data_3S0N # _model_server_result.job_id Xv1hLEndvtQHiu30zOAfvA _model_server_result.datetime_utc '2024-11-24 21:29:45' _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 3s0n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":230}' # _entry.id 3S0N # _exptl.entry_id 3S0N _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 380.46 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '4-{3-[(4-methyl-1-benzothiophen-3-yl)methyl]-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl}butanoic 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 90 _cell.entry_id 3S0N _cell.length_a 73.83 _cell.length_b 73.83 _cell.length_c 48.45 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3S0N _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' # _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 4 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _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 _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 30 A CYS 30 1_555 A SG CYS 46 A CYS 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? disulf ? disulf2 A SG CYS 123 A CYS 123 1_555 A SG CYS 188 A CYS 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.691 ? disulf ? disulf3 A SG CYS 154 A CYS 154 1_555 A SG CYS 167 A CYS 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 59 A ASN 59 1_555 B C1 NAG . A NAG 227 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale2 A ND2 ASN 82 A ASN 82 1_555 C C1 NAG . A NAG 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? metalc ? metalc1 A NE2 HIS 10 A HIS 10 1_555 D ZN ZN . A ZN 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc2 A OE1 GLU 64 A GLU 64 1_555 D ZN ZN . A ZN 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.865 ? # _chem_comp.formula 'C21 H20 N2 O3 S' _chem_comp.formula_weight 380.46 _chem_comp.id 0BB _chem_comp.mon_nstd_flag . _chem_comp.name '4-{3-[(4-methyl-1-benzothiophen-3-yl)methyl]-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl}butanoic 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 N11 C1 0BB sing 1 n n C1 C12 0BB sing 2 n n C1 H1 0BB sing 3 n n C1 H1A 0BB sing 4 n n O1 C10 0BB doub 5 n n C8 C3 0BB doub 6 n y C3 C4 0BB sing 7 n y C3 H3 0BB sing 8 n n C4 C5 0BB doub 9 n y C4 H4 0BB sing 10 n n C6 C5 0BB sing 11 n y C5 H5 0BB sing 12 n n C7 C6 0BB doub 13 n y C6 H6 0BB sing 14 n n C8 C7 0BB sing 15 n y N11 C7 0BB sing 16 n n N9 C8 0BB sing 17 n n C17 N9 0BB sing 18 n n N9 C10 0BB sing 19 n n C10 N11 0BB sing 20 n n C13 C12 0BB sing 21 n n C12 H12 0BB sing 22 n n C12 H12A 0BB sing 23 n n C13 C39 0BB sing 24 n n C13 H13 0BB sing 25 n n C13 H13A 0BB sing 26 n n C18 C17 0BB sing 27 n n C17 H17 0BB sing 28 n n C17 H17A 0BB sing 29 n n C19 C18 0BB sing 30 n y C18 C22 0BB doub 31 n y C23 