data_4J3E # _model_server_result.job_id hXQVAviPupFlHa4LB0MAlw _model_server_result.datetime_utc '2025-01-10 23:09:38' _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 4j3e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4J3E # _exptl.entry_id 4J3E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 581.49 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-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 4J3E _cell.length_a 42.887 _cell.length_b 67.657 _cell.length_c 67.173 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4J3E _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 _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 # _chem_comp.formula 'C30 H30 Cl2 N4 O4' _chem_comp.formula_weight 581.49 _chem_comp.id NUT _chem_comp.mon_nstd_flag . _chem_comp.name 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Nutlin 3a' # 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 O2 C28 NUT doub 237 n n C28 C29 NUT sing 238 n n C28 N3 NUT sing 239 n n C29 N2 NUT sing 240 n n O3 C25 NUT doub 241 n n N3 C27 NUT sing 242 n n C25 N2 NUT sing 243 n n C25 N1 NUT sing 244 n n N2 C26 NUT sing 245 n n C27 C26 NUT sing 246 n n C11 C18 NUT sing 247 n n C11 N NUT sing 248 n n C11 C12 NUT sing 249 n n C3 C2 NUT doub 250 n y C3 C9 NUT sing 251 n y N1 C18 NUT sing 252 n n N1 C10 NUT sing 253 n n C2 C1 NUT sing 254 n y C17 C12 NUT doub 255 n y C17 C16 NUT sing 256 n y C18 C19 NUT sing 257 n n C10 N NUT doub 258 n n C10 C9 NUT sing 259 n n C9 C5 NUT doub 260 n y C O NUT sing 261 n n C12 C13 NUT sing 262 n y C1 O NUT sing 263 n n C1 C4 NUT doub 264 n y C16 C15 NUT doub 265 n y C5 C4 NUT sing 266 n y C5 O1 NUT sing 267 n n C8 C6 NUT sing 268 n n O1 C6 NUT sing 269 n n C19 C24 NUT doub 270 n y C19 C20 NUT sing 271 n y C24 C23 NUT sing 272 n y C13 C14 NUT doub 273 n y C15 C14 NUT sing 274 n y C15 CL NUT sing 275 n n C6 C7 NUT sing 276 n n C20 C21 NUT doub 277 n y C23 C22 NUT doub 278 n y C21 C22 NUT sing 279 n y C22 CL1 NUT sing 280 n n C29 H1 NUT sing 281 n n C29 H2 NUT sing 282 n n N3 H3 NUT sing 283 n n C27 H4 NUT sing 284 n n C27 H5 NUT sing 285 n n C26 H6 NUT sing 286 n n C26 H7 NUT sing 287 n n C3 H9 NUT sing 288 n n C2 H10 NUT sing 289 n n C6 H11 NUT sing 290 n n C8 H12 NUT sing 291 n n C8 H13 NUT sing 292 n n C8 H14 NUT sing 293 n n C7 H15 NUT sing 294 n n C7 H16 NUT sing 295 n n C7 H17 NUT sing 296 n n C4 H18 NUT sing 297 n n C H19 NUT sing 298 n n C H20 NUT sing 299 n n C H21 NUT sing 300 n n C18 H22 NUT sing 301 n n C24 H23 NUT sing 302 n n C23 H24 NUT sing 303 n n C21 H25 NUT sing 304 n n C20 H26 NUT sing 305 n n C11 H27 NUT sing 306 n n C17 H30 NUT sing 307 n n C16 H31 NUT sing 308 n n C14 H32 NUT sing 309 n n C13 H33 NUT sing 310 n n # _atom_sites.entry_id 4J3E _atom_sites.fract_transf_matrix[1][1] 0.023317 _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] 0.01478 _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] 0.014887 _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 NUT A 1 201 1 NUT LIG . C 3 SO4 A 1 202 201 SO4 SO4 . D 4 HOH A 1 301 1 HOH HOH . D 4 HOH A 2 302 2 HOH HOH . D 4 HOH A 3 303 3 HOH HOH . D 4 HOH A 4 304 4 HOH HOH . D 4 HOH A 5 305 5 HOH HOH . D 4 HOH A 6 306 6 HOH HOH . D 4 HOH A 7 307 7 HOH HOH . D 4 HOH A 8 308 8 HOH HOH . D 4 HOH A 9 309 9 HOH HOH . D 4 HOH A 10 310 10 HOH HOH . D 4 HOH A 11 311 11 HOH HOH . D 4 HOH A 12 312 12 HOH HOH . D 4 HOH A 13 313 13 HOH HOH . D 4 HOH A 14 314 14 HOH HOH . D 4 HOH A 15 315 15 HOH HOH . D 4 HOH A 16 316 16 HOH HOH . D 4 HOH A 17 317 17 HOH HOH . D 4 HOH A 18 318 18 HOH HOH . D 4 HOH A 19 319 19 HOH HOH . D 4 HOH A 20 320 20 HOH HOH . D 4 HOH A 21 321 21 HOH HOH . D 4 HOH A 22 322 22 HOH HOH . D 4 HOH A 23 323 23 HOH HOH . D 4 HOH A 24 324 24 HOH HOH . D 4 HOH A 25 325 25 HOH HOH . D 4 HOH A 26 326 26 HOH HOH . D 4 HOH A 27 327 27 HOH HOH . D 4 HOH A 28 328 28 HOH HOH . D 4 HOH A 29 329 29 HOH HOH . D 4 HOH A 30 330 30 HOH HOH . D 4 HOH A 31 331 31 HOH HOH . D 4 HOH A 32 332 32 HOH HOH . D 4 HOH A 33 333 33 HOH HOH . D 4 HOH A 34 334 34 HOH HOH . D 4 HOH A 35 335 35 HOH HOH . D 4 HOH A 36 336 36 HOH HOH . D 4 HOH A 37 337 37 HOH HOH . D 4 HOH A 38 338 38 HOH HOH . D 4 HOH A 39 339 39 HOH HOH . D 4 HOH A 40 340 40 HOH HOH . D 4 HOH A 41 341 41 HOH HOH . D 4 HOH A 42 342 42 HOH HOH . D 4 HOH A 43 343 43 HOH HOH . D 4 HOH A 44 344 44 HOH HOH . D 4 HOH A 45 345 45 HOH HOH . D 4 HOH A 46 346 46 HOH HOH . D 4 HOH A 47 347 47 HOH HOH . D 4 HOH A 48 348 48 HOH HOH . D 4 HOH A 49 349 49 HOH HOH . D 4 HOH A 50 350 50 HOH HOH . D 4 HOH A 51 351 51 HOH HOH . D 4 HOH A 52 352 52 HOH HOH . D 4 HOH A 53 353 53 HOH HOH . D 4 HOH A 54 354 54 HOH HOH . D 4 HOH A 55 355 55 HOH HOH . D 4 HOH A 56 356 56 HOH HOH . D 4 HOH A 57 357 57 HOH HOH . D 4 HOH A 58 358 58 HOH HOH . D 4 HOH A 59 359 59 HOH HOH . D 4 HOH A 60 360 60 HOH HOH . D 4 HOH A 61 361 61 HOH HOH . D 4 HOH A 62 362 62 HOH HOH . D 4 HOH A 63 363 63 HOH HOH . D 4 HOH A 64 364 64 HOH HOH . D 4 HOH A 65 365 65 HOH HOH . D 4 HOH A 66 366 66 HOH HOH . D 4 HOH A 67 367 67 HOH HOH . D 4 HOH A 68 368 68 HOH HOH . D 4 HOH A 69 369 69 HOH HOH . D 4 HOH A 70 370 70 HOH HOH . D 4 HOH A 71 371 71 HOH HOH . D 4 HOH A 72 372 72 HOH HOH . D 4 HOH A 73 373 73 HOH HOH . D 4 HOH A 74 374 74 HOH HOH . D 4 HOH A 75 375 75 HOH HOH . D 4 HOH A 76 376 76 HOH HOH . D 4 HOH A 77 377 77 HOH HOH . D 4 HOH A 78 378 78 HOH HOH . D 4 HOH A 79 379 79 HOH HOH . D 4 HOH A 80 380 80 HOH HOH . D 4 HOH A 81 381 81 HOH HOH . D 4 HOH A 82 382 82 HOH HOH . D 4 HOH A 83 383 83 HOH HOH . D 4 HOH A 84 384 84 HOH HOH . D 4 HOH A 85 385 85 HOH HOH . D 4 HOH A 86 386 86 HOH HOH . D 4 HOH A 87 387 87 HOH HOH . D 4 HOH A 88 388 88 HOH HOH . D 4 HOH A 89 389 89 HOH HOH . D 4 HOH A 90 390 90 HOH HOH . D 4 HOH A 91 391 91 HOH HOH . D 4 HOH A 92 392 92 HOH HOH . D 4 HOH A 93 393 93 HOH HOH . D 4 HOH A 94 394 94 HOH HOH . D 4 HOH A 95 395 95 HOH HOH . D 4 HOH A 96 396 96 HOH HOH . D 4 HOH A 97 397 97 HOH HOH . D 4 HOH A 98 398 98 HOH HOH . D 4 HOH A 99 399 99 HOH HOH . D 4 HOH A 100 400 100 HOH HOH . D 4 HOH A 101 401 101 HOH HOH . D 4 HOH A 102 402 102 HOH HOH . D 4 HOH A 103 403 103 HOH HOH . D 4 HOH A 104 404 104 HOH HOH . D 4 HOH A 105 405 105 HOH HOH . D 4 HOH A 106 406 106 HOH HOH . D 4 HOH A 107 407 107 HOH HOH . D 4 HOH A 108 408 108 HOH HOH . D 4 HOH A 109 409 109 HOH HOH . D 4 HOH A 110 410 110 HOH HOH . D 4 HOH A 111 411 111 HOH HOH . D 4 HOH A 112 412 112 HOH HOH . D 4 HOH A 113 413 113 HOH HOH . D 4 HOH A 114 414 114 HOH HOH . D 4 HOH A 115 415 115 HOH HOH . D 4 HOH A 116 416 116 HOH HOH . D 4 HOH A 117 417 117 HOH HOH . D 4 HOH A 118 418 118 HOH HOH . D 4 HOH A 119 419 119 HOH HOH . D 4 HOH A 120 420 120 HOH HOH . D 4 HOH A 121 421 121 HOH HOH . D 4 HOH A 122 422 122 HOH HOH . D 4 HOH A 123 423 123 HOH HOH . D 4 HOH A 124 424 124 HOH HOH . D 4 HOH A 125 425 125 HOH HOH . D 4 HOH A 126 426 126 HOH HOH . D 4 HOH A 127 427 127 HOH HOH . D 4 HOH A 128 428 128 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 O O3 NUT . . . B 2 7.974 27.233 34.468 1 11.12 ? O3 NUT 201 A 1 HETATM 2 C C25 NUT . . . B 2 8.003 26.745 35.605 1 11.91 ? C25 NUT 201 A 1 HETATM 3 N N2 NUT . . . B 2 7.784 27.496 36.724 1 14.48 ? N2 NUT 201 A 1 HETATM 4 C C29 NUT . . . B 2 7.094 28.784 36.583 1 17.86 ? C29 NUT 201 A 1 HETATM 5 C C28 NUT . . . B 2 8.074 29.891 36.804 1 21.99 ? C28 NUT 201 A 1 HETATM 6 O O2 NUT . . . B 2 8.196 30.861 36.051 1 27.76 ? O2 NUT 201 A 1 HETATM 7 N N3 NUT . . . B 2 8.841 29.767 37.889 1 20.59 ? N3 NUT 201 A 1 HETATM 8 C C27 NUT . . . B 2 8.691 28.598 38.78 1 19.69 ? C27 NUT 201 A 1 HETATM 9 C C26 NUT . . . B 2 8.594 27.297 37.956 1 15.65 ? C26 NUT 201 A 1 HETATM 10 N N1 NUT . . . B 2 8.372 25.39 35.779 1 12.77 ? N1 NUT 201 A 1 HETATM 11 C C10 NUT . . . B 2 8.197 24.578 36.914 1 12.93 ? C10 NUT 201 A 1 HETATM 12 C C9 NUT . . . B 2 7.107 24.798 37.881 1 13.52 ? C9 NUT 201 A 1 HETATM 13 C C3 NUT . . . B 2 7.319 24.528 39.25 1 13.16 ? C3 NUT 201 A 1 HETATM 14 C C2 NUT . . . B 2 6.309 24.744 40.185 1 14.3 ? C2 NUT 201 A 1 HETATM 15 C C5 NUT . . . B 2 5.824 25.265 37.478 1 13.27 ? C5 NUT 201 A 1 HETATM 16 O O1 NUT . . . B 2 5.58 25.434 36.17 1 9.77 ? O1 NUT 201 A 1 HETATM 17 C C6 NUT . . . B 2 4.313 26.009 35.824 1 12.76 ? C6 NUT 201 A 1 HETATM 18 C C8 NUT . . . B 2 4.428 26.762 34.495 1 13.48 ? C8 NUT 201 A 1 HETATM 19 C C7 NUT . . . B 2 3.226 24.932 35.716 1 12.95 ? C7 NUT 201 A 1 HETATM 20 C C4 NUT . . . B 2 4.805 25.513 38.403 1 12.79 ? C4 NUT 201 A 1 HETATM 21 C C1 NUT . . . B 2 5.063 25.234 39.746 1 14.85 ? C1 NUT 201 A 1 HETATM 22 O O NUT . . . B 2 4.087 25.42 40.648 1 16.65 ? O NUT 201 A 1 HETATM 23 C C NUT . . . B 2 4.411 25.041 41.983 1 14.38 ? C NUT 201 A 1 HETATM 24 C C18 NUT . . . B 2 9.362 24.799 34.883 1 10.62 ? C18 NUT 201 A 1 HETATM 25 C C19 NUT . . . B 2 8.653 24.123 33.724 1 10.58 ? C19 NUT 201 A 1 HETATM 26 C C24 NUT . . . B 2 7.278 23.842 33.821 1 10.52 ? C24 NUT 201 A 1 HETATM 27 C C23 NUT . . . B 2 6.618 23.177 32.798 1 10.69 ? C23 NUT 201 A 1 HETATM 28 C C22 NUT . . . B 2 7.351 22.779 31.647 1 10.42 ? C22 NUT 201 A 1 HETATM 29 CL CL1 NUT . . . B 2 6.586 21.91 30.443 1 9.38 ? CL1 NUT 201 A 1 HETATM 30 C C21 NUT . . . B 2 8.726 23.106 31.516 1 10.27 ? C21 NUT 201 A 1 HETATM 31 C C20 NUT . . . B 2 9.36 23.773 32.557 1 10.06 ? C20 NUT 201 A 1 HETATM 32 C C11 NUT . . . B 2 10.041 23.785 35.842 1 11.3 ? C11 NUT 201 A 1 HETATM 33 N N NUT . . . B 2 9.104 23.634 36.96 1 13.13 ? N NUT 201 A 1 HETATM 34 C C12 NUT . . . B 2 10.421 22.469 35.213 1 10.63 ? C12 NUT 201 A 1 HETATM 35 C C17 NUT . . . B 2 11.768 22.242 34.874 1 10.41 ? C17 NUT 201 A 1 HETATM 36 C C16 NUT . . . B 2 12.154 21.071 34.26 1 9.84 ? C16 NUT 201 A 1 HETATM 37 C C15 NUT . . . B 2 11.172 20.095 33.966 1 8.92 ? C15 NUT 201 A 1 HETATM 38 CL CL NUT . . . B 2 11.611 18.721 33.13 1 11.9 ? CL NUT 201 A 1 HETATM 39 C C14 NUT . . . B 2 9.819 20.283 34.356 1 10.23 ? C14 NUT 201 A 1 HETATM 40 C C13 NUT . . . B 2 9.46 21.472 34.975 1 10.62 ? C13 NUT 201 A 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 119 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 40 #