data_T8K # _chem_comp.id T8K _chem_comp.name "[1-[(3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-3-methyl-imidazol-1-ium-2-yl]-nitrooxy-tris(oxidanyl)ruthenium" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H19 N3 O11 Ru" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(4'~{R},6'~{S},7'~{S})-17'-fluoranyl-4',6'-dimethyl-13'-[(4~{S})-4-methyl-2-oxidanylidene-1,3-oxazolidin-3-yl]spiro[1,3-diazinane-5,8'-5,15-dioxa-2,14-diazatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(17),10,12(16),13-tetraene]-2,4,6-trione" _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2023-01-04 _chem_comp.pdbx_modified_date 2024-01-05 _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 458.341 _chem_comp.one_letter_code ? _chem_comp.three_letter_code T8K _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 8C39 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_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 T8K O1 O1 O 0 1 N N N N N N 14.857 -36.059 -14.686 -3.660 -2.053 0.775 O1 T8K 1 T8K O2 O2 O -1 1 N N N N N N 14.355 -36.524 -12.466 -5.358 -0.871 1.184 O2 T8K 2 T8K O3 O3 O 0 1 N N N N N N 12.641 -35.835 -13.892 -3.449 0.209 0.550 O3 T8K 3 T8K N3 N1 N 0 1 Y N N N N N 11.874 -38.639 -12.890 -0.898 2.616 -0.833 N3 T8K 4 T8K O4 O4 O 0 1 N N N N N N 12.223 -34.975 -11.058 -1.191 0.012 1.827 O4 T8K 5 T8K O5 O5 O 0 1 N N N N N N 10.520 -33.860 -13.341 -1.072 -1.842 0.006 O5 T8K 6 T8K N4 N2 N 1 1 Y N N N N N 11.323 -38.393 -10.763 0.802 1.388 -0.324 N4 T8K 7 T8K O6 O6 O 0 1 N N N N N N 9.972 -36.612 -14.077 -2.218 -0.243 -1.697 O6 T8K 8 T8K RU RU1 RU 0 0 N N N N N N 11.027 -35.830 -12.638 -1.704 -0.115 0.065 RU T8K 9 T8K O11 O7 O 0 1 N N N N N N 8.857 -38.911 -9.978 0.634 -1.195 -1.564 O11 T8K 10 T8K C37 C1 C 0 1 N N R N N N 9.645 -38.497 -8.980 1.875 -0.675 -1.083 C37 T8K 11 T8K C36 C2 C 0 1 N N S N N N 8.724 -37.627 -7.984 2.776 -1.831 -0.637 C36 T8K 12 T8K O13 O8 O 0 1 N N N N N N 7.547 -38.272 -7.227 3.084 -2.659 -1.760 O13 T8K 13 T8K C35 C3 C 0 1 N N R N N N 9.614 -37.333 -6.906 4.071 -1.258 -0.052 C35 T8K 14 T8K O15 O9 O 0 1 N N N N N N 9.503 -38.335 -5.891 4.776 -0.539 -1.066 O15 T8K 15 T8K C34 C4 C 0 1 N N R N N N 11.035 -37.328 -7.355 3.726 -0.312 1.101 C34 T8K 16 T8K C38 C5 C 0 1 N N N N N N 11.640 -37.974 -6.142 5.010 0.311 1.652 C38 T8K 17 T8K O17 O10 O 0 1 N N N N N N 11.476 -37.106 -5.066 4.701 1.103 2.800 O17 T8K 18 T8K O10 O11 O 0 1 N N N N N N 11.810 -37.580 -8.642 2.861 0.722 0.624 O10 T8K 19 T8K C33 C6 C 0 1 N N R N N N 10.960 -38.091 -9.528 1.615 0.249 0.109 C33 T8K 20 T8K C29 C7 C 0 1 Y N N N N N 11.483 -37.755 -11.933 -0.501 1.401 -0.395 C29 T8K 21 T8K C32 C8 C 0 1 Y N N N N N 11.630 -39.674 -10.940 1.279 2.580 -0.709 C32 T8K 22 T8K C31 C9 C 0 1 Y N N N N N 11.960 -39.830 -12.197 0.231 3.363 -1.032 C31 T8K 23 T8K C30 C10 C 0 1 N N N N N N 12.153 -38.509 -14.194 -2.279 3.050 -1.059 C30 T8K 24 T8K N N3 N 1 1 N N N N N N 14.000 -36.115 -13.744 -4.190 -0.960 0.850 N T8K 25 T8K H4 H4 H 0 1 N N N N N N 8.013 -39.172 -9.628 0.724 -1.794 -2.318 H4 T8K 26 T8K H5 H5 H 0 1 N N N N N N 9.868 -39.396 -8.386 2.368 -0.116 -1.878 H5 T8K 27 T8K H6 H6 H 0 1 N N N N N N 8.390 -36.715 -8.501 2.262 -2.422 0.122 H6 T8K 28 T8K H7 H7 H 0 1 N N N N N N 7.118 -37.616 -6.690 3.652 -3.412 -1.549 H7 T8K 29 T8K H8 H8 H 0 1 N N N N N N 9.371 -36.347 -6.482 4.694 -2.072 0.319 H8 T8K 30 T8K H9 H9 H 0 1 N N N N N N 10.098 -38.132 -5.179 5.022 -1.078 -1.830 H9 T8K 31 T8K H10 H10 H 0 1 N N N N N N 11.299 -36.276 -7.171 3.224 -0.869 1.892 H10 T8K 32 T8K H11 H11 H 0 1 N N N N N N 11.132 -38.927 -5.934 5.706 -0.480 1.932 H11 T8K 33 T8K H12 H12 H 0 1 N N N N N N 12.711 -38.159 -6.312 5.465 0.941 0.887 H12 T8K 34 T8K H13 H13 H 0 1 N N N N N N 11.852 -37.495 -4.285 5.470 1.529 3.203 H13 T8K 35 T8K H14 H14 H 0 1 N N N N N N 10.586 -37.099 -9.822 1.086 -0.301 0.887 H14 T8K 36 T8K H15 H15 H 0 1 N N N N N N 11.611 -40.445 -10.184 2.320 2.864 -0.753 H15 T8K 37 T8K H16 H16 H 0 1 N N N N N N 12.261 -40.770 -12.636 0.275 4.384 -1.382 H16 T8K 38 T8K H17 H17 H 0 1 N N N N N N 12.006 -37.462 -14.498 -2.569 2.821 -2.085 H17 T8K 39 T8K H18 H18 H 0 1 N N N N N N 13.198 -38.800 -14.376 -2.941 2.528 -0.369 H18 T8K 40 T8K H19 H19 H 0 1 N N N N N N 11.484 -39.158 -14.778 -2.354 4.124 -0.892 H19 T8K 41 T8K H2 H2 H 0 1 N N N N N N 10.930 -33.209 -12.784 -0.162 -1.939 0.319 H2 T8K 42 T8K H3 H3 H 0 1 N N N N N N 9.080 -36.747 -13.779 -1.503 -0.495 -2.298 H3 T8K 43 T8K H1 H1 H 0 1 N N N N N N 13.123 -35.264 -11.150 -0.243 -0.116 1.971 H1 T8K 44 # 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 T8K O1 N DOUB N N 1 T8K C30 N3 SING N N 2 T8K O6 RU SING N N 3 T8K O3 N SING N N 4 T8K O3 RU SING N N 5 T8K N O2 SING N N 6 T8K O5 RU SING N N 7 T8K N3 C31 SING Y N 8 T8K N3 C29 SING Y N 9 T8K RU C29 SING N N 10 T8K RU O4 SING N N 11 T8K C31 C32 DOUB Y N 12 T8K C29 N4 DOUB Y N 13 T8K C32 N4 SING Y N 14 T8K N4 C33 SING N N 15 T8K O11 C37 SING N N 16 T8K C33 C37 SING N N 17 T8K C33 O10 SING N N 18 T8K C37 C36 SING N N 19 T8K O10 C34 SING N N 20 T8K C36 O13 SING N N 21 T8K C36 C35 SING N N 22 T8K C34 C35 SING N N 23 T8K C34 C38 SING N N 24 T8K C35 O15 SING N N 25 T8K C38 O17 SING N N 26 T8K O11 H4 SING N N 27 T8K C37 H5 SING N N 28 T8K C36 H6 SING N N 29 T8K O13 H7 SING N N 30 T8K C35 H8 SING N N 31 T8K O15 H9 SING N N 32 T8K C34 H10 SING N N 33 T8K C38 H11 SING N N 34 T8K C38 H12 SING N N 35 T8K O17 H13 SING N N 36 T8K C33 H14 SING N N 37 T8K C32 H15 SING N N 38 T8K C31 H16 SING N N 39 T8K C30 H17 SING N N 40 T8K C30 H18 SING N N 41 T8K C30 H19 SING N N 42 T8K O5 H2 SING N N 43 T8K O6 H3 SING N N 44 T8K O4 H1 SING N N 45 # 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 T8K InChI InChI 1.06 "InChI=1S/C10H16N2O5.NO3.3H2O.Ru/c1-11-2-3-12(5-11)10-9(16)8(15)7(14)6(4-13)17-10;2-1(3)4;;;;/h2-3,6-10,13-16H,4H2,1H3;;3*1H2;/q+1;-1;;;;+4/p-3/t6-,7+,8+,9-,10-;;;;;/m1...../s1" T8K InChIKey InChI 1.06 YHWXYWLAKQRSBE-BYNJHPACSA-K T8K SMILES_CANONICAL CACTVS 3.385 "Cn1cc[n+]([C@@H]2O[C@H](CO)[C@H](O)[C@H](O)[C@H]2O)c1[Ru](O)(O)(O)O[N+]([O-])=O" T8K SMILES CACTVS 3.385 "Cn1cc[n+]([CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O)c1[Ru](O)(O)(O)O[N+]([O-])=O" T8K SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cn1cc[n+](c1[Ru](O)(O)(O)O[N+](=O)[O-])C2[C@@H]([C@H]([C@H]([C@H](O2)CO)O)O)O" T8K SMILES "OpenEye OEToolkits" 2.0.7 "Cn1cc[n+](c1[Ru](O)(O)(O)O[N+](=O)[O-])C2C(C(C(C(O2)CO)O)O)O" # _pdbx_chem_comp_identifier.comp_id T8K _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[1-[(3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-3-methyl-imidazol-1-ium-2-yl]-nitrooxy-tris(oxidanyl)ruthenium" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site T8K "Create component" 2023-01-04 PDBE T8K "Initial release" 2024-01-10 RCSB #