C19 0BB doub 32 n y C20 C19 0BB sing 33 n y C26 C20 0BB doub 34 n y C20 S21 0BB sing 35 n y S21 C22 0BB sing 36 n y C22 H22 0BB sing 37 n n C24 C23 0BB sing 38 n y C34 C23 0BB sing 39 n n C25 C24 0BB doub 40 n y C24 H24 0BB sing 41 n n C25 C26 0BB sing 42 n y C25 H25 0BB sing 43 n n C26 H26 0BB sing 44 n n C34 H34 0BB sing 45 n n C34 H34A 0BB sing 46 n n C34 H34B 0BB sing 47 n n O40 C39 0BB doub 48 n n C39 O41 0BB sing 49 n n O41 HO41 0BB sing 50 n n # _atom_sites.entry_id 3S0N _atom_sites.fract_transf_matrix[1][1] 0.013545 _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] 0.013545 _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] 0.02064 _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 NAG A 1 227 1 NAG NAG . C 2 NAG A 1 228 2 NAG NAG . D 3 ZN A 1 229 1 ZN ZN . E 4 0BB A 1 230 1 0BB 0BB . F 5 HOH A 1 22 22 HOH HOH . F 5 HOH A 2 23 23 HOH HOH . F 5 HOH A 3 24 24 HOH HOH . F 5 HOH A 4 162 162 HOH HOH . F 5 HOH A 5 171 171 HOH HOH . F 5 HOH A 6 231 1 HOH HOH . F 5 HOH A 7 232 2 HOH HOH . F 5 HOH A 8 233 3 HOH HOH . F 5 HOH A 9 234 4 HOH HOH . F 5 HOH A 10 235 5 HOH HOH . F 5 HOH A 11 236 6 HOH HOH . F 5 HOH A 12 237 7 HOH HOH . F 5 HOH A 13 238 8 HOH HOH . F 5 HOH A 14 239 9 HOH HOH . F 5 HOH A 15 240 10 HOH HOH . F 5 HOH A 16 241 11 HOH HOH . F 5 HOH A 17 242 12 HOH HOH . F 5 HOH A 18 243 13 HOH HOH . F 5 HOH A 19 244 14 HOH HOH . F 5 HOH A 20 245 15 HOH HOH . F 5 HOH A 21 246 16 HOH HOH . F 5 HOH A 22 247 17 HOH HOH . F 5 HOH A 23 248 18 HOH HOH . F 5 HOH A 24 249 19 HOH HOH . F 5 HOH A 25 250 20 HOH HOH . F 5 HOH A 26 251 21 HOH HOH . F 5 HOH A 27 252 25 HOH HOH . F 5 HOH A 28 253 26 HOH HOH . F 5 HOH A 29 254 27 HOH HOH . F 5 HOH A 30 255 28 HOH HOH . F 5 HOH A 31 256 29 HOH HOH . F 5 HOH A 32 257 30 HOH HOH . F 5 HOH A 33 258 31 HOH HOH . F 5 HOH A 34 259 32 HOH HOH . F 5 HOH A 35 260 33 HOH HOH . F 5 HOH A 36 261 34 HOH HOH . F 5 HOH A 37 262 35 HOH HOH . F 5 HOH A 38 263 36 HOH HOH . F 5 HOH A 39 264 37 HOH HOH . F 5 HOH A 40 265 38 HOH HOH . F 5 HOH A 41 266 39 HOH HOH . F 5 HOH A 42 267 40 HOH HOH . F 5 HOH A 43 268 41 HOH HOH . F 5 HOH A 44 269 42 HOH HOH . F 5 HOH A 45 270 43 HOH HOH . F 5 HOH A 46 271 44 HOH HOH . F 5 HOH A 47 272 45 HOH HOH . F 5 HOH A 48 273 46 HOH HOH . F 5 HOH A 49 274 47 HOH HOH . F 5 HOH A 50 275 48 HOH HOH . F 5 HOH A 51 276 49 HOH HOH . F 5 HOH A 52 277 50 HOH HOH . F 5 HOH A 53 278 51 HOH HOH . F 5 HOH A 54 279 52 HOH HOH . F 5 HOH A 55 280 53 HOH HOH . F 5 HOH A 56 281 54 HOH HOH . F 5 HOH A 57 282 55 HOH HOH . F 5 HOH A 58 283 56 HOH HOH . F 5 HOH A 59 284 57 HOH HOH . F 5 HOH A 60 285 58 HOH HOH . F 5 HOH A 61 286 59 HOH HOH . F 5 HOH A 62 287 60 HOH HOH . F 5 HOH A 63 288 61 HOH HOH . F 5 HOH A 64 289 62 HOH HOH . F 5 HOH A 65 290 63 HOH HOH . F 5 HOH A 66 291 64 HOH HOH . F 5 HOH A 67 292 65 HOH HOH . F 5 HOH A 68 293 66 HOH HOH . F 5 HOH A 69 294 67 HOH HOH . F 5 HOH A 70 295 68 HOH HOH . F 5 HOH A 71 296 69 HOH HOH . F 5 HOH A 72 297 70 HOH HOH . F 5 HOH A 73 298 71 HOH HOH . F 5 HOH A 74 299 72 HOH HOH . F 5 HOH A 75 300 73 HOH HOH . F 5 HOH A 76 301 74 HOH HOH . F 5 HOH A 77 302 75 HOH HOH . F 5 HOH A 78 303 76 HOH HOH . F 5 HOH A 79 304 77 HOH HOH . F 5 HOH A 80 305 78 HOH HOH . F 5 HOH A 81 306 79 HOH HOH . F 5 HOH A 82 307 80 HOH HOH . F 5 HOH A 83 308 81 HOH HOH . F 5 HOH A 84 309 82 HOH HOH . F 5 HOH A 85 310 83 HOH HOH . F 5 HOH A 86 311 84 HOH HOH . F 5 HOH A 87 312 85 HOH HOH . F 5 HOH A 88 313 86 HOH HOH . F 5 HOH A 89 314 87 HOH HOH . F 5 HOH A 90 315 88 HOH HOH . F 5 HOH A 91 316 89 HOH HOH . F 5 HOH A 92 317 90 HOH HOH . F 5 HOH A 93 318 91 HOH HOH . F 5 HOH A 94 319 92 HOH HOH . F 5 HOH A 95 320 93 HOH HOH . F 5 HOH A 96 321 94 HOH HOH . F 5 HOH A 97 322 95 HOH HOH . F 5 HOH A 98 323 96 HOH HOH . F 5 HOH A 99 324 97 HOH HOH . F 5 HOH A 100 325 98 HOH HOH . F 5 HOH A 101 326 99 HOH HOH . F 5 HOH A 102 327 100 HOH HOH . F 5 HOH A 103 328 101 HOH HOH . F 5 HOH A 104 329 102 HOH HOH . F 5 HOH A 105 330 103 HOH HOH . F 5 HOH A 106 331 104 HOH HOH . F 5 HOH A 107 332 105 HOH HOH . F 5 HOH A 108 333 106 HOH HOH . F 5 HOH A 109 334 107 HOH HOH . F 5 HOH A 110 335 108 HOH HOH . F 5 HOH A 111 336 109 HOH HOH . F 5 HOH A 112 337 110 HOH HOH . F 5 HOH A 113 338 111 HOH HOH . F 5 HOH A 114 339 112 HOH HOH . F 5 HOH A 115 340 113 HOH HOH . F 5 HOH A 116 341 114 HOH HOH . F 5 HOH A 117 342 115 HOH HOH . F 5 HOH A 118 343 116 HOH HOH . F 5 HOH A 119 344 117 HOH HOH . F 5 HOH A 120 345 118 HOH HOH . F 5 HOH A 121 346 119 HOH HOH . F 5 HOH A 122 347 120 HOH HOH . F 5 HOH A 123 348 121 HOH HOH . F 5 HOH A 124 349 122 HOH HOH . F 5 HOH A 125 350 123 HOH HOH . F 5 HOH A 126 351 124 HOH HOH . F 5 HOH A 127 352 125 HOH HOH . F 5 HOH A 128 353 126 HOH HOH . F 5 HOH A 129 354 127 HOH HOH . F 5 HOH A 130 355 128 HOH HOH . F 5 HOH A 131 356 129 HOH HOH . F 5 HOH A 132 357 130 HOH HOH . F 5 HOH A 133 358 131 HOH HOH . F 5 HOH A 134 359 132 HOH HOH . F 5 HOH A 135 360 133 HOH HOH . F 5 HOH A 136 361 134 HOH HOH . F 5 HOH A 137 362 135 HOH HOH . F 5 HOH A 138 363 136 HOH HOH . F 5 HOH A 139 364 137 HOH HOH . F 5 HOH A 140 365 138 HOH HOH . F 5 HOH A 141 366 139 HOH HOH . F 5 HOH A 142 367 140 HOH HOH . F 5 HOH A 143 368 141 HOH HOH . F 5 HOH A 144 369 142 HOH HOH . F 5 HOH A 145 370 143 HOH HOH . F 5 HOH A 146 371 144 HOH HOH . F 5 HOH A 147 372 145 HOH HOH . F 5 HOH A 148 373 146 HOH HOH . F 5 HOH A 149 374 147 HOH HOH . F 5 HOH A 150 375 148 HOH HOH . F 5 HOH A 151 376 149 HOH HOH . F 5 HOH A 152 377 150 HOH HOH . F 5 HOH A 153 378 