data_9F5D # _model_server_result.job_id lPg0fDzqDTPAgPPfiZao9A _model_server_result.datetime_utc '2024-11-14 19:36:01' _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 9f5d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 9F5D # _exptl.entry_id 9F5D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 217.224 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-[(phenylmethyl)amino]-1~{H}-pyrimidine-2,4-dione _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 93.34 _cell.angle_gamma 90 _cell.entry_id 9F5D _cell.length_a 38.022 _cell.length_b 43.796 _cell.length_c 55.799 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9F5D _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 133 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 130 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C9 _struct_conn.ptnr2_label_comp_id A1H9X _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id A1H9X _struct_conn.ptnr2_auth_seq_id 201 _struct_conn.ptnr2_symmetry 2_556 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id B _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 1.507 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C11 H11 N3 O2' _chem_comp.formula_weight 217.224 _chem_comp.id A1H9X _chem_comp.mon_nstd_flag . _chem_comp.name 5-[(phenylmethyl)amino]-1~{H}-pyrimidine-2,4-dione _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 5-(Benzylamino)pyrimidine-2,4(1h,3h)-dione # 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 O1 C1 A1H9X doub 1 n n C1 N1 A1H9X sing 2 n n N1 C2 A1H9X sing 3 n n C2 C3 A1H9X doub 4 n n C3 N2 A1H9X sing 5 n n N2 C4 A1H9X sing 6 n n C4 C5 A1H9X sing 7 n n C5 C6 A1H9X doub 8 n y C6 C7 A1H9X sing 9 n y C7 C8 A1H9X doub 10 n y C8 C9 A1H9X sing 11 n y C9 C10 A1H9X doub 12 n y C3 C11 A1H9X sing 13 n n C11 O2 A1H9X doub 14 n n C11 N3 A1H9X sing 15 n n C1 N3 A1H9X sing 16 n n C5 C10 A1H9X sing 17 n y N1 H1 A1H9X sing 18 n n N3 H11 A1H9X sing 19 n n C4 H4 A1H9X sing 20 n n C4 H5 A1H9X sing 21 n n C6 H6 A1H9X sing 22 n n C7 H7 A1H9X sing 23 n n C8 H8 A1H9X sing 24 n n C10 H10 A1H9X sing 25 n n C2 H2 A1H9X sing 26 n n C9 H9 A1H9X sing 27 n n N2 H3 A1H9X sing 28 n n # _atom_sites.entry_id 9F5D _atom_sites.fract_transf_matrix[1][1] 0.026301 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001535 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022833 _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] 0.017952 _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 A1H9X A 1 201 1 A1H9X LIG . C 3 HOH A 1 301 65 HOH HOH . C 3 HOH A 2 302 119 HOH HOH . C 3 HOH A 3 303 61 HOH HOH . C 3 HOH A 4 304 114 HOH HOH . C 3 HOH A 5 305 54 HOH HOH . C 3 HOH A 6 306 68 HOH HOH . C 3 HOH A 7 307 125 HOH HOH . C 3 HOH A 8 308 161 HOH HOH . C 3 HOH A 9 309 160 HOH HOH . C 3 HOH A 10 310 63 HOH HOH . C 3 HOH A 11 311 140 HOH HOH . C 3 HOH A 12 312 174 HOH HOH . C 3 HOH A 13 313 16 HOH HOH . C 3 HOH A 14 314 183 HOH HOH . C 3 HOH A 15 315 58 HOH HOH . C 3 HOH A 16 316 37 HOH HOH . C 3 HOH A 17 317 10 HOH HOH . C 3 HOH A 18 318 15 HOH HOH . C 3 HOH A 19 319 85 HOH HOH . C 3 HOH A 20 320 22 HOH HOH . C 3 HOH A 21 321 113 HOH HOH . C 3 HOH A 22 322 2 HOH HOH . C 3 HOH A 23 323 187 HOH HOH . C 3 HOH A 24 324 75 HOH HOH . C 3 HOH A 25 325 8 HOH HOH . C 3 HOH A 26 326 48 HOH HOH . C 3 HOH A 27 327 29 HOH HOH . C 3 HOH A 28 328 11 HOH HOH . C 3 HOH A 29 329 3 HOH HOH . C 3 HOH A 30 330 21 HOH HOH . C 3 HOH A 31 331 145 HOH HOH . C 3 HOH A 32 332 51 HOH HOH . C 3 HOH A 33 333 202 HOH HOH . C 3 HOH A 34 334 28 HOH HOH . C 3 HOH A 35 335 7 HOH HOH . C 3 HOH A 36 336 126 HOH HOH . C 3 HOH A 37 337 184 HOH HOH . C 3 HOH A 38 338 165 HOH HOH . C 3 HOH A 39 339 23 HOH HOH . C 3 HOH A 40 340 6 HOH HOH . C 3 HOH A 41 341 70 HOH HOH . C 3 HOH A 42 342 44 HOH HOH . C 3 HOH A 43 343 79 HOH HOH . C 3 HOH A 44 344 4 HOH HOH . C 3 HOH A 45 345 122 HOH HOH . C 3 HOH A 46 346 1 HOH HOH . C 3 HOH A 47 347 93 HOH HOH . C 3 HOH A 48 348 12 HOH HOH . C 3 HOH A 49 349 52 HOH HOH . C 3 HOH A 50 350 203 HOH HOH . C 3 HOH A 51 351 39 HOH HOH . C 3 HOH A 52 352 19 HOH HOH . C 3 HOH A 53 353 143 HOH HOH . C 3 HOH A 54 354 26 HOH HOH . C 3 HOH A 55 355 81 HOH HOH . C 3 HOH A 56 356 53 HOH HOH . C 3 HOH A 57 357 172 HOH HOH . C 3 HOH A 58 358 102 HOH HOH . C 3 HOH A 59 359 13 HOH HOH . C 3 HOH A 60 360 33 HOH HOH . C 3 HOH A 61 361 73 HOH HOH . C 3 HOH A 62 362 78 HOH HOH . C 3 HOH A 63 363 30 HOH HOH . C 3 HOH A 64 364 72 HOH HOH . C 3 HOH A 65 365 55 HOH HOH . C 3 HOH A 66 366 14 HOH HOH . C 3 HOH A 67 367 9 HOH HOH . C 3 HOH A 68 368 27 HOH HOH . C 3 HOH A 69 369 139 HOH HOH . C 3 HOH A 70 370 17 HOH HOH . C 3 HOH A 71 371 95 HOH HOH . C 3 HOH A 72 372 104 HOH HOH . C 3 HOH A 73 373 84 HOH HOH . C 3 HOH A 74 374 46 HOH HOH . C 3 HOH A 75 375 36 HOH HOH . C 3 HOH A 76 376 82 HOH HOH . C 3 HOH A 77 377 59 HOH HOH . C 3 HOH A 78 378 108 HOH HOH . C 3 HOH A 79 379 40 HOH HOH . C 3 HOH A 80 380 24 HOH HOH . C 3 HOH A 81 381 67 HOH HOH . C 3 HOH A 82 382 115 HOH HOH . C 3 HOH A 83 383 88 HOH HOH . C 3 HOH A 84 384 110 HOH HOH . C 3 HOH A 85 385 56 HOH HOH . C 3 HOH A 86 386 35 HOH HOH . C 3 HOH A 87 387 45 HOH HOH . C 3 HOH A 88 388 207 HOH HOH . C 3 HOH A 89 389 43 HOH HOH . C 3 HOH A 90 390 66 HOH HOH . C 3 HOH A 91 391 133 HOH HOH . C 3 HOH A 92 392 71 HOH HOH . C 3 HOH A 93 393 123 HOH HOH . C 3 HOH A 94 394 186 HOH HOH . C 3 HOH A 95 395 171 HOH HOH . C 3 HOH A 96 396 197 HOH HOH . C 3 HOH A 97 397 62 HOH HOH . C 3 HOH A 98 398 144 HOH HOH . C 3 HOH A 99 399 5 HOH HOH . C 3 