 5 N N A1JKO N1 C17 SING N N 6 N N A1JKO N1 C19 SING N N 7 N N A1JKO C2 C3 SING Y N 8 N N A1JKO C2 C10 DOUB Y N 9 N N A1JKO C2 RU SING N N 10 Y Y A1JKO C19 N2 SING N N 11 N N A1JKO N2 C20 SING N N 12 N N A1JKO N2 C21 SING N N 13 N N A1JKO C3 C4 DOUB Y N 14 N N A1JKO C3 RU SING N N 15 Y Y A1JKO C17 N3 SING N N 16 N N A1JKO N3 C18 SING N N 17 N N A1JKO C21 N3 SING N N 18 N N A1JKO C4 C5 DOUB Y N 19 N N A1JKO C4 RU SING N N 20 Y Y A1JKO C5 C9 DOUB Y N 21 N N A1JKO C5 RU SING N N 22 Y Y A1JKO C9 C10 SING Y N 23 N N A1JKO C9 RU SING N N 24 Y Y A1JKO C10 RU SING N N 25 Y Y A1JKO C16 H16A SING N N 26 N N A1JKO C16 H16B SING N N 27 N N A1JKO C17 H17A SING N N 28 N N A1JKO C17 H17B SING N N 29 N N A1JKO C18 H18A SING N N 30 N N A1JKO C18 H18B SING N N 31 N N A1JKO C19 H19A SING N N 32 N N A1JKO C19 H19B SING N N 33 N N A1JKO C20 H20A SING N N 34 N N A1JKO C20 H20B SING N N 35 N N A1JKO C21 H21A SING N N 36 N N A1JKO C21 H21B SING N N 37 N N A1JKO C3 H1 SING N N 38 N N A1JKO C9 H5 SING N N 39 N N A1JKO H2 C2 SING N N 40 N N A1JKO H3 C4 SING N N 41 N N A1JKO H4 C5 SING N N 42 N N A1JKO H6 C10 SING N N 43 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 A1JKO InChI InChI 1.06 "InChI=1S/C6H12N3P.C6H6.Ru/c1-7-2-9-3-8(1)5-10(4-7)6-9;1-2-4-6-5-3-1;/h1-6H2;1-6H;/q;;-1/p+1" A1JKO InChIKey InChI 1.06 IDTLIGTZEVFYSG-UHFFFAOYSA-O A1JKO SMILES_CANONICAL CACTVS 3.385 "C1N2CN3CN1CP(C2)C3.[Ru]4[C@@H]=5=CC=CC=[C@@H]4=5" A1JKO SMILES CACTVS 3.385 "C1N2CN3CN1CP(C2)C3.[Ru]4[CH]=5=CC=CC=[CH]4=5" A1JKO SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C1N2CN3CN1C[P](C2)(C3)[Ru]45678[CH]=9=[CH]4=[CH]5[CH]6=[CH]7[CH]98" A1JKO SMILES "OpenEye OEToolkits" 3.1.0.0 "C1N2CN3CN1C[P](C2)(C3)[Ru]45678[CH]=9=[CH]4=[CH]5[CH]6=[CH]7[CH]98" # _pdbx_chem_comp_atom_coordination.geometry_id 1 _pdbx_chem_comp_atom_coordination.comp_id A1JKO _pdbx_chem_comp_atom_coordination.atom_id RU _pdbx_chem_comp_atom_coordination.number 9 _pdbx_chem_comp_atom_coordination.geometry_calculated sandwich_6_3 _pdbx_chem_comp_atom_coordination.geometry_generic "sandwich 6 3" _pdbx_chem_comp_atom_coordination.geometry_abbr SAS _pdbx_chem_comp_atom_coordination.provenance MetalCoord _pdbx_chem_comp_atom_coordination.representative_entry_id 9RY3 # 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 A1JKO RU "@SAS{Ru,O,C,C,C,O,P,C,C,C}" MetalCoord 9RY3 2 1 A1JKO RU "@SAS{Ru,N,C,C,C,O,P,C,C,C}" MetalCoord 9RY3 # 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 A1JKO GLU None "Metal coordination" "Any position" RU OE2 ? ? "Amino-acid side chain" 2 A1JKO GLU None "Metal coordination" "Any position" RU OE1 ? ? "Amino-acid side chain" 3 A1JKO 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 A1JKO "Create component" 2025-07-16 PDBE A1JKO "Other modification" 2025-07-16 PDBE A1JKO "Initial release" 2026-07-22 RCSB A1JKO "Other modification" 2026-07-28 RCSB A1JKO "Other modification" 2026-07-31 RCSB A1JKO "Modify aromatic_flag" 2026-08-27 RCSB A1JKO "Other modification" 2026-09-01 RCSB #