data_6TPY # _model_server_result.job_id hkZMn0e2LCd3yfz53UTVDg _model_server_result.datetime_utc '2024-10-19 12:34:42' _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 6tpy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":204}' # _entry.id 6TPY # _exptl.entry_id 6TPY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 337.416 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,3-dimethyl-5-[1-(oxan-4-ylmethyl)benzimidazol-2-yl]pyridin-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 90 _cell.entry_id 6TPY _cell.length_a 38.694 _cell.length_b 43.252 _cell.length_c 79.181 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6TPY _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C20 H23 N3 O2' _chem_comp.formula_weight 337.416 _chem_comp.id NUB _chem_comp.mon_nstd_flag . _chem_comp.name 1,3-dimethyl-5-[1-(oxan-4-ylmethyl)benzimidazol-2-yl]pyridin-2-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1,3-dimethyl-5-(1-((tetrahydro-2H-pyran-4-yl)methyl)-1H-benzo[d]imidazol-2-yl)pyridin-2(1H)-one # 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 C43 O42 NUB sing 246 n n C43 C46 NUB sing 247 n n O42 C39 NUB sing 248 n n C46 C34 NUB sing 249 n n C39 C36 NUB sing 250 n n C34 C36 NUB sing 251 n n C34 C31 NUB sing 252 n n C31 N30 NUB sing 253 n n C27 C25 NUB doub 254 n y C27 C29 NUB sing 255 n y N30 C29 NUB sing 256 n y N30 C18 NUB sing 257 n y C01 C05 NUB sing 258 n n C25 C23 NUB sing 259 n y C29 C20 NUB doub 260 n y C06 C05 NUB doub 261 n n C06 C08 NUB sing 262 n n C05 C16 NUB sing 263 n n C18 C08 NUB sing 264 n n C18 N19 NUB doub 265 n y C08 C09 NUB doub 266 n n C16 O17 NUB doub 267 n n C16 N11 NUB sing 268 n n C23 C21 NUB doub 269 n y C20 N19 NUB sing 270 n y C20 C21 NUB sing 271 n y C09 N11 NUB sing 272 n n N11 C12 NUB sing 273 n n C21 H1 NUB sing 274 n n C01 H2 NUB sing 275 n n C01 H3 NUB sing 276 n n C01 H4 NUB sing 277 n n C06 H5 NUB sing 278 n n C09 H6 NUB sing 279 n n C12 H7 NUB sing 280 n n C12 H8 NUB sing 281 n n C12 H9 NUB sing 282 n n C23 H10 NUB sing 283 n n C25 H11 NUB sing 284 n n C27 H12 NUB sing 285 n n C31 H13 NUB sing 286 n n C31 H14 NUB sing 287 n n C34 H15 NUB sing 288 n n C36 H16 NUB sing 289 n n C36 H17 NUB sing 290 n n C39 H18 NUB sing 291 n n C39 H19 NUB sing 292 n n C43 H20 NUB sing 293 n n C43 H21 NUB sing 294 n n C46 H22 NUB sing 295 n n C46 H23 NUB sing 296 n n # _atom_sites.entry_id 6TPY _atom_sites.fract_transf_matrix[1][1] 0.025844 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.02312 _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] 0.012629 _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 B 2 EDO AAA 1 201 1 EDO EDO . C 2 EDO AAA 1 202 2 EDO EDO . D 2 EDO AAA 1 203 3 EDO EDO . E 3 NUB AAA 1 204 1 NUB LIG . F 4 HOH AAA 1 301 67 HOH HOH . F 4 HOH AAA 2 302 196 HOH HOH . F 4 HOH AAA 