HOH A 100 400 150 HOH HOH . C 3 HOH A 101 401 94 HOH HOH . C 3 HOH A 102 402 192 HOH HOH . C 3 HOH A 103 403 69 HOH HOH . C 3 HOH A 104 404 64 HOH HOH . C 3 HOH A 105 405 47 HOH HOH . C 3 HOH A 106 406 101 HOH HOH . C 3 HOH A 107 407 91 HOH HOH . C 3 HOH A 108 408 31 HOH HOH . C 3 HOH A 109 409 137 HOH HOH . C 3 HOH A 110 410 34 HOH HOH . C 3 HOH A 111 411 149 HOH HOH . C 3 HOH A 112 412 49 HOH HOH . C 3 HOH A 113 413 134 HOH HOH . C 3 HOH A 114 414 121 HOH HOH . C 3 HOH A 115 415 178 HOH HOH . C 3 HOH A 116 416 173 HOH HOH . C 3 HOH A 117 417 32 HOH HOH . C 3 HOH A 118 418 162 HOH HOH . C 3 HOH A 119 419 42 HOH HOH . C 3 HOH A 120 420 109 HOH HOH . C 3 HOH A 121 421 38 HOH HOH . C 3 HOH A 122 422 103 HOH HOH . C 3 HOH A 123 423 199 HOH HOH . C 3 HOH A 124 424 96 HOH HOH . C 3 HOH A 125 425 117 HOH HOH . C 3 HOH A 126 426 148 HOH HOH . C 3 HOH A 127 427 142 HOH HOH . C 3 HOH A 128 428 130 HOH HOH . C 3 HOH A 129 429 57 HOH HOH . C 3 HOH A 130 430 198 HOH HOH . C 3 HOH A 131 431 90 HOH HOH . C 3 HOH A 132 432 120 HOH HOH . C 3 HOH A 133 433 131 HOH HOH . C 3 HOH A 134 434 194 HOH HOH . C 3 HOH A 135 435 180 HOH HOH . C 3 HOH A 136 436 99 HOH HOH . C 3 HOH A 137 437 92 HOH HOH . C 3 HOH A 138 438 181 HOH HOH . C 3 HOH A 139 439 158 HOH HOH . C 3 HOH A 140 440 175 HOH HOH . C 3 HOH A 141 441 86 HOH HOH . C 3 HOH A 142 442 80 HOH HOH . C 3 HOH A 143 443 98 HOH HOH . C 3 HOH A 144 444 182 HOH HOH . C 3 HOH A 145 445 141 HOH HOH . C 3 HOH A 146 446 111 HOH HOH . C 3 HOH A 147 447 136 HOH HOH . C 3 HOH A 148 448 87 HOH HOH . C 3 HOH A 149 449 18 HOH HOH . C 3 HOH A 150 450 153 HOH HOH . C 3 HOH A 151 451 41 HOH HOH . C 3 HOH A 152 452 159 HOH HOH . C 3 HOH A 153 453 118 HOH HOH . C 3 HOH A 154 454 20 HOH HOH . C 3 HOH A 155 455 179 HOH HOH . C 3 HOH A 156 456 60 HOH HOH . C 3 HOH A 157 457 170 HOH HOH . C 3 HOH A 158 458 201 HOH HOH . C 3 HOH A 159 459 100 HOH HOH . C 3 HOH A 160 460 128 HOH HOH . C 3 HOH A 161 461 129 HOH HOH . C 3 HOH A 162 462 89 HOH HOH . C 3 HOH A 163 463 127 HOH HOH . C 3 HOH A 164 464 50 HOH HOH . C 3 HOH A 165 465 176 HOH HOH . C 3 HOH A 166 466 205 HOH HOH . C 3 HOH A 167 467 106 HOH HOH . C 3 HOH A 168 468 83 HOH HOH . C 3 HOH A 169 469 77 HOH HOH . C 3 HOH A 170 470 152 HOH HOH . C 3 HOH A 171 471 124 HOH HOH . C 3 HOH A 172 472 105 HOH HOH . C 3 HOH A 173 473 190 HOH HOH . C 3 HOH A 174 474 76 HOH HOH . C 3 HOH A 175 475 146 HOH HOH . C 3 HOH A 176 476 193 HOH HOH . C 3 HOH A 177 477 74 HOH HOH . C 3 HOH A 178 478 189 HOH HOH . C 3 HOH A 179 479 135 HOH HOH . C 3 HOH A 180 480 116 HOH HOH . C 3 HOH A 181 481 164 HOH HOH . C 3 HOH A 182 482 107 HOH HOH . C 3 HOH A 183 483 204 HOH HOH . C 3 HOH A 184 484 97 HOH HOH . C 3 HOH A 185 485 154 HOH HOH . C 3 HOH A 186 486 147 HOH HOH . C 3 HOH A 187 487 188 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 N N1 A1H9X . A . B 2 -0.91 -10.436 31.05 0.66 35.14 ? N1 A1H9X 201 A 1 HETATM 2 N N1 A1H9X . B . B 2 -3.989 -8.872 28.08 0.34 35.77 ? N1 A1H9X 201 A 1 HETATM 3 N N3 A1H9X . A . B 2 -0.601 -8.147 31.044 0.66 36.89 ? N3 A1H9X 201 A 1 HETATM 4 N N3 A1H9X . B . B 2 -4.978 -10.759 27.194 0.34 35.49 ? N3 A1H9X 201 A 1 HETATM 5 C C4 A1H9X . A . B 2 -4.29 -9.568 28.441 0.66 38.21 ? C4 A1H9X 201 A 1 HETATM 6 C C4 A1H9X . B . B 2 -1.151 -11.591 29.9 0.34 33.68 ? C4 A1H9X 201 A 1 HETATM 7 C C5 A1H9X . A . B 2 -4.481 -10.967 27.903 0.66 35.5 ? C5 A1H9X 201 A 1 HETATM 8 C C5 A1H9X . B . B 2 -0.736 -10.651 31.007 0.34 34.85 ? C5 A1H9X 201 A 1 HETATM 9 C C6 A1H9X . A . B 2 -4.858 -11.175 26.586 0.66 37.38 ? C6 A1H9X 201 A 1 HETATM 10 C C6 A1H9X . B . B 2 -0.636 -9.288 30.778 0.34 35.38 ? C6 A1H9X 201 A 1 HETATM 11 C C7 A1H9X . A . B 2 -5.039 -12.46 26.101 0.66 41.04 ? C7 A1H9X 201 A 1 HETATM 12 C C7 A1H9X . B . B 2 -0.259 -8.431 31.796 0.34 35.43 ? C7 A1H9X 201 A 1 HETATM 13 C C8 A1H9X . A . B 2 -4.846 -13.545 26.925 0.66 38.15 ? C8 A1H9X 201 A 1 HETATM 14 C C8 A1H9X . B . B 2 0.036 -8.925 33.045 0.34 38.92 ? C8 A1H9X 201 A 1 HETATM 15 C C10 A1H9X . A . B 2 -4.291 -12.069 28.723 0.66 38.92 ? C10 A1H9X 201 A 1 HETATM 16 C C10 A1H9X . B . B 2 -0.44 -11.136 32.27 0.34 37.57 ? C10 A1H9X 201 A 1 HETATM 17 C C1 A1H9X . A . B 2 -0.297 -9.353 31.615 0.66 35.73 ? C1 A1H9X 201 A 1 HETATM 18 C C1 A1H9X . B . B 2 -4.888 -9.394 27.197 0.34 32.26 ? C1 A1H9X 201 A 1 HETATM 19 C C11 A1H9X . A . B 2 -1.454 -7.936 29.981 0.66 30.42 ? C11 A1H9X 201 A 1 HETATM 20 C C11 A1H9X . B . B 2 -4.265 -11.627 27.993 0.34 37.68 ? C11 A1H9X 201 A 1 HETATM 21 C C2 A1H9X . A . B 2 -1.762 -10.34 30.025 0.66 32.93 ? C2 A1H9X 201 A 1 HETATM 22 C C2 A1H9X . B . B 2 -3.246 -9.627 28.892 0.34 32.29 ? C2 A1H9X 201 A 1 HETATM 23 C C3 A1H9X . A . B 2 -2.056 -9.129 29.448 0.66 31.15 ? C3 A1H9X 201 A 1 HETATM 24 C C3 A1H9X . B . B 2 -3.341 -10.992 28.888 0.34 34 ? C3 A1H9X 201 A 1 HETATM 25 C C9 A1H9X . A . B 2 -4.474 -13.352 28.233 0.66 39.09 ? C9 A1H9X 201 A 1 HETATM 26 C C9 A1H9X . B . B 2 -0.056 -10.274 33.284 0.34 39.58 ? C9 A1H9X 201 A 1 HETATM 27 N N2 A1H9X . A . B 2 -2.938 -9.048 28.398 0.66 34.38 ? N2 A1H9X 201 A 1 HETATM 28 N N2 A1H9X . B . B 2 -2.579 -11.75 29.739 0.34 32.5 ? N2 A1H9X 201 A 1 HETATM 29 O O1 A1H9X . A . B 2 0.474 -9.447 32.562 0.66 39.72 ? O1 A1H9X 201 A 1 HETATM 30 O O1 A1H9X . B . B 2 -5.567 -8.694 26.457 0.34 39.17 ? O1 A1H9X 201 A 1 HETATM 31 O O2 A1H9X . A . B 2 -1.632 -6.786 29.576 0.66 29.98 ? O2 A1H9X 201 A 1 HETATM 32 O O2 A1H9X . B . B 2 -4.454 -12.84 27.887 0.34 39.08 ? O2 A1H9X 201 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #