data_9RU # _chem_comp.id 9RU _chem_comp.name "[1-[4-[[5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]methyl]-2,6-dimethyl-phenyl]-3-(2,4,6-trimethylphenyl)-4,5-dihydroimidazol-2-yl]-bis(chloranyl)ruthenium" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C31 H41 Cl2 N5 O2 Ru S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge ? _chem_comp.pdbx_initial_date 2015-12-02 _chem_comp.pdbx_modified_date 2026-09-16 _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 719.731 _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 MetalCoord _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 5F2B _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI _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 9RU O1 O1 O 0 1 N N N N N N 14.092 29.416 -7.938 -8.270 -3.997 1.348 O1 9RU 1 9RU C1 C1 C 0 1 N N N N N N 15.332 29.343 -8.264 -8.440 -2.956 0.696 C1 9RU 2 9RU N2 N1 N 0 1 N N N N N N 16.288 29.543 -7.403 -9.426 -2.730 -0.190 N2 9RU 3 9RU C2 C2 C 0 1 N N R N N N 17.639 29.455 -7.926 -9.392 -1.400 -0.760 C2 9RU 4 9RU C3 C3 C 0 1 N N N N N N 18.324 28.156 -7.441 -10.584 -0.538 -0.346 C3 9RU 5 9RU S1 S1 S 0 1 N N N N N N 17.785 26.802 -8.497 -10.117 0.267 1.181 S1 9RU 6 9RU N1 N2 N 0 1 N N N N N N 15.783 29.189 -9.559 -7.665 -1.857 0.743 N1 9RU 7 9RU C4 C4 C 0 1 N N S N N N 17.252 29.219 -9.523 -8.095 -0.804 -0.154 C4 9RU 8 9RU C5 C5 C 0 1 N N S N N N 17.879 27.891 -9.920 -8.453 0.574 0.514 C5 9RU 9 9RU C6 C6 C 0 1 N N N N N N 17.267 27.191 -11.193 -7.517 1.167 1.575 C6 9RU 10 9RU C7 C7 C 0 1 N N N N N N 18.106 26.048 -11.727 -6.226 1.822 1.062 C7 9RU 11 9RU C8 C8 C 0 1 N N N N N N 17.309 25.531 -12.988 -5.128 2.044 2.115 C8 9RU 12 9RU C9 C9 C 0 1 N N N N N N 18.154 24.390 -13.622 -3.731 2.352 1.576 C9 9RU 13 9RU C10 C10 C 0 1 N N N N N N 19.404 24.942 -14.268 -2.936 1.108 1.240 C10 9RU 14 9RU O2 O2 O 0 1 N N N N N N 19.364 26.058 -14.835 -2.345 0.493 2.139 O2 9RU 15 9RU N3 N3 N 0 1 N N N N N N 20.522 24.278 -14.251 -2.915 0.707 -0.037 N3 9RU 16 9RU C11 C11 C 0 1 N N N N N N 21.438 24.104 -15.502 -2.123 -0.410 -0.550 C11 9RU 17 9RU C12 C12 C 0 1 Y N N N N N 22.731 24.846 -15.269 -0.646 -0.090 -0.592 C12 9RU 18 9RU C13 C13 C 0 1 Y N N N N N 23.908 24.222 -15.672 0.215 -0.569 0.378 C13 9RU 19 9RU C14 C14 C 0 1 Y N N N N N 25.189 24.805 -15.490 1.585 -0.302 0.365 C14 9RU 20 9RU C15 C15 C 0 1 N N N N N N 26.419 24.032 -15.957 2.410 -0.872 1.492 C15 9RU 21 9RU C16 C16 C 0 1 Y N N N N N 25.295 26.058 -14.844 2.089 0.565 -0.634 C16 9RU 22 9RU C17 C17 C 0 1 Y N N N N N 24.096 26.707 -14.446 1.234 1.033 -1.662 C17 9RU 23 9RU C18 C18 C 0 1 N N N N N N 24.096 28.055 -13.807 1.676 1.893 -2.821 C18 9RU 24 9RU C19 C19 C 0 1 Y N N N N N 22.818 26.116 -14.642 -0.122 0.708 -1.592 C19 9RU 25 9RU N4 N4 N 0 1 N N N N N N 26.594 26.623 -14.615 3.514 0.846 -0.687 N4 9RU 26 9RU C20 C20 C -2 1 N N N N N N 27.336 27.567 -15.370 4.494 -0.022 -0.460 C20 9RU 27 9RU RU1 RU1 RU ? 0 N N N N N N 26.753 28.308 -16.890 4.619 1.221 2.203 RU1 9RU 28 9RU N5 N5 N 0 1 N N N N N N 28.580 27.793 -14.700 5.692 0.423 -0.853 N5 9RU 29 9RU C21 C21 C 0 1 N N N N N N 28.674 27.007 -13.503 5.598 1.894 -1.065 C21 9RU 30 9RU C22 C22 C 0 1 N N N N N N 27.378 26.233 -13.433 4.135 2.199 -0.686 C22 9RU 31 9RU C23 C23 C 0 1 Y N N N N N 29.584 29.120 -14.967 6.910 -0.364 -0.886 C23 9RU 32 9RU C24 C24 C 0 1 Y N N N N N 30.449 29.106 -16.120 7.738 -0.340 -2.031 C24 9RU 33 9RU C25 C25 C 0 1 N N N N N N 30.582 28.108 -17.157 7.364 0.326 -3.332 C25 9RU 34 9RU C26 C26 C 0 1 Y N N N N N 31.304 30.138 -16.302 8.916 -1.089 -2.003 C26 9RU 35 9RU C27 C27 C 0 1 Y N N N N N 31.392 31.242 -15.402 9.346 -1.772 -0.884 C27 9RU 36 9RU C28 C28 C 0 1 N N N N N N 32.353 32.408 -15.615 10.644 -2.549 -0.889 C28 9RU 37 9RU C29 C29 C 0 1 Y N N N N N 30.532 31.269 -14.328 8.547 -1.726 0.239 C29 9RU 38 9RU C30 C30 C 0 1 Y N N N N N 29.635 30.230 -14.141 7.342 -1.025 0.286 C30 9RU 39 9RU C31 C31 C 0 1 N N N N N N 28.729 30.289 -12.976 6.564 -1.045 1.577 C31 9RU 40 9RU CL1 CL1 CL -1 0 N N N N N N 27.966 26.881 -18.092 2.667 2.598 2.675 CL1 9RU 41 9RU CL2 CL2 CL -1 0 N N N N N N 25.836 30.003 -15.662 6.469 2.768 2.367 CL2 9RU 42 9RU H1 H1 H 0 1 N N N N N N 16.103 29.745 -6.441 -10.014 -3.330 -0.387 H1 9RU 43 9RU H2 H2 H 0 1 N N N N N N 18.255 30.355 -7.784 -9.325 -1.453 -1.743 H2 9RU 44 9RU H3 H3 H 0 1 N N N N N N 19.417 28.266 -7.506 -11.387 -1.101 -0.210 H3 9RU 45 9RU H4 H4 H 0 1 N N N N N N 18.037 27.951 -6.399 -10.785 0.134 -1.046 H4 9RU 46 9RU H5 H5 H 0 1 N N N N N N 15.214 29.077 -10.374 -6.975 -1.812 1.260 H5 9RU 47 9RU H6 H6 H 0 1 N N N N N N 17.661 30.046 -10.122 -7.417 -0.674 -0.859 H6 9RU 48 9RU H7 H7 H 0 1 N N N N N N 18.952 28.050 -10.103 -8.543 1.250 -0.218 H7 9RU 49 9RU H8 H8 H 0 1 N N N N N N 16.274 26.798 -10.929 -7.277 0.454 2.205 H8 9RU 50 9RU H9 H9 H 0 1 N N N N N N 17.163 27.945 -11.987 -8.018 1.840 2.081 H9 9RU 51 9RU H10 H10 H 0 1 N N N N N N 19.106 26.402 -12.017 -6.452 2.692 0.668 H10 9RU 52 9RU H11 H11 H 0 1 N N N N N N 18.203 25.252 -10.974 -5.852 1.270 0.339 H11 9RU 53 9RU H12 H12 H 0 1 N N N N N N 16.325 25.147 -12.682 -5.073 1.244 2.684 H12 9RU 54 9RU H13 H13 H 0 1 N N N N N N 17.175 26.349 -13.712 -5.408 2.787 2.693 H13 9RU 55 9RU H14 H14 H 0 1 N N N N N N 18.440 23.674 -12.837 -3.239 2.865 2.252 H14 9RU 56 9RU H15 H15 H 0 1 N N N N N N 17.551 23.876 -14.385 -3.807 2.916 0.775 H15 9RU 57 9RU H16 H16 H 0 1 N N N N N N 20.810 23.857 -13.391 -3.415 1.125 -0.639 H16 9RU 58 9RU H17 H17 H 0 1 N N N N N N 21.649 23.036 -15.660 -2.431 -0.630 -1.455 H17 9RU 59 9RU H18 H18 H 0 1 N N N N N N 20.933 24.513 -16.389 -2.273 -1.196 0.018 H18 9RU 60 9RU H19 H19 H 0 1 N N N N N N 23.844 23.252 -16.143 -0.137 -1.111 1.071 H19 9RU 61 9RU H20 H20 H 0 1 N N N N N N 26.654 24.308 -16.995 2.980 -1.583 1.154 H20 9RU 62 9RU H21 H21 H 0 1 N N N N N N 27.274 24.278 -15.310 1.832 -1.240 2.182 H21 9RU 63 9RU H22 H22 H 0 1 N N N N N N 26.216 22.952 -15.902 2.951 -0.176 1.884 H22 9RU 64 9RU H23 H23 H 0 1 N N N N N N 24.031 28.830 -14.585 1.042 1.817 -3.555 H23 9RU 65 9RU H24 H24 H 0 1 N N N N N N 23.232 28.140 -13.131 2.547 1.600 -3.135 H24 9RU 66 9RU H25 H25 H 0 1 N N N N N N 25.025 28.189 -13.233 1.725 2.821 -2.538 H25 9RU 67 9RU H26 H26 H 0 1 N N N N N N 21.924 26.628 -14.318 -0.705 1.040 -2.261 H26 9RU 68 9RU H27 H27 H 0 1 N N N N N N 29.531 26.320 -13.559 5.771 2.145 -2.001 H27 9RU 69 9RU H28 H28 H 0 1 N N N N N N 26.832 26.489 -12.513 4.082 2.615 0.205 H28 9RU 70 9RU H29 H29 H 0 1 N N N N N N 29.895 28.343 -17.983 7.836 -0.093 -4.072 H29 9RU 71 9RU H30 H30 H 0 1 N N N N N N 31.616 28.104 -17.531 7.600 1.268 -3.296 H30 9RU 72 9RU H31 H31 H 0 1 N N N N N N 30.336 27.118 -16.746 6.408 0.237 -3.483 H31 9RU 73 9RU H32 H32 H 0 1 N N N N N N 31.949 30.126 -17.168 9.456 -1.117 -2.781 H32 9RU 74 9RU H33 H33 H 0 1 N N N N N N 31.865 33.178 -16.230 11.013 -2.581 0.010 H33 9RU 75 9RU H34 H34 H 0 1 N N N N N N 32.630 32.838 -14.641 11.284 -2.117 -1.481 H34 9RU 76 9RU H35 H35 H 0 1 N N N N N N 33.258 32.049 -16.127 10.479 -3.455 -1.201 H35 9RU 77 9RU H36 H36 H 0 1 N N N N N N 30.556 32.096 -13.634 8.834 -2.191 1.013 H36 9RU 78 9RU H37 H37 H 0 1 N N N N N N 29.215 29.818 -12.109 7.035 -1.569 2.247 H37 9RU 79 9RU H38 H38 H 0 1 N N N N N N 28.500 31.339 -12.742 5.692 -1.444 1.431 H38 9RU 80 9RU H39 H39 H 0 1 N N N N N N 27.797 29.754 -13.209 6.461 -0.138 1.904 H39 9RU 81 9RU H40 H40 H 0 1 N N N N N N 28.783 27.657 -12.622 6.227 2.380 -0.483 H40 9RU 82 9RU H41 H41 H 0 1 N N N N N N 27.580 25.152 -13.451 3.723 2.805 -1.342 H41 9RU 83 # 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 9RU O1 C1 DOUB N N 1 N N 9RU C1 N2 SING N N 2 N N 9RU C1 N1 SING N N 3 N N 9RU N2 C2 SING N N 4 N N 9RU C2 C3 SING N N 5 N N 9RU C2 C4 SING N N 6 N N 9RU C3 S1 SING N N 7 N N 9RU S1 C5 SING N N 8 N N 9RU N1 C4 SING N N 9 N N 9RU C4 C5 SING N N 10 N N 9RU C5 C6 SING N N 11 N N 9RU C6 C7 SING N N 12 N N 9RU C7 C8 SING N N 13 N N 9RU C8 C9 SING N N 14 N N 9RU C9 C10 SING N N 15 N N 9RU C10 O2 DOUB N N 16 N N 9RU C10 N3 SING N N 17 N N 9RU N3 C11 SING N N 18 N N 9RU C11 C12 SING N N 19 N N 9RU C12 C13 DOUB Y N 20 N N 9RU C12 C19 SING Y N 21 N N 9RU C13 C14 SING Y N 22 N N 9RU C14 C15 SING N N 23 N N 9RU C14 C16 DOUB Y N 24 N N 9RU C16 C17 SING Y N 25 N N 9RU C16 N4 SING N N 26 N N 9RU C17 C18 SING N N 27 N N 9RU C17 C19 DOUB Y N 28 N N 9RU N4 C20 SING N N 29 N N 9RU N4 C22 SING N N 30 N N 9RU C20 RU1 SING N N 31 Y N 9RU C20 N5 SING N N 32 N N 9RU RU1 CL1 SING N N 33 Y N 9RU RU1 CL2 SING N N 34 Y N 9RU N5 C21 SING N N 35 N N 9RU C21 C22 SING N N 36 N N 9RU C23 C24 DOUB Y N 37 N N 9RU C23 C30 SING Y N 38 N N 9RU C24 C25 SING N N 39 N N 9RU C24 C26 SING Y N 40 N N 9RU C26 C27 DOUB Y N 41 N N 9RU C27 C28 SING N N 42 N N 9RU C27 C29 SING Y N 43 N N 9RU C29 C30 DOUB Y N 44 N N 9RU C30 C31 SING N N 45 N N 9RU N5 C23 SING N N 46 N N 9RU N2 H1 SING N N 47 N N 9RU C2 H2 SING N N 48 N N 9RU C3 H3 SING N N 49 N N 9RU C3 H4 SING N N 50 N N 9RU N1 H5 SING N N 51 N N 9RU C4 H6 SING N N 52 N N 9RU C5 H7 SING N N 53 N N 9RU C6 H8 SING N N 54 N N 9RU C6 H9 SING N N 55 N N 9RU C7 H10 SING N N 56 N N 9RU C7 H11 SING N N 57 N N 9RU C8 H12 SING N N 58 N N 9RU C8 H13 SING N N 59 N N 9RU C9 H14 SING N N 60 N N 9RU C9 H15 SING N N 61 N N 9RU N3 H16 SING N N 62 N N 9RU C11 H17 SING N N 63 N N 9RU C11 H18 SING N N 64 N N 9RU C13 H19 SING N N 65 N N 9RU C15 H20 SING N N 66 N N 9RU C15 H21 SING N N 67 N N 9RU C15 H22 SING N N 68 N N 9RU C18 H23 SING N N 69 N N 9RU C18 H24 SING N N 70 N N 9RU C18 H25 SING N N 71 N N 9RU C19 H26 SING N N 72 N N 9RU C21 H27 SING N N 73 N N 9RU C22 H28 SING N N 74 N N 9RU C25 H29 SING N N 75 N N 9RU C25 H30 SING N N 76 N N 9RU C25 H31 SING N N 77 N N 9RU C26 H32 SING N N 78 N N 9RU C28 H33 SING N N 79 N N 9RU C28 H34 SING N N 80 N N 9RU C28 H35 SING N N 81 N N 9RU C29 H36 SING N N 82 N N 9RU C31 H37 SING N N 83 N N 9RU C31 H38 SING N N 84 N N 9RU C31 H39 SING N N 85 N N 9RU C21 H40 SING N N 86 N N 9RU C22 H41 SING N N 87 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 9RU SMILES ACDLabs 14.52 "O=C1NC2C(CCCCC(=O)NCc3cc(C)c(N4CCN(c5c(C)cc(C)cc5C)C4[Ru](Cl)Cl)c(C)c3)SCC2N1" 9RU InChI InChI 1.06 "InChI=1S/C31H42N5O2S.2ClH.Ru/c1-19-12-20(2)29(21(3)13-19)35-10-11-36(18-35)30-22(4)14-24(15-23(30)5)16-32-27(37)9-7-6-8-26-28-25(17-39-26)33-31(38)34-28;;;/h12-15,18,25-26,28H,6-11,16-17H2,1-5H3,(H,32,37)(H2,33,34,38);2*1H;/q;;;+2/p-2/t25-,26-,28-;;;/m0.../s1" 9RU InChIKey InChI 1.06 LMVDBENAALZRIZ-ZYPDNKHZSA-L 9RU SMILES_CANONICAL CACTVS 3.385 "Cc1cc(C)c(N2CN(CC2)c3c(C)cc(CNC(=O)CCCC[C@@H]4SC[C@@H]5NC(=O)N[C@H]45)cc3C)c(C)c1.Cl[Ru]Cl" 9RU SMILES CACTVS 3.385 "Cc1cc(C)c(N2CN(CC2)c3c(C)cc(CNC(=O)CCCC[CH]4SC[CH]5NC(=O)N[CH]45)cc3C)c(C)c1.Cl[Ru]Cl" 9RU SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "Cc1cc(c(c(c1)C)N2CCN([C]2[Ru](Cl)Cl)c3c(cc(cc3C)CNC(=O)CCCC[C@H]4[C@@H]5[C@H](CS4)NC(=O)N5)C)C" 9RU SMILES "OpenEye OEToolkits" 3.1.0.0 "Cc1cc(c(c(c1)C)N2CCN([C]2[Ru](Cl)Cl)c3c(cc(cc3C)CNC(=O)CCCCC4C5C(CS4)NC(=O)N5)C)C" # 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 9RU "SYSTEMATIC NAME" ACDLabs 14.52 "dichlorido[(2S)-1-[2,6-dimethyl-4-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamido}methyl)phenyl]-3-(2,4,6-trimethylphenyl)imidazolidin-2-yl]ruthenium" 9RU "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "[1-[4-[[5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]methyl]-2,6-dimethyl-phenyl]-3-(2,4,6-trimethylphenyl)-4,5-dihydroimidazol-2-yl]-bis(chloranyl)ruthenium" # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id 9RU _pdbx_chem_comp_pcm.modified_residue_id LYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Metal coordination" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom RU1 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom NZ _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? _pdbx_chem_comp_pcm.position "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 9RU "Create component" 2015-12-02 EBI 9RU "Initial release" 2016-08-31 RCSB 9RU "Other modification" 2026-07-08 RCSB 9RU "Other modification" 2026-07-17 RCSB 9RU "Other modification" 2026-07-31 RCSB 9RU "Other modification" 2026-09-16 RCSB #