151 HOH HOH . F 5 HOH A 154 379 152 HOH HOH . F 5 HOH A 155 380 153 HOH HOH . F 5 HOH A 156 381 154 HOH HOH . F 5 HOH A 157 382 155 HOH HOH . F 5 HOH A 158 383 156 HOH HOH . F 5 HOH A 159 384 157 HOH HOH . F 5 HOH A 160 385 158 HOH HOH . F 5 HOH A 161 386 159 HOH HOH . F 5 HOH A 162 387 160 HOH HOH . F 5 HOH A 163 388 161 HOH HOH . F 5 HOH A 164 389 163 HOH HOH . F 5 HOH A 165 390 164 HOH HOH . F 5 HOH A 166 391 165 HOH HOH . F 5 HOH A 167 392 166 HOH HOH . F 5 HOH A 168 393 167 HOH HOH . F 5 HOH A 169 394 168 HOH HOH . F 5 HOH A 170 395 169 HOH HOH . F 5 HOH A 171 396 170 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 C1 0BB . . . E 4 20.998 29.042 8.684 1 37.88 ? C1 0BB 230 A 1 HETATM 2 O O1 0BB . . . E 4 21.381 28.735 5.76 1 33.05 ? O1 0BB 230 A 1 HETATM 3 C C3 0BB . . . E 4 20.391 24.249 7.16 1 26.02 ? C3 0BB 230 A 1 HETATM 4 C C4 0BB . . . E 4 20.116 23.751 8.408 1 26.72 ? C4 0BB 230 A 1 HETATM 5 C C5 0BB . . . E 4 20.084 24.627 9.63 1 26.78 ? C5 0BB 230 A 1 HETATM 6 C C6 0BB . . . E 4 20.326 25.979 9.585 1 27.2 ? C6 0BB 230 A 1 HETATM 7 C C7 0BB . . . E 4 20.633 26.591 8.244 1 29.49 ? C7 0BB 230 A 1 HETATM 8 C C8 0BB . . . E 4 20.665 25.72 7.032 1 27.76 ? C8 0BB 230 A 1 HETATM 9 N N9 0BB . . . E 4 20.96 26.506 5.996 1 28.41 ? N9 0BB 230 A 1 HETATM 10 C C10 0BB . . . E 4 21.106 27.785 6.475 1 31.03 ? C10 0BB 230 A 1 HETATM 11 N N11 0BB . . . E 4 20.915 27.836 7.834 1 32.97 ? N11 0BB 230 A 1 HETATM 12 C C12 0BB . . . E 4 22.434 29.297 9.187 1 44.63 ? C12 0BB 230 A 1 HETATM 13 C C13 0BB . . . E 4 22.954 30.695 8.793 1 50.28 ? C13 0BB 230 A 1 HETATM 14 C C17 0BB . . . E 4 21.106 26.127 4.581 1 23.73 ? C17 0BB 230 A 1 HETATM 15 C C18 0BB . . . E 4 22.528 25.823 4.069 1 21.12 ? C18 0BB 230 A 1 HETATM 16 C C19 0BB . . . E 4 22.89 25.229 2.744 1 18.8 ? C19 0BB 230 A 1 HETATM 17 C C20 0BB . . . E 4 24.344 25.11 2.659 1 20.54 ? C20 0BB 230 A 1 HETATM 18 S S21 0BB . . . E 4 25.129 25.672 4.052 1 22.99 ? S21 0BB 230 A 1 HETATM 19 C C22 0BB . . . E 4 23.692 26.088 4.833 1 22.15 ? C22 0BB 230 A 1 HETATM 20 C C23 0BB . . . E 4 22.112 24.785 1.617 1 17.22 ? C23 0BB 230 A 1 HETATM 21 C C24 0BB . . . E 4 22.764 24.246 0.466 1 18.46 ? C24 0BB 230 A 1 HETATM 22 C C25 0BB . . . E 4 24.17 24.143 0.413 1 20.45 ? C25 0BB 230 A 1 HETATM 23 C C26 0BB . . . E 4 24.943 24.579 1.513 1 21.36 ? C26 0BB 230 A 1 HETATM 24 C C34 0BB . . . E 4 20.604 24.859 1.581 1 16.7 ? C34 0BB 230 A 1 HETATM 25 C C39 0BB . . . E 4 24.395 30.988 9.275 1 53.28 ? C39 0BB 230 A 1 HETATM 26 O O40 0BB . . . E 4 24.943 32 8.84 1 54.97 ? O40 0BB 230 A 1 HETATM 27 O O41 0BB . . . E 4 24.954 30.218 10.07 1 53.94 ? O41 0BB 230 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 413 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #