data_7ZWV # _model_server_result.job_id 5aSJDwKLMmlcxZQr3i_JEg _model_server_result.datetime_utc '2025-01-10 01:55:34' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 7zwv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 7ZWV # _exptl.entry_id 7ZWV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 377.463 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,3-dimethyl-5-[[6-(phenylmethylsulfanyl)pyrimidin-4-yl]amino]benzimidazol-2-one _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 7ZWV _cell.length_a 67.231 _cell.length_b 67.231 _cell.length_c 165.202 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ZWV _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 12_545 x,x-y-1,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 33.6155 -58.223754 27.533667 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C20 H19 N5 O S' _chem_comp.formula_weight 377.463 _chem_comp.id KA9 _chem_comp.mon_nstd_flag . _chem_comp.name 1,3-dimethyl-5-[[6-(phenylmethylsulfanyl)pyrimidin-4-yl]amino]benzimidazol-2-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag S C6 KA9 sing 204 n n S C8 KA9 sing 205 n n N3 C6 KA9 doub 206 n y N3 C5 KA9 sing 207 n y C6 C7 KA9 sing 208 n y C8 C9 KA9 sing 209 n n C5 N2 KA9 doub 210 n y C9 C10 KA9 doub 211 n y C9 C14 KA9 sing 212 n y C10 C11 KA9 sing 213 n y C7 C4 KA9 doub 214 n y N2 C4 KA9 sing 215 n y C14 C13 KA9 doub 216 n y C4 N1 KA9 sing 217 n n C11 C12 KA9 doub 218 n y C13 C12 KA9 sing 219 n y N1 C3 KA9 sing 220 n n C3 C15 KA9 doub 221 n y C3 C2 KA9 sing 222 n y C15 C16 KA9 sing 223 n y C2 C1 KA9 doub 224 n y C16 C17 KA9 doub 225 n y C1 C17 KA9 sing 226 n y C1 N KA9 sing 227 n n C17 N4 KA9 sing 228 n n N C19 KA9 sing 229 n n N C KA9 sing 230 n n N4 C18 KA9 sing 231 n n N4 C KA9 sing 232 n n C O KA9 doub 233 n n C2 H1 KA9 sing 234 n n C5 H2 KA9 sing 235 n n C7 H3 KA9 sing 236 n n C12 H4 KA9 sing 237 n n C13 H5 KA9 sing 238 n n C14 H6 KA9 sing 239 n n C15 H7 KA9 sing 240 n n C16 H8 KA9 sing 241 n n C19 H9 KA9 sing 242 n n C19 H10 KA9 sing 243 n n C19 H11 KA9 sing 244 n n C18 H12 KA9 sing 245 n n C18 H13 KA9 sing 246 n n C18 H14 KA9 sing 247 n n N1 H15 KA9 sing 248 n n C8 H16 KA9 sing 249 n n C8 H17 KA9 sing 250 n n C11 H18 KA9 sing 251 n n C10 H19 KA9 sing 252 n n # _atom_sites.entry_id 7ZWV _atom_sites.fract_transf_matrix[1][1] 0.014874 _atom_sites.fract_transf_matrix[1][2] 0.008588 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017175 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.006053 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 KA9 A 1 201 200 KA9 065 . D 4 EDO A 1 202 1 EDO EDO . E 4 EDO A 1 203 3 EDO EDO . F 4 EDO A 1 204 4 EDO EDO . G 4 EDO A 1 205 5 EDO EDO . H 4 EDO A 1 206 6 EDO EDO . I 4 EDO A 1 207 7 EDO EDO . J 4 EDO A 1 208 8 EDO EDO . K 4 EDO A 1 209 9 EDO EDO . L 4 EDO A 1 210 10 EDO EDO . M 5 GOL A 1 211 1 GOL GOL . N 5 GOL A 1 212 2 GOL GOL . O 6 DMS A 1 213 1 DMS DMS . P 7 HOH A 1 301 191 HOH HOH . P 7 HOH A 2 302 130 HOH HOH . P 7 HOH A 3 303 9 HOH HOH . P 7 HOH A 4 304 24 HOH HOH . P 7 HOH A 5 305 180 HOH HOH . P 7 HOH A 6 306 80 HOH HOH . P 7 HOH A 7 307 188 HOH HOH . P 7 HOH A 8 308 15 HOH HOH . P 7 HOH A 9 309 197 HOH HOH . P 7 HOH A 10 310 7 HOH HOH . P 7 HOH A 11 311 157 HOH HOH . P 7 HOH A 12 312 74 HOH HOH . P 7 HOH A 13 313 87 HOH HOH . P 7 HOH A 14 314 153 HOH HOH . P 7 HOH A 15 315 126 HOH HOH . P 7 HOH A 16 316 29 HOH HOH . P 7 HOH A 17 317 35 HOH HOH . P 7 HOH A 18 318 41 HOH HOH . P 7 HOH A 19 319 64 HOH HOH . P 7 HOH A 20 320 52 HOH HOH . P 7 HOH A 21 321 60 HOH HOH . P 7 HOH A 22 322 164 HOH HOH . P 7 HOH A 23 323 17 HOH HOH . P 7 HOH A 24 324 118 HOH HOH . P 7 HOH A 25 325 147 HOH HOH . P 7 HOH A 26 326 13 HOH HOH . P 7 HOH A 27 327 168 HOH HOH . P 7 HOH A 28 328 72 HOH HOH . P 7 HOH A 29 329 10 HOH HOH . P 7 HOH A 30 330 99 HOH HOH . P 7 HOH A 31 331 36 HOH HOH . P 7 HOH A 32 332 42 HOH HOH . P 7 HOH A 33 333 93 HOH HOH . P 7 HOH A 34 334 122 HOH HOH . P 7 HOH A 35 335 185 HOH HOH . P 7 HOH A 36 336 162 HOH HOH . P 7 HOH A 37 337 167 HOH HOH . P 7 HOH A 38 338 113 HOH HOH . P 7 HOH A 39 339 106 HOH HOH . P 7 HOH A 40 340 203 HOH HOH . P 7 HOH A 41 341 20 HOH HOH . P 7 HOH A 42 342 43 HOH HOH . P 7 HOH A 43 343 175 HOH HOH . P 7 HOH A 44 344 119 HOH HOH . P 7 HOH A 45 345 62 HOH HOH . P 7 HOH A 46 346 133 HOH HOH . P 7 HOH A 47 347 81 HOH HOH . P 7 HOH A 48 348 40 HOH HOH . P 7 HOH A 49 349 202 HOH HOH . P 7 HOH A 50 350 88 HOH HOH . P 7 HOH A 51 351 28 HOH HOH . P 7 HOH A 52 352 16 HOH HOH . P 7 HOH A 53 353 49 HOH HOH . P 7 HOH A 54 354 83 HOH HOH . P 7 HOH A 55 355 95 HOH HOH . P 7 HOH A 56 356 5 HOH HOH . P 7 HOH A 57 357 92 HOH HOH . P 7 HOH A 58 358 171 HOH HOH . P 7 HOH A 59 359 61 HOH HOH . P 7 HOH A 60 360 142 HOH HOH . P 7 HOH A 61 361 25 HOH HOH . P 7 HOH A 62 362 112 HOH HOH . P 7 HOH A 63 363 32 HOH HOH . P 7 HOH A 64 364 84 HOH HOH . P 7 HOH A 65 365 90 HOH HOH . P 7 HOH A 66 366 73 HOH HOH . P 7 HOH A 67 367 63 HOH HOH . P 7 HOH A 68 368 3 HOH HOH . P 7 HOH A 69 369 70 HOH HOH . P 7 HOH A 70 370 71 HOH HOH . P 7 HOH A 71 371 105 HOH HOH . P 7 HOH A 72 372 50 HOH HOH . P 7 HOH A 73 373 173 HOH HOH . P 7 HOH A 74 374 37 HOH HOH . P 7 HOH A 75 375 6 HOH HOH . P 7 HOH A 76 376 85 HOH HOH . P 7 HOH A 77 377 89 HOH HOH . P 7 HOH A 78 378 115 HOH HOH . P 7 HOH A 79 379 56 HOH HOH . P 7 HOH A 80 380 53 HOH HOH . P 7 HOH A 81 381 131 HOH HOH . P 7 HOH A 82 382 205 HOH HOH . P 7 HOH A 83 383 8 HOH HOH . P 7 HOH A 84 384 27 HOH HOH . P 7 HOH A 85 385 124 HOH HOH . P 7 HOH A 86 386 140 HOH HOH . P 7 HOH A 87 387 34 HOH HOH . P 7 HOH A 88 388 129 HOH HOH . P 7 HOH A 89 389 163 HOH HOH . P 7 HOH A 90 390 104 HOH HOH . P 7 HOH A 91 391 66 HOH HOH . P 7 HOH A 92 392 209 HOH HOH . P 7 HOH A 93 393 31 HOH HOH . P 7 HOH A 94 394 11 HOH HOH . P 7 HOH A 95 395 169 HOH HOH . P 7 HOH A 96 396 98 HOH HOH . P 7 HOH A 97 397 170 HOH HOH . P 7 HOH A 98 398 101 HOH HOH . P 7 HOH A 99 399 48 HOH HOH . P 7 HOH A 100 400 152 HOH HOH . P 7 HOH A 101 401 54 HOH HOH . P 7 HOH A 102 402 125 HOH HOH . P 7 HOH A 103 403 117 HOH HOH . P 7 HOH A 104 404 55 HOH HOH . P 7 HOH A 105 405 160 HOH HOH . P 7 HOH A 106 406 97 HOH HOH . P 7 HOH A 107 407 51 HOH HOH . P 7 HOH A 108 408 158 HOH HOH . P 7 HOH A 109 409 204 HOH HOH . P 7 HOH A 110 410 58 HOH HOH . P 7 HOH A 111 411 186 HOH HOH . P 7 HOH A 112 412 136 HOH HOH . P 7 HOH A 113 413 166 HOH HOH . P 7 HOH A 114 414 79 HOH HOH . P 7 HOH A 115 415 134 HOH HOH . P 7 HOH A 116 416 77 HOH HOH . P 7 HOH A 117 417 154 HOH HOH . P 7 HOH A 118 418 68 HOH HOH . P 7 HOH A 119 419 193 HOH HOH . P 7 HOH A 120 420 69 HOH HOH . P 7 HOH A 121 421 161 HOH HOH . P 7 HOH A 122 422 172 HOH HOH . P 7 HOH A 123 423 4 HOH HOH . P 7 HOH A 124 424 190 HOH HOH . P 7 HOH A 125 425 96 HOH HOH . P 7 HOH A 126 426 177 HOH HOH . P 7 HOH A 127 427 110 HOH HOH . P 7 HOH A 128 428 174 HOH HOH . P 7 HOH A 129 429 120 HOH HOH . P 7 HOH A 130 430 82 HOH HOH . P 7 HOH A 131 431 76 HOH HOH . P 7 HOH A 132 432 182 HOH HOH . P 7 HOH A 133 433 150 HOH HOH . P 7 HOH A 134 434 45 HOH HOH . P 7 HOH A 135 435 194 HOH HOH . P 7 HOH A 136 436 135 HOH HOH . P 7 HOH A 137 437 137 HOH HOH . P 7 HOH A 138 438 146 HOH HOH . P 7 HOH A 139 439 144 HOH HOH . P 7 HOH A 140 440 94 HOH HOH . P 7 HOH A 141 441 148 HOH HOH . P 7 HOH A 142 442 192 HOH HOH . P 7 HOH A 143 443 109 HOH HOH . P 7 HOH A 144 444 181 HOH HOH . P 7 HOH A 145 445 187 HOH HOH . P 7 HOH A 146 446 143 HOH HOH . P 7 HOH A 147 447 121 HOH HOH . P 7 HOH A 148 448 206 HOH HOH . P 7 HOH A 149 449 102 HOH HOH . P 7 HOH A 150 450 151 HOH HOH . P 7 HOH A 151 451 208 HOH HOH . P 7 HOH A 152 452 184 HOH HOH . P 7 HOH A 153 453 138 HOH HOH . Q 7 HOH B 1 101 195 HOH HOH . Q 7 HOH B 2 102 107 HOH HOH . Q 7 HOH B 3 103 65 HOH HOH . Q 7 HOH B 4 104 75 HOH HOH . Q 7 HOH B 5 105 159 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C2 KA9 . . . C 3 24.792 -10.734 17.173 0.76 23.14 ? C2 KA9 201 A 1 HETATM 2 C C3 KA9 . . . C 3 25.418 -9.827 16.326 0.76 23.73 ? C3 KA9 201 A 1 HETATM 3 C C4 KA9 . . . C 3 26.465 -10.139 14.065 0.76 23.08 ? C4 KA9 201 A 1 HETATM 4 C C5 KA9 . . . C 3 27.616 -10.498 12.175 0.76 23.87 ? C5 KA9 201 A 1 HETATM 5 C C6 KA9 . . . C 3 25.775 -9.236 12.005 0.76 24.6 ? C6 KA9 201 A 1 HETATM 6 C C7 KA9 . . . C 3 25.52 -9.386 13.361 0.76 23.99 ? C7 KA9 201 A 1 HETATM 7 C C12 KA9 . . . C 3 23.688 -4.9 15.007 0.76 36.81 ? C12 KA9 201 A 1 HETATM 8 C C13 KA9 . . . C 3 22.484 -5.549 14.874 0.76 36.82 ? C13 KA9 201 A 1 HETATM 9 C C14 KA9 . . . C 3 22.329 -6.541 13.925 0.76 34.89 ? C14 KA9 201 A 1 HETATM 10 C C15 KA9 . . . C 3 25.072 -8.476 16.347 0.76 22.35 ? C15 KA9 201 A 1 HETATM 11 C C16 KA9 . . . C 3 24.093 -8.006 17.206 0.76 25.42 ? C16 KA9 201 A 1 HETATM 12 C C17 KA9 . . . C 3 23.463 -8.911 18.043 0.76 26.76 ? C17 KA9 201 A 1 HETATM 13 C C19 KA9 . . . C 3 23.033 -12.329 19.222 0.76 25.35 ? C19 KA9 201 A 1 HETATM 14 O O KA9 . . . C 3 21.259 -10.228 20.329 0.76 29.76 ? O KA9 201 A 1 HETATM 15 C C KA9 . . . C 3 22.135 -9.987 19.529 0.76 29.71 ? C KA9 201 A 1 HETATM 16 N N4 KA9 . . . C 3 22.443 -8.757 18.976 0.76 28.22 ? N4 KA9 201 A 1 HETATM 17 C C18 KA9 . . . C 3 21.809 -7.487 19.318 0.76 29.47 ? C18 KA9 201 A 1 HETATM 18 C C1 KA9 . . . C 3 23.811 -10.255 18.021 0.76 23.76 ? C1 KA9 201 A 1 HETATM 19 N N KA9 . . . C 3 22.993 -10.899 18.938 0.76 25.59 ? N KA9 201 A 1 HETATM 20 N N1 KA9 . . . C 3 26.388 -10.3 15.43 0.76 22.28 ? N1 KA9 201 A 1 HETATM 21 N N3 KA9 . . . C 3 26.818 -9.78 11.392 0.76 24.79 ? N3 KA9 201 A 1 HETATM 22 N N2 KA9 . . . C 3 27.514 -10.716 13.485 0.76 20.72 ? N2 KA9 201 A 1 HETATM 23 S S KA9 . . . C 3 24.616 -8.371 10.991 0.76 30.83 ? S KA9 201 A 1 HETATM 24 C C8 KA9 . . . C 3 23.228 -8.033 12.118 0.76 32.8 ? C8 KA9 201 A 1 HETATM 25 C C9 KA9 . . . C 3 23.382 -6.905 13.101 0.76 34.28 ? C9 KA9 201 A 1 HETATM 26 C C11 KA9 . . . C 3 24.737 -5.24 14.187 0.76 35.96 ? C11 KA9 201 A 1 HETATM 27 C C10 KA9 . . . C 3 24.586 -6.236 13.239 0.76 34.66 ? C10 KA9 201 A 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 76 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 1316 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 27 #