data_KYT # _chem_comp.id KYT _chem_comp.name "(3AS,4S,6AR)-4-(5-((3R,4R)-3,4-DIAMINOPYRROLIDIN-1-YL)-5-OXOPENTYL)TETRAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-2(3H)-ONE-P-CYMENE-CHLORO-RUTHENIUM(III)" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C24 H39 Cl N5 O2 Ru S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2009-08-10 _chem_comp.pdbx_modified_date 2011-06-04 _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 598.187 _chem_comp.one_letter_code ? _chem_comp.three_letter_code KYT _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 2WPU _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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.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 KYT CL1 CL1 CL 0 0 N N N 5.617 -4.982 2.805 5.617 -4.982 2.805 CL1 KYT 1 KYT RU1 RU1 RU 1 0 N N N 3.890 -5.979 0.796 3.890 -5.979 0.796 RU1 KYT 2 KYT N1 N1 N 0 1 N N N 5.241 -7.679 1.273 5.241 -7.679 1.273 N1 KYT 3 KYT C1 C1 C 0 1 N N R 6.107 -7.724 0.098 6.107 -7.724 0.098 C1 KYT 4 KYT C2 C2 C 0 1 N N N 7.365 -8.604 0.127 7.365 -8.604 0.127 C2 KYT 5 KYT C3 C3 C 0 1 Y N N 2.268 -4.617 0.400 2.268 -4.617 0.400 C3 KYT 6 KYT C4 C4 C 0 1 N N N 2.239 -3.139 0.371 2.239 -3.139 0.371 C4 KYT 7 KYT C5 C5 C 0 1 N N N 3.506 -2.493 -0.261 3.506 -2.493 -0.261 C5 KYT 8 KYT C6 C6 C 0 1 N N N 0.936 -2.613 -0.294 0.936 -2.613 -0.294 C6 KYT 9 KYT C7 C7 C 0 1 Y N N 1.989 -5.303 1.575 1.989 -5.303 1.575 C7 KYT 10 KYT C8 C8 C 0 1 Y N N 2.016 -6.653 1.629 2.016 -6.653 1.629 C8 KYT 11 KYT C9 C9 C 0 1 Y N N 2.242 -7.395 0.484 2.242 -7.395 0.484 C9 KYT 12 KYT C10 C10 C 0 1 N N N 2.184 -8.856 0.507 2.184 -8.856 0.507 C10 KYT 13 KYT C11 C11 C 0 1 Y N N 2.490 -5.362 -0.717 2.490 -5.362 -0.717 C11 KYT 14 KYT C12 C12 C 0 1 Y N N 2.502 -6.739 -0.675 2.502 -6.739 -0.675 C12 KYT 15 KYT N2 N2 N 0 1 N N N 5.611 -5.433 -0.534 5.611 -5.433 -0.534 N2 KYT 16 KYT C13 C13 C 0 1 N N R 6.693 -6.327 -0.111 6.693 -6.327 -0.111 C13 KYT 17 KYT C14 C14 C 0 1 N N N 7.851 -6.622 -1.078 7.851 -6.622 -1.078 C14 KYT 18 KYT N3 N3 N 0 1 N N N 8.243 -7.935 -0.746 8.243 -7.935 -0.746 N3 KYT 19 KYT C15 C15 C 0 1 N N N 9.335 -8.484 -1.227 9.335 -8.484 -1.227 C15 KYT 20 KYT O1 O1 O 0 1 N N N 9.503 -8.470 -2.440 9.503 -8.470 -2.440 O1 KYT 21 KYT C16 C16 C 0 1 N N N 10.330 -9.123 -0.367 10.330 -9.123 -0.367 C16 KYT 22 KYT C17 C17 C 0 1 N N N 11.745 -9.321 -0.987 11.745 -9.321 -0.987 C17 KYT 23 KYT C18 C18 C 0 1 N N N 12.731 -10.030 -0.018 12.731 -10.030 -0.018 C18 KYT 24 KYT C19 C19 C 0 1 N N N 14.184 -10.107 -0.564 14.184 -10.107 -0.564 C19 KYT 25 KYT C20 C20 C 0 1 N N S 15.164 -10.813 0.418 15.164 -10.813 0.418 C20 KYT 26 KYT C21 C21 C 0 1 N N S 16.550 -11.208 -0.163 16.550 -11.208 -0.163 C21 KYT 27 KYT N4 N4 N 0 1 N N N 17.100 -10.286 -1.038 17.100 -10.286 -1.038 N4 KYT 28 KYT S1 S1 S 0 1 N N N 15.610 -9.803 1.870 15.610 -9.803 1.870 S1 KYT 29 KYT C22 C22 C 0 1 N N N 17.131 -10.707 2.301 17.131 -10.707 2.301 C22 KYT 30 KYT C23 C23 C 0 1 N N R 17.647 -11.260 0.945 17.647 -11.260 0.945 C23 KYT 31 KYT N5 N5 N 0 1 N N N 18.625 -10.449 0.396 18.625 -10.449 0.396 N5 KYT 32 KYT C24 C24 C 0 1 N N N 18.264 -9.902 -0.694 18.264 -9.902 -0.694 C24 KYT 33 KYT O2 O2 O 0 1 N N N 18.948 -9.119 -1.331 18.948 -9.119 -1.331 O2 KYT 34 KYT HAF1 HAF1 H 0 0 N N N 4.718 -8.549 1.380 4.718 -8.549 1.380 HAF1 KYT 35 KYT HAF2 HAF2 H 0 0 N N N 5.783 -7.470 2.112 5.783 -7.470 2.112 HAF2 KYT 36 KYT H1 H1 H 0 1 N N N 1.754 -4.803 2.403 1.754 -4.803 2.403 H1 KYT 37 KYT H2 H2 H 0 1 N N N 1.808 -7.104 2.489 1.808 -7.104 2.489 H2 KYT 38 KYT H5 H5 H 0 1 N N N 2.647 -4.920 -1.594 2.647 -4.920 -1.594 H5 KYT 39 KYT H4 H4 H 0 1 N N N 2.676 -7.247 -1.514 2.676 -7.247 -1.514 H4 KYT 40 KYT HAI1 HAI1 H 0 0 N N N 5.366 -5.612 -1.509 5.366 -5.612 -1.509 HAI1 KYT 41 KYT HAI2 HAI2 H 0 0 N N N 5.880 -4.454 -0.410 5.880 -4.454 -0.410 HAI2 KYT 42 KYT HAE HAE H 0 1 N N N 5.490 -8.007 -0.764 5.490 -8.007 -0.764 HAE KYT 43 KYT HAD1 HAD1 H 0 0 N N N 7.780 -8.657 1.138 7.780 -8.657 1.138 HAD1 KYT 44 KYT HAD2 HAD2 H 0 0 N N N 7.124 -9.613 -0.217 7.124 -9.613 -0.217 HAD2 KYT 45 KYT HAH HAH H 0 1 N N N 7.098 -5.936 0.830 7.098 -5.936 0.830 HAH KYT 46 KYT H10 H10 H 0 1 N N N 2.219 -2.758 1.399 2.219 -2.758 1.399 H10 KYT 47 KYT H81C H81C H 0 0 N N N 3.487 -1.411 -0.109 3.487 -1.411 -0.109 H81C KYT 48 KYT H82C H82C H 0 0 N N N 4.411 -2.877 0.213 4.411 -2.877 0.213 H82C KYT 49 KYT H83C H83C H 0 0 N N N 3.559 -2.685 -1.335 3.559 -2.685 -1.335 H83C KYT 50 KYT H71C H71C H 0 0 N N N 0.897 -1.523 -0.239 0.897 -1.523 -0.239 H71C KYT 51 KYT H72C H72C H 0 0 N N N 0.880 -2.907 -1.344 0.880 -2.907 -1.344 H72C KYT 52 KYT H73C H73C H 0 0 N N N 0.060 -3.007 0.227 0.060 -3.007 0.227 H73C KYT 53 KYT H91C H91C H 0 0 N N N 1.280 -9.195 -0.002 1.280 -9.195 -0.002 H91C KYT 54 KYT H92C H92C H 0 0 N N N 3.050 -9.284 -0.002 3.050 -9.284 -0.002 H92C KYT 55 KYT H93C H93C H 0 0 N N N 2.171 -9.256 1.523 2.171 -9.256 1.523 H93C KYT 56 KYT HAG1 HAG1 H 0 0 N N N 8.663 -5.905 -0.925 8.663 -5.905 -0.925 HAG1 KYT 57 KYT HAG2 HAG2 H 0 0 N N N 7.511 -6.562 -2.117 7.511 -6.562 -2.117 HAG2 KYT 58 KYT H401 H401 H 0 0 N N N 9.942 -10.100 -0.065 9.942 -10.100 -0.065 H401 KYT 59 KYT H402 H402 H 0 0 N N N 10.444 -8.513 0.535 10.444 -8.513 0.535 H402 KYT 60 KYT H451 H451 H 0 0 N N N 12.150 -8.344 -1.261 12.150 -8.344 -1.261 H451 KYT 61 KYT H452 H452 H 0 0 N N N 11.666 -9.921 -1.898 11.666 -9.921 -1.898 H452 KYT 62 KYT H461 H461 H 0 0 N N N 12.368 -11.046 0.164 12.368 -11.046 0.164 H461 KYT 63 KYT H462 H462 H 0 0 N N N 12.738 -9.497 0.935 12.738 -9.497 0.935 H462 KYT 64 KYT H471 H471 H 0 0 N N N 14.546 -9.097 -0.778 14.546 -9.097 -0.778 H471 KYT 65 KYT H472 H472 H 0 0 N N N 14.171 -10.667 -1.502 14.171 -10.667 -1.502 H472 KYT 66 KYT H48 H48 H 0 1 N N N 14.700 -11.728 0.796 14.700 -11.728 0.796 H48 KYT 67 KYT H49 H49 H 0 1 N N N 16.471 -12.167 -0.681 16.471 -12.167 -0.681 H49 KYT 68 KYT H53 H53 H 0 1 N N N 16.668 -9.981 -1.811 16.668 -9.981 -1.811 H53 KYT 69 KYT H50 H50 H 0 1 N N N 18.040 -12.274 1.068 18.040 -12.274 1.068 H50 KYT 70 KYT H55 H55 H 0 1 N N N 19.467 -10.321 0.784 19.467 -10.321 0.784 H55 KYT 71 KYT H511 H511 H 0 0 N N N 16.868 -11.531 2.970 16.868 -11.531 2.970 H511 KYT 72 KYT H512 H512 H 0 0 N N N 17.848 -10.047 2.797 17.848 -10.047 2.797 H512 KYT 73 # 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 KYT CL1 RU1 SING N N 1 KYT N1 C1 SING N N 2 KYT N1 HAF1 SING N N 3 KYT N1 HAF2 SING N N 4 KYT C1 C2 SING N N 5 KYT C1 C13 SING N N 6 KYT C1 HAE SING N N 7 KYT C2 N3 SING N N 8 KYT C2 HAD1 SING N N 9 KYT C2 HAD2 SING N N 10 KYT C3 C4 SING N N 11 KYT C3 C7 SING Y N 12 KYT C3 C11 DOUB Y N 13 KYT C4 C5 SING N N 14 KYT C4 C6 SING N N 15 KYT C4 H10 SING N N 16 KYT C5 H81C SING N N 17 KYT C5 H82C SING N N 18 KYT C5 H83C SING N N 19 KYT C6 H71C SING N N 20 KYT C6 H72C SING N N 21 KYT C6 H73C SING N N 22 KYT C7 C8 DOUB Y N 23 KYT C7 H1 SING N N 24 KYT C8 C9 SING Y N 25 KYT C8 H2 SING N N 26 KYT C9 C10 SING N N 27 KYT C9 C12 DOUB Y N 28 KYT C10 H91C SING N N 29 KYT C10 H92C SING N N 30 KYT C10 H93C SING N N 31 KYT C11 C12 SING Y N 32 KYT C11 H5 SING N N 33 KYT C12 H4 SING N N 34 KYT N2 C13 SING N N 35 KYT N2 HAI1 SING N N 36 KYT N2 HAI2 SING N N 37 KYT C13 C14 SING N N 38 KYT C13 HAH SING N N 39 KYT C14 N3 SING N N 40 KYT C14 HAG1 SING N N 41 KYT C14 HAG2 SING N N 42 KYT N3 C15 SING N N 43 KYT C15 O1 DOUB N N 44 KYT C15 C16 SING N N 45 KYT C16 C17 SING N N 46 KYT C16 H401 SING N N 47 KYT C16 H402 SING N N 48 KYT C17 C18 SING N N 49 KYT C17 H451 SING N N 50 KYT C17 H452 SING N N 51 KYT C18 C19 SING N N 52 KYT C18 H461 SING N N 53 KYT C18 H462 SING N N 54 KYT C19 C20 SING N N 55 KYT C19 H471 SING N N 56 KYT C19 H472 SING N N 57 KYT C20 C21 SING N N 58 KYT C20 S1 SING N N 59 KYT C20 H48 SING N N 60 KYT C21 N4 SING N N 61 KYT C21 C23 SING N N 62 KYT C21 H49 SING N N 63 KYT N4 C24 SING N N 64 KYT N4 H53 SING N N 65 KYT S1 C22 SING N N 66 KYT C22 C23 SING N N 67 KYT C22 H511 SING N N 68 KYT C22 H512 SING N N 69 KYT C23 N5 SING N N 70 KYT C23 H50 SING N N 71 KYT N5 C24 SING N N 72 KYT N5 H55 SING N N 73 KYT C24 O2 DOUB N N 74 KYT N2 RU1 SING N N 75 KYT N1 RU1 SING N N 76 KYT C3 RU1 SING N N 77 KYT C8 RU1 SING N N 78 KYT C12 RU1 SING N N 79 # 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 KYT SMILES ACDLabs 11.02 "O=C1NC2C(SCC2N1)CCCCC(=O)N7CC6N[Ru+]45(Cl)(C3=CC5(=CC4=C3C)C(C)C)NC6C7" KYT SMILES_CANONICAL CACTVS 3.352 "CC(C)C1|2=CC|3=C(C)C(=C1)|[Ru+]|4|2|3(|N[C@@H]5CN(C[C@H]5N|4)C(=O)CCCC[C@@H]6SC[C@@H]7NC(=O)N[C@H]67)Cl" KYT SMILES CACTVS 3.352 "CC(C)C1|2=CC|3=C(C)C(=C1)|[Ru+]|4|2|3(|N[CH]5CN(C[CH]5N|4)C(=O)CCCC[CH]6SC[CH]7NC(=O)N[CH]67)Cl" KYT SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CC1=[CH]2C=C3([Ru+]24([CH]1=C3)([NH2][C@@H]5CN(C[C@H]5[NH2]4)C(=O)CCCC[C@H]6[C@@H]7[C@H](CS6)NC(=O)N7)Cl)C(C)C" KYT SMILES "OpenEye OEToolkits" 1.7.0 "CC1=[CH]2C=C3([Ru+]24([CH]1=C3)([NH2]C5CN(CC5[NH2]4)C(=O)CCCCC6C7C(CS6)NC(=O)N7)Cl)C(C)C" KYT InChI InChI 1.03 "InChI=1S/C14H25N5O2S.C10H14.ClH.Ru/c15-8-5-19(6-9(8)16)12(20)4-2-1-3-11-13-10(7-22-11)17-14(21)18-13;1-8(2)10-6-4-9(3)5-7-10;;/h8-11,13H,1-7,15-16H2,(H2,17,18,21);4-8H,1-3H3;1H;/q;;;+2/p-1/t8-,9-,10+,11+,13+;;;/m1.../s1" KYT InChIKey InChI 1.03 OJIBJWGHGYGDGX-SNKMZJELSA-M # 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 KYT "SYSTEMATIC NAME" ACDLabs 11.02 "chloro[(3aS,4S,6aR)-4-{5-[(3R,4R)-3,4-di(amino-kappaN)pyrrolidin-1-yl]-5-oxopentyl}tetrahydro-1H-thieno[3,4-d]imidazol-2(3H)-one][1-methyl-4-(propan-2-yl)benzene-kappa~3~C~2~,C~4~,C~6~]ruthenium(1+)" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site KYT "Create component" 2009-08-10 EBI KYT "Modify aromatic_flag" 2011-06-04 RCSB KYT "Modify descriptor" 2011-06-04 RCSB #