3 303 76 HOH HOH . F 4 HOH AAA 4 304 187 HOH HOH . F 4 HOH AAA 5 305 145 HOH HOH . F 4 HOH AAA 6 306 28 HOH HOH . F 4 HOH AAA 7 307 146 HOH HOH . F 4 HOH AAA 8 308 178 HOH HOH . F 4 HOH AAA 9 309 182 HOH HOH . F 4 HOH AAA 10 310 86 HOH HOH . F 4 HOH AAA 11 311 99 HOH HOH . F 4 HOH AAA 12 312 107 HOH HOH . F 4 HOH AAA 13 313 11 HOH HOH . F 4 HOH AAA 14 314 40 HOH HOH . F 4 HOH AAA 15 315 24 HOH HOH . F 4 HOH AAA 16 316 36 HOH HOH . F 4 HOH AAA 17 317 96 HOH HOH . F 4 HOH AAA 18 318 193 HOH HOH . F 4 HOH AAA 19 319 116 HOH HOH . F 4 HOH AAA 20 320 31 HOH HOH . F 4 HOH AAA 21 321 156 HOH HOH . F 4 HOH AAA 22 322 127 HOH HOH . F 4 HOH AAA 23 323 54 HOH HOH . F 4 HOH AAA 24 324 57 HOH HOH . F 4 HOH AAA 25 325 32 HOH HOH . F 4 HOH AAA 26 326 189 HOH HOH . F 4 HOH AAA 27 327 75 HOH HOH . F 4 HOH AAA 28 328 72 HOH HOH . F 4 HOH AAA 29 329 117 HOH HOH . F 4 HOH AAA 30 330 190 HOH HOH . F 4 HOH AAA 31 331 181 HOH HOH . F 4 HOH AAA 32 332 43 HOH HOH . F 4 HOH AAA 33 333 158 HOH HOH . F 4 HOH AAA 34 334 23 HOH HOH . F 4 HOH AAA 35 335 4 HOH HOH . F 4 HOH AAA 36 336 38 HOH HOH . F 4 HOH AAA 37 337 25 HOH HOH . F 4 HOH AAA 38 338 42 HOH HOH . F 4 HOH AAA 39 339 49 HOH HOH . F 4 HOH AAA 40 340 186 HOH HOH . F 4 HOH AAA 41 341 103 HOH HOH . F 4 HOH AAA 42 342 26 HOH HOH . F 4 HOH AAA 43 343 9 HOH HOH . F 4 HOH AAA 44 344 157 HOH HOH . F 4 HOH AAA 45 345 79 HOH HOH . F 4 HOH AAA 46 346 165 HOH HOH . F 4 HOH AAA 47 347 52 HOH HOH . F 4 HOH AAA 48 348 128 HOH HOH . F 4 HOH AAA 49 349 85 HOH HOH . F 4 HOH AAA 50 350 192 HOH HOH . F 4 HOH AAA 51 351 164 HOH HOH . F 4 HOH AAA 52 352 105 HOH HOH . F 4 HOH AAA 53 353 29 HOH HOH . F 4 HOH AAA 54 354 155 HOH HOH . F 4 HOH AAA 55 355 30 HOH HOH . F 4 HOH AAA 56 356 139 HOH HOH . F 4 HOH AAA 57 357 161 HOH HOH . F 4 HOH AAA 58 358 17 HOH HOH . F 4 HOH AAA 59 359 83 HOH HOH . F 4 HOH AAA 60 360 1 HOH HOH . F 4 HOH AAA 61 361 65 HOH HOH . F 4 HOH AAA 62 362 73 HOH HOH . F 4 HOH AAA 63 363 61 HOH HOH . F 4 HOH AAA 64 364 60 HOH HOH . F 4 HOH AAA 65 365 176 HOH HOH . F 4 HOH AAA 66 366 48 HOH HOH . F 4 HOH AAA 67 367 138 HOH HOH . F 4 HOH AAA 68 368 175 HOH HOH . F 4 HOH AAA 69 369 74 HOH HOH . F 4 HOH AAA 70 370 122 HOH HOH . F 4 HOH AAA 71 371 91 HOH HOH . F 4 HOH AAA 72 372 177 HOH HOH . F 4 HOH AAA 73 373 50 HOH HOH . F 4 HOH AAA 74 374 37 HOH HOH . F 4 HOH AAA 75 375 144 HOH HOH . F 4 HOH AAA 76 376 35 HOH HOH . F 4 HOH AAA 77 377 10 HOH HOH . F 4 HOH AAA 78 378 27 HOH HOH . F 4 HOH AAA 79 379 77 HOH HOH . F 4 HOH AAA 80 380 5 HOH HOH . F 4 HOH AAA 81 381 8 HOH HOH . F 4 HOH AAA 82 382 18 HOH HOH . F 4 HOH AAA 83 383 167 HOH HOH . F 4 HOH AAA 84 384 41 HOH HOH . F 4 HOH AAA 85 385 160 HOH HOH . F 4 HOH AAA 86 386 82 HOH HOH . F 4 HOH AAA 87 387 118 HOH HOH . F 4 HOH AAA 88 388 45 HOH HOH . F 4 HOH AAA 89 389 3 HOH HOH . F 4 HOH AAA 90 390 33 HOH HOH . F 4 HOH AAA 91 391 102 HOH HOH . F 4 HOH AAA 92 392 169 HOH HOH . F 4 HOH AAA 93 393 21 HOH HOH . F 4 HOH AAA 94 394 130 HOH HOH . F 4 HOH AAA 95 395 22 HOH HOH . F 4 HOH AAA 96 396 12 HOH HOH . F 4 HOH AAA 97 397 71 HOH HOH . F 4 HOH AAA 98 398 2 HOH HOH . F 4 HOH AAA 99 399 19 HOH HOH . F 4 HOH AAA 100 400 20 HOH HOH . F 4 HOH AAA 101 401 183 HOH HOH . F 4 HOH AAA 102 402 7 HOH HOH . F 4 HOH AAA 103 403 69 HOH HOH . F 4 HOH AAA 104 404 13 HOH HOH . F 4 HOH AAA 105 405 126 HOH HOH . F 4 HOH AAA 106 406 53 HOH HOH . F 4 HOH AAA 107 407 16 HOH HOH . F 4 HOH AAA 108 408 68 HOH HOH . F 4 HOH AAA 109 409 133 HOH HOH . F 4 HOH AAA 110 410 63 HOH HOH . F 4 HOH AAA 111 411 44 HOH HOH . F 4 HOH AAA 112 412 6 HOH HOH . F 4 HOH AAA 113 413 124 HOH HOH . F 4 HOH AAA 114 414 15 HOH HOH . F 4 HOH AAA 115 415 195 HOH HOH . F 4 HOH AAA 116 416 108 HOH HOH . F 4 HOH AAA 117 417 120 HOH HOH . F 4 HOH AAA 118 418 173 HOH HOH . F 4 HOH AAA 119 419 125 HOH HOH . F 4 HOH AAA 120 420 149 HOH HOH . F 4 HOH AAA 121 421 113 HOH HOH . F 4 HOH AAA 122 422 179 HOH HOH . F 4 HOH AAA 123 423 171 HOH HOH . F 4 HOH AAA 124 424 153 HOH HOH . F 4 HOH AAA 125 425 172 HOH HOH . F 4 HOH AAA 126 426 123 HOH HOH . F 4 HOH AAA 127 427 64 HOH HOH . F 4 HOH AAA 128 428 150 HOH HOH . F 4 HOH AAA 129 429 185 HOH HOH . F 4 HOH AAA 130 430 66 HOH HOH . F 4 HOH AAA 131 431 106 HOH HOH . F 4 HOH AAA 132 432 78 HOH HOH . F 4 HOH AAA 133 433 46 HOH HOH . F 4 HOH AAA 134 434 170 HOH HOH . F 4 HOH AAA 135 435 180 HOH HOH . F 4 HOH AAA 136 436 81 HOH HOH . F 4 HOH AAA 137 437 141 HOH HOH . F 4 HOH AAA 138 438 151 HOH HOH . F 4 HOH AAA 139 439 184 HOH HOH . F 4 HOH AAA 140 440 131 HOH HOH . F 4 HOH AAA 141 441 92 HOH HOH . F 4 HOH AAA 142 442 97 HOH HOH . F 4 HOH AAA 143 443 111 HOH HOH . F 4 HOH AAA 144 444 147 HOH HOH . F 4 HOH AAA 145 445 142 HOH HOH . F 4 HOH AAA 146 446 95 HOH HOH . F 4 HOH AAA 147 447 55 HOH HOH . F 4 HOH AAA 148 448 88 HOH HOH . F 4 HOH AAA 149 449 39 HOH HOH . F 4 HOH AAA 150 450 84 HOH HOH . F 4 HOH AAA 151 451 34 HOH HOH . F 4 HOH AAA 152 452 140 HOH HOH . F 4 HOH AAA 153 453 162 HOH HOH . F 4 HOH AAA 154 454 58 HOH HOH . F 4 HOH AAA 155 455 129 HOH HOH . F 4 HOH AAA 156 456 87 HOH HOH . F 4 HOH AAA 157 457 154 HOH HOH . F 4 HOH AAA 158 458 59 HOH HOH . F 4 HOH AAA 159 459 100 HOH HOH . F 4 HOH AAA 160 460 104 HOH HOH . F 4 HOH AAA 161 461 148 HOH HOH . F 4 HOH AAA 162 462 51 HOH HOH . F 4 HOH AAA 163 463 168 HOH HOH . F 4 HOH AAA 164 464 114 HOH HOH . F 4 HOH AAA 165 465 174 HOH HOH . F 4 HOH AAA 166 466 47 HOH HOH . F 4 HOH AAA 167 467 98 HOH HOH . F 4 HOH AAA 168 468 119 HOH HOH . F 4 HOH AAA 169 469 132 HOH HOH . F 4 HOH AAA 170 470 14 HOH HOH . F 4 HOH AAA 171 471 135 HOH HOH . F 4 HOH AAA 172 472 110 HOH HOH . F 4 HOH AAA 173 473 115 HOH HOH . F 4 HOH AAA 174 474 134 HOH HOH . F 4 HOH AAA 175 475 163 HOH HOH . F 4 HOH AAA 176 476 137 HOH HOH . F 4 HOH AAA 177 477 121 HOH HOH . F 4 HOH AAA 178 478 152 HOH HOH . F 4 HOH AAA 179 479 70 HOH HOH . F 4 HOH AAA 180 480 56 HOH HOH . F 4 HOH AAA 181 481 80 HOH HOH . F 4 HOH AAA 182 482 93 HOH HOH . F 4 HOH AAA 183 483 62 HOH HOH . F 4 HOH AAA 184 484 143 HOH HOH . F 4 HOH AAA 185 485 90 HOH HOH . F 4 HOH AAA 186 486 159 HOH HOH . F 4 HOH AAA 187 487 89 HOH HOH . F 4 HOH AAA 188 488 109 HOH HOH . F 4 HOH AAA 189 489 136 HOH HOH . F 4 HOH AAA 190 490 188 HOH HOH . F 4 HOH AAA 191 491 101 HOH HOH . F 4 HOH AAA 192 492 112 HOH HOH . F 4 HOH AAA 193 493 194 HOH HOH . F 4 HOH AAA 194 494 94 HOH HOH . F 4 HOH AAA 195 495 166 HOH HOH . F 4 HOH AAA 196 496 191 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 C20 NUB . . . E 3 30.743 50.758 0.816 1 19.82 ? C20 NUB 204 AAA 1 HETATM 2 C C21 NUB . . . E 3 31.85 51.256 1.501 1 18.53 ? C21 NUB 204 AAA 1 HETATM 3 C C01 NUB . . . E 3 24.131 49.824 -0.864 1 15.09 ? C01 NUB 204 AAA 1 HETATM 4 C C05 NUB . . . E 3 25.334 49.149 -0.271 1 15.24 ? C05 NUB 204 AAA 1 HETATM 5 C C06 NUB . . . E 3 26.559 49.708 -0.313 1 16.06 ? C06 NUB 204 AAA 1 HETATM 6 C C08 NUB . . . E 3 27.699 49.077 0.286 1 16.6 ? C08 NUB 204 AAA 1 HETATM 7 C C09 NUB . . . E 3 27.499 47.926 0.928 1 16.11 ? C09 NUB 204 AAA 1 HETATM 8 N N11 NUB . . . E 3 26.274 47.33 0.963 1 16.63 ? N11 NUB 204 AAA 1 HETATM 9 C C12 NUB . . . E 3 26.092 46.067 1.666 1 17.23 ? C12 NUB 204 AAA 1 HETATM 10 C C16 NUB . . . E 3 25.144 47.926 0.396 1 15.33 ? C16 NUB 204 AAA 1 HETATM 11 O O17 NUB . . . E 3 24.052 47.343 0.46 1 17.98 ? O17 NUB 204 AAA 1 HETATM 12 C C18 NUB . . . E 3 28.934 49.788 0.211 1 17.57 ? C18 NUB 204 AAA 1 HETATM 13 N N19 NUB . . . E 3 29.678 49.982 1.275 1 19.95 ? N19 NUB 204 AAA 1 HETATM 14 C C23 NUB . . . E 3 32.767 52.025 0.806 1 18.98 ? C23 NUB 204 AAA 1 HETATM 15 C C25 NUB . . . E 3 32.587 52.307 -0.534 1 17.45 ? C25 NUB 204 AAA 1 HETATM 16 C C27 NUB . . . E 3 31.504 51.807 -1.228 1 19.38 ? C27 NUB 204 AAA 1 HETATM 17 C C29 NUB . . . E 3 30.582 51.055 -0.521 1 18.48 ? C29 NUB 204 AAA 1 HETATM 18 N N30 NUB . . . E 3 29.392 50.452 -0.904 1 17.81 ? N30 NUB 204 AAA 1 HETATM 19 C C31 NUB . . . E 3 28.906 50.471 -2.29 1 19.54 ? C31 NUB 204 AAA 1 HETATM 20 C C34 NUB . . . E 3 29.277 49.219 -3.051 1 20.16 ? C34 NUB 204 AAA 1 HETATM 21 C C36 NUB . . . E 3 30.715 48.791 -2.831 1 22.83 ? C36 NUB 204 AAA 1 HETATM 22 C C39 NUB . . . E 3 31.043 47.554 -3.636 1 22.39 ? C39 NUB 204 AAA 1 HETATM 23 O O42 NUB . . . E 3 30.736 47.732 -5.013 1 22.2 ? O42 NUB 204 AAA 1 HETATM 24 C C43 NUB . . . E 3 29.378 48.099 -5.202 1 21.34 ? C43 NUB 204 AAA 1 HETATM 25 C C46 NUB . . . E 3 29.053 49.399 -4.515 1 20.35 ? C46 NUB 204 AAA 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #