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 
# 
