data_8GD5 # _model_server_result.job_id IT6ZTMi0UnlSKsVN61j-Cg _model_server_result.datetime_utc '2025-01-26 17:35:45' _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 8gd5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":512}' # _entry.id 8GD5 # _exptl.entry_id 8GD5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 456.896 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '{4-[(3S,5R)-3-[(4-chloro-3-fluorophenyl)carbamoyl]-5-(hydroxymethyl)piperidine-1-carbonyl]piperazin-1-yl}acetic 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 8GD5 _cell.length_a 63.395 _cell.length_b 66.792 _cell.length_c 92.123 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GD5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 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,E,F,G,H,I,J,K,L,M,N _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 M _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 13 A CYS 54 1_555 A SG CYS 33 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 78 A CYS 119 1_555 A SG CYS 91 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 104 A CYS 218 1_555 A SG CYS 133 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf4 A SG CYS 114 A CYS 228 1_555 A SG CYS 125 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? disulf ? disulf5 A SG CYS 182 A CYS 296 1_555 A SG CYS 201 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf6 A SG CYS 247 A CYS 378 1_555 A SG CYS 308 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf7 A SG CYS 254 A CYS 385 1_555 A SG CYS 281 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf8 A SG CYS 264 A CYS 395 1_555 A SG CYS 273 A CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 120 A ASN 234 1_555 B C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale2 A ND2 ASN 127 A ASN 241 1_555 C C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale3 A ND2 ASN 148 A ASN 262 1_555 D C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 A ND2 ASN 162 A ASN 276 1_555 E C1 NAG . A NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 A ND2 ASN 175 A ASN 289 1_555 F C1 NAG . A NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale6 A ND2 ASN 181 A ASN 295 1_555 G C1 NAG . A NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale7 A ND2 ASN 204 A ASN 334 1_555 H C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale8 A ND2 ASN 255 A ASN 386 1_555 I C1 NAG . A NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale9 A ND2 ASN 311 A ASN 448 1_555 J C1 NAG . A NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale10 A ND2 ASN 324 A ASN 461 1_555 K C1 NAG . A NAG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? # _chem_comp.formula 'C20 H26 Cl F N4 O5' _chem_comp.formula_weight 456.896 _chem_comp.id Z2O _chem_comp.mon_nstd_flag . _chem_comp.name '{4-[(3S,5R)-3-[(4-chloro-3-fluorophenyl)carbamoyl]-5-(hydroxymethyl)piperidine-1-carbonyl]piperazin-1-yl}acetic 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 CL1 C19 Z2O sing 439 n n C21 C19 Z2O doub 440 n y C21 C22 Z2O sing 441 n y C19 C17 Z2O sing 442 n y C22 C15 Z2O doub 443 n y C17 F18 Z2O sing 444 n n C17 C16 Z2O doub 445 n y C15 C16 Z2O sing 446 n y C15 N14 Z2O sing 447 n n N14 C12 Z2O sing 448 n n C12 O13 Z2O doub 449 n n C12 C11 Z2O sing 450 n n C11 C23 Z2O sing 451 n n C11 C10 Z2O sing 452 n n C23 C24 Z2O sing 453 n n C24 C25 Z2O sing 454 n n C24 C27 Z2O sing 455 n n C10 N09 Z2O sing 456 n n C25 O26 Z2O sing 457 n n C29 N07 Z2O sing 458 n n C29 C30 Z2O sing 459 n n N09 C27 Z2O sing 460 n n N09 C08 Z2O sing 461 n n N07 C08 Z2O sing 462 n n N07 C06 Z2O sing 463 n n C08 O28 Z2O doub 464 n n C06 C05 Z2O sing 465 n n C30 N04 Z2O sing 466 n n N04 C05 Z2O sing 467 n n N04 C03 Z2O sing 468 n n C03 C02 Z2O sing 469 n n O1 C02 Z2O doub 470 n n C02 O31 Z2O sing 471 n n C03 H1 Z2O sing 472 n n C03 H2 Z2O sing 473 n n C05 H3 Z2O sing 474 n n C05 H4 Z2O sing 475 n n C06 H5 Z2O sing 476 n n C06 H6 Z2O sing 477 n n C10 H7 Z2O sing 478 n n C10 H8 Z2O sing 479 n n C11 H9 Z2O sing 480 n n C16 H10 Z2O sing 481 n n C21 H11 Z2O sing 482 n n C22 H12 Z2O sing 483 n n C23 H13 Z2O sing 484 n n C23 H14 Z2O sing 485 n n C24 H15 Z2O sing 486 n n C25 H16 Z2O sing 487 n n C25 H17 Z2O sing 488 n n C27 H18 Z2O sing 489 n n C27 H19 Z2O sing 490 n n C29 H20 Z2O sing 491 n n C29 H21 Z2O sing 492 n n C30 H22 Z2O sing 493 n n C30 H23 Z2O sing 494 n n N14 H25 Z2O sing 495 n n O26 H26 Z2O sing 496 n n O31 H27 Z2O sing 497 n n # _atom_sites.entry_id 8GD5 _atom_sites.fract_transf_matrix[1][1] 0.015774 _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] 0.014972 _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] 0.010855 _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 1 501 501 NAG NAG . C 2 NAG A 1 502 502 NAG NAG . D 2 NAG A 1 503 503 NAG NAG . E 2 NAG A 1 504 504 NAG NAG . F 2 NAG A 1 505 505 NAG NAG . G 2 NAG A 1 506 506 NAG NAG . H 2 NAG A 1 507 507 NAG NAG . I 2 NAG A 1 508 508 NAG NAG . J 2 NAG A 1 509 510 NAG NAG . K 2 NAG A 1 510 511 NAG NAG . L 3 EPE A 1 511 513 EPE EPE . M 4 Z2O A 1 512 1 Z2O MW0 . N 5 HOH A 1 601 2 HOH HOH . N 5 HOH A 2 602 1 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 C02 Z2O . . . M 4 -2.125 13.091 -7.965 1 137.51 ? C02 Z2O 512 A 1 HETATM 2 C C03 Z2O . . . M 4 -1.214 13.966 -8.817 1 139.52 ? C03 Z2O 512 A 1 HETATM 3 C C05 Z2O . . . M 4 0.76 13.289 -9.889 1 147.07 ? C05 Z2O 512 A 1 HETATM 4 C C06 Z2O . . . M 4 1.352 14.071 -11.066 1 156.6 ? C06 Z2O 512 A 1 HETATM 5 C C08 Z2O . . . M 4 0.524 16.498 -11.48 1 129.53 ? C08 Z2O 512 A 1 HETATM 6 C C10 Z2O . . . M 4 -1.83 17.282 -12.662 1 118.94 ? C10 Z2O 512 A 1 HETATM 7 C C11 Z2O . . . M 4 -1.658 17.967 -14.037 1 114.17 ? C11 Z2O 512 A 1 HETATM 8 C C12 Z2O . . . M 4 -2.751 17.583 -15.075 1 108.09 ? C12 Z2O 512 A 1 HETATM 9 C C15 Z2O . . . M 4 -3.259 17.405 -17.587 1 107.98 ? C15 Z2O 512 A 1 HETATM 10 C C16 Z2O . . . M 4 -4.636 17.418 -17.457 1 106.18 ? C16 Z2O 512 A 1 HETATM 11 C C17 Z2O . . . M 4 -5.423 17.117 -18.551 1 116.56 ? C17 Z2O 512 A 1 HETATM 12 C C19 Z2O . . . M 4 -4.833 16.813 -19.771 1 120.75 ? C19 Z2O 512 A 1 HETATM 13 C C21 Z2O . . . M 4 -3.457 16.805 -19.906 1 127.61 ? C21 Z2O 512 A 1 HETATM 14 C C22 Z2O . . . M 4 -2.674 17.104 -18.808 1 111.43 ? C22 Z2O 512 A 1 HETATM 15 C C23 Z2O . . . M 4 -1.642 19.418 -13.868 1 109.26 ? C23 Z2O 512 A 1 HETATM 16 C C24 Z2O . . . M 4 -0.466 19.834 -13.076 1 112.18 ? C24 Z2O 512 A 1 HETATM 17 C C25 Z2O . . . M 4 -0.713 21.299 -12.611 1 121.4 ? C25 Z2O 512 A 1 HETATM 18 C C27 Z2O . . . M 4 -0.247 18.957 -11.818 1 125.79 ? C27 Z2O 512 A 1 HETATM 19 C C29 Z2O . . . M 4 -0.703 14.264 -12.135 1 142.22 ? C29 Z2O 512 A 1 HETATM 20 C C30 Z2O . . . M 4 -1.456 13.56 -11.033 1 137.73 ? C30 Z2O 512 A 1 HETATM 21 F F18 Z2O . . . M 4 -6.78 17.126 -18.425 1 123 ? F18 Z2O 512 A 1 HETATM 22 N N04 Z2O . . . M 4 -0.676 13.174 -9.894 1 133.34 ? N04 Z2O 512 A 1 HETATM 23 N N07 Z2O . . . M 4 0.403 15.036 -11.585 1 136.11 ? N07 Z2O 512 A 1 HETATM 24 N N09 Z2O . . . M 4 -0.488 17.468 -11.965 1 123.48 ? N09 Z2O 512 A 1 HETATM 25 N N14 Z2O . . . M 4 -2.39 17.713 -16.473 1 109.24 ? N14 Z2O 512 A 1 HETATM 26 O O1 Z2O . . . M 4 -2.003 11.842 -8.048 1 129.54 ? O1 Z2O 512 A 1 HETATM 27 O O13 Z2O . . . M 4 -3.807 17.222 -14.7 1 110.39 ? O13 Z2O 512 A 1 HETATM 28 O O26 Z2O . . . M 4 -0.296 21.467 -11.287 1 128.02 ? O26 Z2O 512 A 1 HETATM 29 O O28 Z2O . . . M 4 1.496 16.967 -10.972 1 139.14 ? O28 Z2O 512 A 1 HETATM 30 O O31 Z2O . . . M 4 -2.992 13.604 -7.202 1 127.67 ? O31 Z2O 512 A 1 HETATM 31 CL CL1 Z2O . . . M 4 -5.856 16.429 -21.178 1 163.1 ? CL1 Z2O 512 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 560 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #