data_KA9 # _chem_comp.id KA9 _chem_comp.name "1,3-dimethyl-5-[[6-(phenylmethylsulfanyl)pyrimidin-4-yl]amino]benzimidazol-2-one" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H19 N5 O S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-05-23 _chem_comp.pdbx_modified_date 2022-11-11 _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 377.463 _chem_comp.one_letter_code ? _chem_comp.three_letter_code KA9 _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 7ZWV _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.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 KA9 C2 C1 C 0 1 Y N N 24.792 -10.734 17.173 -3.545 1.227 0.244 C2 KA9 1 KA9 C3 C2 C 0 1 Y N N 25.418 -9.827 16.326 -2.441 0.425 0.495 C3 KA9 2 KA9 C4 C3 C 0 1 Y N N 26.465 -10.139 14.065 -0.041 0.331 0.250 C4 KA9 3 KA9 C5 C4 C 0 1 Y N N 27.616 -10.498 12.175 0.931 -1.464 -0.821 C5 KA9 4 KA9 C6 C5 C 0 1 Y N N 25.775 -9.236 12.005 2.333 0.126 0.082 C6 KA9 5 KA9 C7 C6 C 0 1 Y N N 25.520 -9.386 13.361 1.223 0.843 0.522 C7 KA9 6 KA9 C12 C7 C 0 1 Y N N 23.688 -4.900 15.007 9.094 0.272 0.026 C12 KA9 7 KA9 C13 C8 C 0 1 Y N N 22.484 -5.549 14.874 8.399 0.734 -1.076 C13 KA9 8 KA9 C14 C9 C 0 1 Y N N 22.329 -6.541 13.925 7.052 0.455 -1.211 C14 KA9 9 KA9 C15 C10 C 0 1 Y N N 25.072 -8.476 16.347 -2.585 -0.956 0.576 C15 KA9 10 KA9 C16 C11 C 0 1 Y N N 24.093 -8.006 17.206 -3.827 -1.535 0.407 C16 KA9 11 KA9 C17 C12 C 0 1 Y N N 23.463 -8.911 18.043 -4.934 -0.739 0.156 C17 KA9 12 KA9 C19 C13 C 0 1 N N N 23.033 -12.329 19.222 -6.387 2.588 -0.336 C19 KA9 13 KA9 O O1 O 0 1 N N N 21.259 -10.228 20.329 -8.124 0.257 -0.467 O KA9 14 KA9 C C14 C 0 1 N N N 22.135 -9.987 19.529 -6.931 0.146 -0.254 C KA9 15 KA9 N4 N1 N 0 1 N N N 22.443 -8.757 18.976 -6.285 -1.018 -0.054 N4 KA9 16 KA9 C18 C15 C 0 1 N N N 21.809 -7.487 19.318 -6.895 -2.350 -0.057 C18 KA9 17 KA9 C1 C16 C 0 1 Y N N 23.811 -10.255 18.021 -4.792 0.648 0.074 C1 KA9 18 KA9 N N2 N 0 1 N N N 22.993 -10.899 18.938 -6.059 1.169 -0.178 N KA9 19 KA9 N1 N3 N 0 1 N N N 26.388 -10.300 15.430 -1.179 1.006 0.667 N1 KA9 20 KA9 N3 N4 N 0 1 Y N N 26.818 -9.780 11.392 2.145 -1.015 -0.579 N3 KA9 21 KA9 N2 N5 N 0 1 Y N N 27.514 -10.716 13.485 -0.144 -0.816 -0.421 N2 KA9 22 KA9 S S1 S 0 1 N N N 24.616 -8.371 10.991 3.962 0.721 0.394 S KA9 23 KA9 C8 C17 C 0 1 N N N 23.228 -8.033 12.118 4.931 -0.591 -0.390 C8 KA9 24 KA9 C9 C18 C 0 1 Y N N 23.382 -6.905 13.101 6.400 -0.287 -0.243 C9 KA9 25 KA9 C11 C19 C 0 1 Y N N 24.737 -5.240 14.187 8.444 -0.474 0.990 C11 KA9 26 KA9 C10 C20 C 0 1 Y N N 24.586 -6.236 13.239 7.095 -0.749 0.859 C10 KA9 27 KA9 H1 H1 H 0 1 N N N 25.063 -11.779 17.169 -3.432 2.300 0.186 H1 KA9 28 KA9 H2 H2 H 0 1 N N N 28.457 -10.966 11.685 0.813 -2.391 -1.363 H2 KA9 29 KA9 H3 H3 H 0 1 N N N 24.654 -8.952 13.838 1.340 1.772 1.060 H3 KA9 30 KA9 H4 H4 H 0 1 N N N 23.809 -4.127 15.752 10.147 0.491 0.131 H4 KA9 31 KA9 H5 H5 H 0 1 N N N 21.656 -5.283 15.514 8.908 1.314 -1.832 H5 KA9 32 KA9 H6 H6 H 0 1 N N N 21.376 -7.039 13.824 6.509 0.815 -2.072 H6 KA9 33 KA9 H7 H7 H 0 1 N N N 25.575 -7.787 15.684 -1.724 -1.577 0.771 H7 KA9 34 KA9 H8 H8 H 0 1 N N N 23.827 -6.959 17.223 -3.936 -2.608 0.470 H8 KA9 35 KA9 H9 H9 H 0 1 N N N 22.281 -12.573 19.987 -6.297 2.867 -1.385 H9 KA9 36 KA9 H10 H10 H 0 1 N N N 22.816 -12.892 18.302 -7.409 2.764 0.001 H10 KA9 37 KA9 H11 H11 H 0 1 N N N 24.033 -12.602 19.591 -5.700 3.188 0.260 H11 KA9 38 KA9 H12 H12 H 0 1 N N N 21.037 -7.656 20.083 -7.219 -2.603 0.952 H12 KA9 39 KA9 H13 H13 H 0 1 N N N 22.567 -6.793 19.710 -7.755 -2.354 -0.727 H13 KA9 40 KA9 H14 H14 H 0 1 N N N 21.346 -7.055 18.419 -6.165 -3.083 -0.399 H14 KA9 41 KA9 H15 H15 H 0 1 N N N 27.130 -10.830 15.842 -1.100 1.881 1.077 H15 KA9 42 KA9 H16 H16 H 0 1 N N N 22.348 -7.809 11.497 4.708 -1.544 0.091 H16 KA9 43 KA9 H17 H17 H 0 1 N N N 23.045 -8.950 12.697 4.676 -0.649 -1.448 H17 KA9 44 KA9 H18 H18 H 0 1 N N N 25.683 -4.728 14.283 8.988 -0.839 1.849 H18 KA9 45 KA9 H19 H19 H 0 1 N N N 25.417 -6.495 12.599 6.586 -1.328 1.615 H19 KA9 46 # 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 KA9 S C6 SING N N 1 KA9 S C8 SING N N 2 KA9 N3 C6 DOUB Y N 3 KA9 N3 C5 SING Y N 4 KA9 C6 C7 SING Y N 5 KA9 C8 C9 SING N N 6 KA9 C5 N2 DOUB Y N 7 KA9 C9 C10 DOUB Y N 8 KA9 C9 C14 SING Y N 9 KA9 C10 C11 SING Y N 10 KA9 C7 C4 DOUB Y N 11 KA9 N2 C4 SING Y N 12 KA9 C14 C13 DOUB Y N 13 KA9 C4 N1 SING N N 14 KA9 C11 C12 DOUB Y N 15 KA9 C13 C12 SING Y N 16 KA9 N1 C3 SING N N 17 KA9 C3 C15 DOUB Y N 18 KA9 C3 C2 SING Y N 19 KA9 C15 C16 SING Y N 20 KA9 C2 C1 DOUB Y N 21 KA9 C16 C17 DOUB Y N 22 KA9 C1 C17 SING Y N 23 KA9 C1 N SING N N 24 KA9 C17 N4 SING N N 25 KA9 N C19 SING N N 26 KA9 N C SING N N 27 KA9 N4 C18 SING N N 28 KA9 N4 C SING N N 29 KA9 C O DOUB N N 30 KA9 C2 H1 SING N N 31 KA9 C5 H2 SING N N 32 KA9 C7 H3 SING N N 33 KA9 C12 H4 SING N N 34 KA9 C13 H5 SING N N 35 KA9 C14 H6 SING N N 36 KA9 C15 H7 SING N N 37 KA9 C16 H8 SING N N 38 KA9 C19 H9 SING N N 39 KA9 C19 H10 SING N N 40 KA9 C19 H11 SING N N 41 KA9 C18 H12 SING N N 42 KA9 C18 H13 SING N N 43 KA9 C18 H14 SING N N 44 KA9 N1 H15 SING N N 45 KA9 C8 H16 SING N N 46 KA9 C8 H17 SING N N 47 KA9 C11 H18 SING N N 48 KA9 C10 H19 SING N N 49 # 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 KA9 InChI InChI 1.06 "InChI=1S/C20H19N5OS/c1-24-16-9-8-15(10-17(16)25(2)20(24)26)23-18-11-19(22-13-21-18)27-12-14-6-4-3-5-7-14/h3-11,13H,12H2,1-2H3,(H,21,22,23)" KA9 InChIKey InChI 1.06 UFPZSUZTGMULLK-UHFFFAOYSA-N KA9 SMILES_CANONICAL CACTVS 3.385 "CN1C(=O)N(C)c2cc(Nc3cc(SCc4ccccc4)ncn3)ccc12" KA9 SMILES CACTVS 3.385 "CN1C(=O)N(C)c2cc(Nc3cc(SCc4ccccc4)ncn3)ccc12" KA9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN1c2ccc(cc2N(C1=O)C)Nc3cc(ncn3)SCc4ccccc4" KA9 SMILES "OpenEye OEToolkits" 2.0.7 "CN1c2ccc(cc2N(C1=O)C)Nc3cc(ncn3)SCc4ccccc4" # _pdbx_chem_comp_identifier.comp_id KA9 _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-dimethyl-5-[[6-(phenylmethylsulfanyl)pyrimidin-4-yl]amino]benzimidazol-2-one" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site KA9 "Create component" 2022-05-23 PDBE KA9 "Modify descriptor" 2022-08-22 RCSB KA9 "Initial release" 2022-11-16 RCSB #