data_5SBK # _model_server_result.job_id hAiRIhbq6FiwHESVCKYA3Q _model_server_result.datetime_utc '2024-11-23 02:43:02' _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 5sbk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5SBK # _exptl.entry_id 5SBK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 204.268 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[(3R)-piperidin-3-yl]benzamide _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 117.85 _cell.angle_gamma 90 _cell.entry_id 5SBK _cell.length_a 30.7 _cell.length_b 81.45 _cell.length_c 31.98 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5SBK _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _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,D,E,F,G _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 # 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 10 A CYS 32 1_555 A SG CYS 112 A CYS 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf2 A SG CYS 35 A CYS 57 1_555 A SG CYS 101 A CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 59 A CYS 81 1_555 A SG CYS 79 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? # _chem_comp.formula 'C12 H16 N2 O' _chem_comp.formula_weight 204.268 _chem_comp.id 89W _chem_comp.mon_nstd_flag . _chem_comp.name N-[(3R)-piperidin-3-yl]benzamide _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 C07 C06 89W sing 1 n n C07 N08 89W sing 2 n n C06 C05 89W sing 3 n n N08 C09 89W sing 4 n n C05 C04 89W sing 5 n n C09 C04 89W sing 6 n n C04 N03 89W sing 7 n n N03 C02 89W sing 8 n n O01 C02 89W doub 9 n n C02 C10 89W sing 10 n n C10 C15 89W doub 11 n y C10 C11 89W sing 12 n y C15 C14 89W sing 13 n y C11 C12 89W doub 14 n y C14 C13 89W doub 15 n y C12 C13 89W sing 16 n y C13 H1 89W sing 17 n n C15 H2 89W sing 18 n n N03 H3 89W sing 19 n n C04 H4 89W sing 20 n n C05 H5 89W sing 21 n n C05 H6 89W sing 22 n n C06 H7 89W sing 23 n n C06 H8 89W sing 24 n n C07 H9 89W sing 25 n n C07 H10 89W sing 26 n n N08 H11 89W sing 27 n n C09 H13 89W sing 28 n n C09 H14 89W sing 29 n n C11 H15 89W sing 30 n n C12 H16 89W sing 31 n n C14 H17 89W sing 32 n n # _atom_sites.entry_id 5SBK _atom_sites.fract_transf_matrix[1][1] 0.032573 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.01721 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012277 _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] 0.035366 _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 89W A 1 201 201 89W LIG . C 3 DMS A 1 202 1 DMS DMS . D 3 DMS A 1 203 2 DMS DMS . E 4 EDO A 1 204 1 EDO EDO . F 4 EDO A 1 205 2 EDO EDO . G 5 HOH A 1 301 278 HOH HOH . G 5 HOH A 2 302 41 HOH HOH . G 5 HOH A 3 303 163 HOH HOH . G 5 HOH A 4 304 32 HOH HOH . G 5 HOH A 5 305 103 HOH HOH . G 5 HOH A 6 306 175 HOH HOH . G 5 HOH A 7 307 71 HOH HOH . G 5 HOH A 8 308 120 HOH HOH . G 5 HOH A 9 309 50 HOH HOH . G 5 HOH A 10 310 60 HOH HOH . G 5 HOH A 11 311 62 HOH HOH . G 5 HOH A 12 312 161 HOH HOH . G 5 HOH A 13 313 115 HOH HOH . G 5 HOH A 14 314 91 HOH HOH . G 5 HOH A 15 315 21 HOH HOH . G 5 HOH A 16 316 76 HOH HOH . G 5 HOH A 17 317 4 HOH HOH . G 5 HOH A 18 318 255 HOH HOH . G 5 HOH A 19 319 2 HOH HOH . G 5 HOH A 20 320 114 HOH HOH . G 5 HOH A 21 321 5 HOH HOH . G 5 HOH A 22 322 85 HOH HOH . G 5 HOH A 23 323 78 HOH HOH . G 5 HOH A 24 324 14 HOH HOH . G 5 HOH A 25 325 180 HOH HOH . G 5 HOH A 26 326 26 HOH HOH . G 5 HOH A 27 327 254 HOH HOH . G 5 HOH A 28 328 231 HOH HOH . G 5 HOH A 29 329 3 HOH HOH . G 5 HOH A 30 330 144 HOH HOH . G 5 HOH A 31 331 34 HOH HOH . G 5 HOH A 32 332 18 HOH HOH . G 5 HOH A 33 333 46 HOH HOH . G 5 HOH A 34 334 57 HOH HOH . G 5 HOH A 35 335 49 HOH HOH . G 5 HOH A 36 336 31 HOH HOH . G 5 HOH A 37 337 197 HOH HOH . G 5 HOH A 38 338 10 HOH HOH . G 5 HOH A 39 339 28 HOH HOH . G 5 HOH A 40 340 102 HOH HOH . G 5 HOH A 41 341 158 HOH HOH . G 5 HOH A 42 342 259 HOH HOH . G 5 HOH A 43 343 44 HOH HOH . G 5 HOH A 44 344 195 HOH HOH . G 5 HOH A 45 345 55 HOH HOH . G 5 HOH A 46 346 54 HOH HOH . G 5 HOH A 47 347 193 HOH HOH . G 5 HOH A 48 348 68 HOH HOH . G 5 HOH A 49 349 110 HOH HOH . G 5 HOH A 50 350 27 HOH HOH . G 5 HOH A 51 351 137 HOH HOH . G 5 HOH A 52 352 271 HOH HOH . G 5 HOH A 53 353 11 HOH HOH . G 5 HOH A 54 354 79 HOH HOH . G 5 HOH A 55 355 126 HOH HOH . G 5 HOH A 56 356 51 HOH HOH . G 5 HOH A 57 357 73 HOH HOH . G 5 HOH A 58 358 159 HOH HOH . G 5 HOH A 59 359 38 HOH HOH . G 5 HOH A 60 360 82 HOH HOH . G 5 HOH A 61 361 22 HOH HOH . G 5 HOH A 62 362 100 HOH HOH . G 5 HOH A 63 363 45 HOH HOH . G 5 HOH A 64 364 178 HOH HOH . G 5 HOH A 65 365 109 HOH HOH . G 5 HOH A 66 366 48 HOH HOH . G 5 HOH A 67 367 154 HOH HOH . G 5 HOH A 68 368 47 HOH HOH . G 5 HOH A 69 369 7 HOH HOH . G 5 HOH A 70 370 13 HOH HOH . G 5 HOH A 71 371 1 HOH HOH . G 5 HOH A 72 372 9 HOH HOH . G 5 HOH A 73 373 33 HOH HOH . G 5 HOH A 74 374 29 HOH HOH . G 5 HOH A 75 375 127 HOH HOH . G 5 HOH A 76 376 56 HOH HOH . G 5 HOH A 77 377 15 HOH HOH . G 5 HOH A 78 378 160 HOH HOH . G 5 HOH A 79 379 63 HOH HOH . G 5 HOH A 80 380 147 HOH HOH . G 5 HOH A 81 381 174 HOH HOH . G 5 HOH A 82 382 121 HOH HOH . G 5 HOH A 83 383 130 HOH HOH . G 5 HOH A 84 384 19 HOH HOH . G 5 HOH A 85 385 112 HOH HOH . G 5 HOH A 86 386 95 HOH HOH . G 5 HOH A 87 387 270 HOH HOH . G 5 HOH A 88 388 101 HOH HOH . G 5 HOH A 89 389 156 HOH HOH . G 5 HOH A 90 390 17 HOH HOH . G 5 HOH A 91 391 248 HOH HOH . G 5 HOH A 92 392 42 HOH HOH . G 5 HOH A 93 393 66 HOH HOH . G 5 HOH A 94 394 192 HOH HOH . G 5 HOH A 95 395 39 HOH HOH . G 5 HOH A 96 396 43 HOH HOH . G 5 HOH A 97 397 35 HOH HOH . G 5 HOH A 98 398 36 HOH HOH . G 5 HOH A 99 399 155 HOH HOH . G 5 HOH A 100 400 167 HOH HOH . G 5 HOH A 101 401 261 HOH HOH . G 5 HOH A 102 402 228 HOH HOH . G 5 HOH A 103 403 87 HOH HOH . G 5 HOH A 104 404 119 HOH HOH . G 5 HOH A 105 405 106 HOH HOH . G 5 HOH A 106 406 92 HOH HOH . G 5 HOH A 107 407 25 HOH HOH . G 5 HOH A 108 408 266 HOH HOH . G 5 HOH A 109 409 40 HOH HOH . G 5 HOH A 110 410 89 HOH HOH . G 5 HOH A 111 411 177 HOH HOH . G 5 HOH A 112 412 107 HOH HOH . G 5 HOH A 113 413 139 HOH HOH . G 5 HOH A 114 414 70 HOH HOH . G 5 HOH A 115 415 200 HOH HOH . G 5 HOH A 116 416 64 HOH HOH . G 5 HOH A 117 417 116 HOH HOH . G 5 HOH A 118 418 72 HOH HOH . G 5 HOH A 119 419 77 HOH HOH . G 5 HOH A 120 420 67 HOH HOH . G 5 HOH A 121 421 6 HOH HOH . G 5 HOH A 122 422 24 HOH HOH . G 5 HOH A 123 423 20 HOH HOH . G 5 HOH A 124 424 98 HOH HOH . G 5 HOH A 125 425 23 HOH HOH . G 5 HOH A 126 426 221 HOH HOH . G 5 HOH A 127 427 84 HOH HOH . G 5 HOH A 128 428 12 HOH HOH . G 5 HOH A 129 429 274 HOH HOH . G 5 HOH A 130 430 86 HOH HOH . G 5 HOH A 131 431 290 HOH HOH . G 5 HOH A 132 432 122 HOH HOH . G 5 HOH A 133 433 152 HOH HOH . G 5 HOH A 134 434 269 HOH HOH . G 5 HOH A 135 435 226 HOH HOH . G 5 HOH A 136 436 289 HOH HOH . G 5 HOH A 137 437 258 HOH HOH . G 5 HOH A 138 438 58 HOH HOH . G 5 HOH A 139 439 108 HOH HOH . G 5 HOH A 140 440 146 HOH HOH . G 5 HOH A 141 441 179 HOH HOH . G 5 HOH A 142 442 272 HOH HOH . G 5 HOH A 143 443 53 HOH HOH . G 5 HOH A 144 444 149 HOH HOH . G 5 HOH A 145 445 105 HOH HOH . G 5 HOH A 146 446 227 HOH HOH . G 5 HOH A 147 447 222 HOH HOH . G 5 HOH A 148 448 281 HOH HOH . G 5 HOH A 149 449 201 HOH HOH . G 5 HOH A 150 450 8 HOH HOH . G 5 HOH A 151 451 80 HOH HOH . G 5 HOH A 152 452 94 HOH HOH . G 5 HOH A 153 453 249 HOH HOH . G 5 HOH A 154 454 134 HOH HOH . G 5 HOH A 155 455 219 HOH HOH . G 5 HOH A 156 456 140 HOH HOH . G 5 HOH A 157 457 284 HOH HOH . G 5 HOH A 158 458 97 HOH HOH . G 5 HOH A 159 459 69 HOH HOH . G 5 HOH A 160 460 83 HOH HOH . G 5 HOH A 161 461 136 HOH HOH . G 5 HOH A 162 462 291 HOH HOH . G 5 HOH A 163 463 173 HOH HOH . G 5 HOH A 164 464 165 HOH HOH . G 5 HOH A 165 465 240 HOH HOH . G 5 HOH A 166 466 138 HOH HOH . G 5 HOH A 167 467 191 HOH HOH . G 5 HOH A 168 468 135 HOH HOH . G 5 HOH A 169 469 113 HOH HOH . G 5 HOH A 170 470 247 HOH HOH . G 5 HOH A 171 471 61 HOH HOH . G 5 HOH A 172 472 129 HOH HOH . G 5 HOH A 173 473 235 HOH HOH . G 5 HOH A 174 474 37 HOH HOH . G 5 HOH A 175 475 244 HOH HOH . G 5 HOH A 176 476 104 HOH HOH . G 5 HOH A 177 477 59 HOH HOH . G 5 HOH A 178 478 265 HOH HOH . G 5 HOH A 179 479 184 HOH HOH . G 5 HOH A 180 480 168 HOH HOH . G 5 HOH A 181 481 181 HOH HOH . G 5 HOH A 182 482 209 HOH HOH . G 5 HOH A 183 483 230 HOH HOH . G 5 HOH A 184 484 132 HOH HOH . G 5 HOH A 185 485 145 HOH HOH . G 5 HOH A 186 486 148 HOH HOH . G 5 HOH A 187 487 142 HOH HOH . G 5 HOH A 188 488 288 HOH HOH . G 5 HOH A 189 489 172 HOH HOH . G 5 HOH A 190 490 202 HOH HOH . G 5 HOH A 191 491 234 HOH HOH . G 5 HOH A 192 492 162 HOH HOH . G 5 HOH A 193 493 213 HOH HOH . G 5 HOH A 194 494 170 HOH HOH . G 5 HOH A 195 495 90 HOH HOH . G 5 HOH A 196 496 251 HOH HOH . G 5 HOH A 197 497 143 HOH HOH . G 5 HOH A 198 498 242 HOH HOH . G 5 HOH A 199 499 141 HOH HOH . G 5 HOH A 200 500 164 HOH HOH . G 5 HOH A 201 501 30 HOH HOH . G 5 HOH A 202 502 220 HOH HOH . G 5 HOH A 203 503 118 HOH HOH . G 5 HOH A 204 504 243 HOH HOH . G 5 HOH A 205 505 190 HOH HOH . G 5 HOH A 206 506 65 HOH HOH . G 5 HOH A 207 507 93 HOH HOH . G 5 HOH A 208 508 198 HOH HOH . G 5 HOH A 209 509 99 HOH HOH . G 5 HOH A 210 510 287 HOH HOH . G 5 HOH A 211 511 262 HOH HOH . G 5 HOH A 212 512 74 HOH HOH . G 5 HOH A 213 513 171 HOH HOH . G 5 HOH A 214 514 199 HOH HOH . G 5 HOH A 215 515 257 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 C10 89W . . . B 2 0.498 4.012 -8.396 0.74 12.97 ? C10 89W 201 A 1 HETATM 2 C C13 89W . . . B 2 -0.915 4.045 -6.069 0.74 12.98 ? C13 89W 201 A 1 HETATM 3 C C15 89W . . . B 2 -0.042 2.833 -7.895 0.74 13.06 ? C15 89W 201 A 1 HETATM 4 O O01 89W . . . B 2 2.292 4.566 -9.851 0.74 13.31 ? O01 89W 201 A 1 HETATM 5 C C02 89W . . . B 2 1.282 3.963 -9.69 0.74 13.16 ? C02 89W 201 A 1 HETATM 6 N N03 89W . . . B 2 0.737 3.125 -10.71 0.74 13.36 ? N03 89W 201 A 1 HETATM 7 C C04 89W . . . B 2 1.473 2.993 -11.925 0.74 14 ? C04 89W 201 A 1 HETATM 8 C C05 89W . . . B 2 0.864 3.817 -13.011 0.74 14.97 ? C05 89W 201 A 1 HETATM 9 C C06 89W . . . B 2 1.417 3.478 -14.346 0.74 15.11 ? C06 89W 201 A 1 HETATM 10 C C07 89W . . . B 2 1.317 1.977 -14.658 0.74 15.31 ? C07 89W 201 A 1 HETATM 11 N N08 89W . . . B 2 1.727 1.081 -13.535 0.74 15.15 ? N08 89W 201 A 1 HETATM 12 C C09 89W . . . B 2 1.383 1.489 -12.154 0.74 14.26 ? C09 89W 201 A 1 HETATM 13 C C11 89W . . . B 2 0.347 5.229 -7.762 0.74 13.04 ? C11 89W 201 A 1 HETATM 14 C C12 89W . . . B 2 -0.386 5.225 -6.59 0.74 12.79 ? C12 89W 201 A 1 HETATM 15 C C14 89W . . . B 2 -0.765 2.827 -6.705 0.74 12.66 ? C14 89W 201 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #