data_4YK5 # _model_server_result.job_id MHk0DOWnueM7dQv4TPMDEQ _model_server_result.datetime_utc '2024-11-22 00:32:37' _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 4yk5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4YK5 # _exptl.entry_id 4YK5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 540.067 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3-[1-(4-chlorobenzyl)-5-(2-fluoro-2'-methylbiphenyl-4-yl)-3-methyl-1H-indol-2-yl]-2,2-dimethylpropanoic acid" _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 4YK5 _cell.length_a 76.6 _cell.length_b 76.6 _cell.length_c 123.736 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YK5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 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 'C34 H31 Cl F N O2' _chem_comp.formula_weight 540.067 _chem_comp.id 4DV _chem_comp.mon_nstd_flag . _chem_comp.name "3-[1-(4-chlorobenzyl)-5-(2-fluoro-2'-methylbiphenyl-4-yl)-3-methyl-1H-indol-2-yl]-2,2-dimethylpropanoic acid" _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 C20 C19 4DV doub 1 n y C20 C21 4DV sing 2 n y C19 C18 4DV sing 3 n y C22 C21 4DV sing 4 n n C21 C16 4DV doub 5 n y C18 C17 4DV doub 6 n y C16 C17 4DV sing 7 n y C16 C13 4DV sing 8 n n C13 C14 4DV doub 9 n y C13 C12 4DV sing 10 n y F1 C12 4DV sing 11 n n C14 C15 4DV sing 12 n y C12 C11 4DV doub 13 n y C15 C10 4DV doub 14 n y C11 C10 4DV sing 15 n y C10 C6 4DV sing 16 n n C6 C5 4DV doub 17 n y C6 C7 4DV sing 18 n y C5 C4 4DV sing 19 n y C3 C2 4DV sing 20 n n C7 C8 4DV doub 21 n y C4 C2 4DV sing 22 n y C4 C9 4DV doub 23 n y C2 C1 4DV doub 24 n y C8 C9 4DV sing 25 n y C9 N1 4DV sing 26 n y C25 C24 4DV sing 27 n n C1 N1 4DV sing 28 n y C1 C23 4DV sing 29 n n N1 C28 4DV sing 30 n n C23 C24 4DV sing 31 n n C24 C26 4DV sing 32 n n C24 C27 4DV sing 33 n n C28 C29 4DV sing 34 n n C27 O1 4DV doub 35 n n C27 O2 4DV sing 36 n n C30 C29 4DV doub 37 n y C30 C31 4DV sing 38 n y C29 C34 4DV sing 39 n y C31 C32 4DV doub 40 n y C34 C33 4DV doub 41 n y C32 C33 4DV sing 42 n y C32 CL1 4DV sing 43 n n C7 H1 4DV sing 44 n n O2 H2 4DV sing 45 n n C5 H3 4DV sing 46 n n C3 H4 4DV sing 47 n n C3 H5 4DV sing 48 n n C3 H6 4DV sing 49 n n C31 H7 4DV sing 50 n n C30 H8 4DV sing 51 n n C33 H9 4DV sing 52 n n C34 H10 4DV sing 53 n n C28 H11 4DV sing 54 n n C28 H12 4DV sing 55 n n C23 H13 4DV sing 56 n n C23 H14 4DV sing 57 n n C26 H15 4DV sing 58 n n C26 H16 4DV sing 59 n n C26 H17 4DV sing 60 n n C25 H18 4DV sing 61 n n C25 H19 4DV sing 62 n n C25 H20 4DV sing 63 n n C8 H21 4DV sing 64 n n C15 H22 4DV sing 65 n n C14 H23 4DV sing 66 n n C11 H24 4DV sing 67 n n C22 H25 4DV sing 68 n n C22 H26 4DV sing 69 n n C22 H27 4DV sing 70 n n C20 H28 4DV sing 71 n n C19 H29 4DV sing 72 n n C18 H30 4DV sing 73 n n C17 H31 4DV sing 74 n n # _atom_sites.entry_id 4YK5 _atom_sites.fract_transf_matrix[1][1] 0.013055 _atom_sites.fract_transf_matrix[1][2] 0.007537 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015074 _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] 0.008082 _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 4DV A 1 201 1 4DV SX1 . C 3 PG0 A 1 202 1 PG0 PG4 . D 4 GSH A 1 203 2 GSH GTT . E 5 JZR A 1 204 3 JZR BOG . F 6 BOG A 1 205 4 BOG BOG . G 7 PG4 A 1 206 5 PG4 PG4 . H 8 HOH A 1 301 81 HOH HOH . H 8 HOH A 2 302 63 HOH HOH . H 8 HOH A 3 303 37 HOH HOH . H 8 HOH A 4 304 33 HOH HOH . H 8 HOH A 5 305 12 HOH HOH . H 8 HOH A 6 306 18 HOH HOH . H 8 HOH A 7 307 23 HOH HOH . H 8 HOH A 8 308 31 HOH HOH . H 8 HOH A 9 309 10 HOH HOH . H 8 HOH A 10 310 87 HOH HOH . H 8 HOH A 11 311 144 HOH HOH . H 8 HOH A 12 312 96 HOH HOH . H 8 HOH A 13 313 32 HOH HOH . H 8 HOH A 14 314 16 HOH HOH . H 8 HOH A 15 315 34 HOH HOH . H 8 HOH A 16 316 58 HOH HOH . H 8 HOH A 17 317 64 HOH HOH . H 8 HOH A 18 318 22 HOH HOH . H 8 HOH A 19 319 47 HOH HOH . H 8 HOH A 20 320 20 HOH HOH . H 8 HOH A 21 321 7 HOH HOH . H 8 HOH A 22 322 51 HOH HOH . H 8 HOH A 23 323 6 HOH HOH . H 8 HOH A 24 324 9 HOH HOH . H 8 HOH A 25 325 19 HOH HOH . H 8 HOH A 26 326 55 HOH HOH . H 8 HOH A 27 327 74 HOH HOH . H 8 HOH A 28 328 44 HOH HOH . H 8 HOH A 29 329 43 HOH HOH . H 8 HOH A 30 330 27 HOH HOH . H 8 HOH A 31 331 26 HOH HOH . H 8 HOH A 32 332 108 HOH HOH . H 8 HOH A 33 333 50 HOH HOH . H 8 HOH A 34 334 59 HOH HOH . H 8 HOH A 35 335 105 HOH HOH . H 8 HOH A 36 336 41 HOH HOH . H 8 HOH A 37 337 110 HOH HOH . H 8 HOH A 38 338 57 HOH HOH . H 8 HOH A 39 339 121 HOH HOH . H 8 HOH A 40 340 17 HOH HOH . H 8 HOH A 41 341 29 HOH HOH . H 8 HOH A 42 342 91 HOH HOH . H 8 HOH A 43 343 24 HOH HOH . H 8 HOH A 44 344 15 HOH HOH . H 8 HOH A 45 345 122 HOH HOH . H 8 HOH A 46 346 13 HOH HOH . H 8 HOH A 47 347 14 HOH HOH . H 8 HOH A 48 348 77 HOH HOH . H 8 HOH A 49 349 38 HOH HOH . H 8 HOH A 50 350 124 HOH HOH . H 8 HOH A 51 351 88 HOH HOH . H 8 HOH A 52 352 48 HOH HOH . H 8 HOH A 53 353 90 HOH HOH . H 8 HOH A 54 354 130 HOH HOH . H 8 HOH A 55 355 113 HOH HOH . H 8 HOH A 56 356 123 HOH HOH . H 8 HOH A 57 357 84 HOH HOH . H 8 HOH A 58 358 139 HOH HOH . H 8 HOH A 59 359 116 HOH HOH . H 8 HOH A 60 360 36 HOH HOH . H 8 HOH A 61 361 71 HOH HOH . H 8 HOH A 62 362 107 HOH HOH . H 8 HOH A 63 363 35 HOH HOH . H 8 HOH A 64 364 70 HOH HOH . H 8 HOH A 65 365 3 HOH HOH . H 8 HOH A 66 366 80 HOH HOH . H 8 HOH A 67 367 1 HOH HOH . H 8 HOH A 68 368 2 HOH HOH . H 8 HOH A 69 369 4 HOH HOH . H 8 HOH A 70 370 5 HOH HOH . H 8 HOH A 71 371 8 HOH HOH . H 8 HOH A 72 372 11 HOH HOH . H 8 HOH A 73 373 21 HOH HOH . H 8 HOH A 74 374 25 HOH HOH . H 8 HOH A 75 375 28 HOH HOH . H 8 HOH A 76 376 30 HOH HOH . H 8 HOH A 77 377 39 HOH HOH . H 8 HOH A 78 378 40 HOH HOH . H 8 HOH A 79 379 42 HOH HOH . H 8 HOH A 80 380 45 HOH HOH . H 8 HOH A 81 381 46 HOH HOH . H 8 HOH A 82 382 49 HOH HOH . H 8 HOH A 83 383 52 HOH HOH . H 8 HOH A 84 384 53 HOH HOH . H 8 HOH A 85 385 54 HOH HOH . H 8 HOH A 86 386 56 HOH HOH . H 8 HOH A 87 387 60 HOH HOH . H 8 HOH A 88 388 61 HOH HOH . H 8 HOH A 89 389 62 HOH HOH . H 8 HOH A 90 390 65 HOH HOH . H 8 HOH A 91 391 66 HOH HOH . H 8 HOH A 92 392 67 HOH HOH . H 8 HOH A 93 393 68 HOH HOH . H 8 HOH A 94 394 69 HOH HOH . H 8 HOH A 95 395 72 HOH HOH . H 8 HOH A 96 396 73 HOH HOH . H 8 HOH A 97 397 75 HOH HOH . H 8 HOH A 98 398 76 HOH HOH . H 8 HOH A 99 399 78 HOH HOH . H 8 HOH A 100 400 79 HOH HOH . H 8 HOH A 101 401 82 HOH HOH . H 8 HOH A 102 402 83 HOH HOH . H 8 HOH A 103 403 85 HOH HOH . H 8 HOH A 104 404 86 HOH HOH . H 8 HOH A 105 405 89 HOH HOH . H 8 HOH A 106 406 92 HOH HOH . H 8 HOH A 107 407 93 HOH HOH . H 8 HOH A 108 408 94 HOH HOH . H 8 HOH A 109 409 95 HOH HOH . H 8 HOH A 110 410 97 HOH HOH . H 8 HOH A 111 411 98 HOH HOH . H 8 HOH A 112 412 99 HOH HOH . H 8 HOH A 113 413 100 HOH HOH . H 8 HOH A 114 414 101 HOH HOH . H 8 HOH A 115 415 102 HOH HOH . H 8 HOH A 116 416 103 HOH HOH . H 8 HOH A 117 417 104 HOH HOH . H 8 HOH A 118 418 106 HOH HOH . H 8 HOH A 119 419 109 HOH HOH . H 8 HOH A 120 420 111 HOH HOH . H 8 HOH A 121 421 112 HOH HOH . H 8 HOH A 122 422 114 HOH HOH . H 8 HOH A 123 423 115 HOH HOH . H 8 HOH A 124 424 117 HOH HOH . H 8 HOH A 125 425 118 HOH HOH . H 8 HOH A 126 426 119 HOH HOH . H 8 HOH A 127 427 120 HOH HOH . H 8 HOH A 128 428 125 HOH HOH . H 8 HOH A 129 429 126 HOH HOH . H 8 HOH A 130 430 127 HOH HOH . H 8 HOH A 131 431 128 HOH HOH . H 8 HOH A 132 432 129 HOH HOH . H 8 HOH A 133 433 131 HOH HOH . H 8 HOH A 134 434 132 HOH HOH . H 8 HOH A 135 435 133 HOH HOH . H 8 HOH A 136 436 134 HOH HOH . H 8 HOH A 137 437 135 HOH HOH . H 8 HOH A 138 438 136 HOH HOH . H 8 HOH A 139 439 137 HOH HOH . H 8 HOH A 140 440 138 HOH HOH . H 8 HOH A 141 441 140 HOH HOH . H 8 HOH A 142 442 141 HOH HOH . H 8 HOH A 143 443 142 HOH HOH . H 8 HOH A 144 444 143 HOH HOH . H 8 HOH A 145 445 145 HOH HOH . H 8 HOH A 146 446 146 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 O1 4DV . . . B 2 18.402 18.725 32.539 1 30.86 ? O1 4DV 201 A 1 HETATM 2 C C7 4DV . . . B 2 10.103 17.704 28.237 1 20.64 ? C7 4DV 201 A 1 HETATM 3 O O2 4DV . . . B 2 17.048 17.211 33.457 1 20.53 ? O2 4DV 201 A 1 HETATM 4 C C6 4DV . . . B 2 10.792 17.129 27.153 1 18.82 ? C6 4DV 201 A 1 HETATM 5 C C1 4DV . . . B 2 14.177 17.116 30.372 1 19.62 ? C1 4DV 201 A 1 HETATM 6 N N1 4DV . . . B 2 12.927 17.631 30.718 1 20.41 ? N1 4DV 201 A 1 HETATM 7 C C5 4DV . . . B 2 12.139 16.753 27.35 1 17.44 ? C5 4DV 201 A 1 HETATM 8 C C4 4DV . . . B 2 12.786 16.961 28.588 1 17.69 ? C4 4DV 201 A 1 HETATM 9 C C3 4DV . . . B 2 15.183 16.064 28.214 1 17.76 ? C3 4DV 201 A 1 HETATM 10 C C2 4DV . . . B 2 14.107 16.691 29.048 1 17.15 ? C2 4DV 201 A 1 HETATM 11 CL CL1 4DV . . . B 2 10.096 12.721 34.39 1 28.52 ? CL1 4DV 201 A 1 HETATM 12 C C32 4DV . . . B 2 10.758 14.158 33.731 1 23.53 ? C32 4DV 201 A 1 HETATM 13 C C31 4DV . . . B 2 9.923 15.037 33.044 1 24.64 ? C31 4DV 201 A 1 HETATM 14 C C30 4DV . . . B 2 10.459 16.211 32.504 1 28.16 ? C30 4DV 201 A 1 HETATM 15 C C33 4DV . . . B 2 12.117 14.434 33.897 1 35.62 ? C33 4DV 201 A 1 HETATM 16 C C34 4DV . . . B 2 12.651 15.611 33.359 1 31.65 ? C34 4DV 201 A 1 HETATM 17 C C29 4DV . . . B 2 11.826 16.513 32.658 1 23.7 ? C29 4DV 201 A 1 HETATM 18 C C28 4DV . . . B 2 12.423 17.78 32.088 1 22.93 ? C28 4DV 201 A 1 HETATM 19 C C9 4DV . . . B 2 12.069 17.544 29.632 1 18.28 ? C9 4DV 201 A 1 HETATM 20 C C23 4DV . . . B 2 15.356 17.054 31.316 1 20.18 ? C23 4DV 201 A 1 HETATM 21 C C24 4DV . . . B 2 16.281 18.3 31.407 1 21.44 ? C24 4DV 201 A 1 HETATM 22 C C27 4DV . . . B 2 17.345 18.111 32.497 1 24.22 ? C27 4DV 201 A 1 HETATM 23 C C26 4DV . . . B 2 15.544 19.637 31.613 1 24.7 ? C26 4DV 201 A 1 HETATM 24 C C25 4DV . . . B 2 17.037 18.429 30.057 1 24.38 ? C25 4DV 201 A 1 HETATM 25 C C8 4DV . . . B 2 10.721 17.924 29.477 1 20.27 ? C8 4DV 201 A 1 HETATM 26 C C10 4DV . A . B 2 10.125 16.882 25.862 0.65 16.59 ? C10 4DV 201 A 1 HETATM 27 C C10 4DV . B . B 2 10.129 16.885 25.86 0.35 18.53 ? C10 4DV 201 A 1 HETATM 28 C C15 4DV . A . B 2 9.047 17.663 25.388 0.65 16.51 ? C15 4DV 201 A 1 HETATM 29 C C15 4DV . B . B 2 10.406 15.7 25.16 0.35 19.73 ? C15 4DV 201 A 1 HETATM 30 C C14 4DV . A . B 2 8.433 17.375 24.154 0.65 15.43 ? C14 4DV 201 A 1 HETATM 31 C C14 4DV . B . B 2 9.798 15.414 23.937 0.35 19.36 ? C14 4DV 201 A 1 HETATM 32 C C13 4DV . A . B 2 8.882 16.295 23.369 0.65 16.58 ? C13 4DV 201 A 1 HETATM 33 C C13 4DV . B . B 2 8.884 16.303 23.367 0.35 18.28 ? C13 4DV 201 A 1 HETATM 34 C C12 4DV . A . B 2 9.943 15.524 23.853 0.65 16.33 ? C12 4DV 201 A 1 HETATM 35 C C12 4DV . B . B 2 8.6 17.486 24.065 0.35 18.49 ? C12 4DV 201 A 1 HETATM 36 F F1 4DV . A . B 2 10.401 14.485 23.139 0.65 17.12 ? F1 4DV 201 A 1 HETATM 37 F F1 4DV . B . B 2 7.733 18.381 23.569 0.35 19.97 ? F1 4DV 201 A 1 HETATM 38 C C11 4DV . A . B 2 10.556 15.804 25.072 0.65 14.78 ? C11 4DV 201 A 1 HETATM 39 C C11 4DV . B . B 2 9.207 17.778 25.29 0.35 18.75 ? C11 4DV 201 A 1 HETATM 40 C C16 4DV . . . B 2 8.267 15.952 22.077 1 17.87 ? C16 4DV 201 A 1 HETATM 41 C C21 4DV . . . B 2 8.702 16.469 20.825 1 24.54 ? C21 4DV 201 A 1 HETATM 42 C C22 4DV . . . B 2 9.837 17.452 20.679 1 36.32 ? C22 4DV 201 A 1 HETATM 43 C C20 4DV . . . B 2 8.041 16.055 19.65 1 25.1 ? C20 4DV 201 A 1 HETATM 44 C C19 4DV . . . B 2 6.977 15.147 19.689 1 21.45 ? C19 4DV 201 A 1 HETATM 45 C C18 4DV . . . B 2 6.554 14.632 20.911 1 19.51 ? C18 4DV 201 A 1 HETATM 46 C C17 4DV . . . B 2 7.195 15.03 22.087 1 16.19 ? C17 4DV 201 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 27 _model_server_stats.element_count 46 #