data_8GD3 # _model_server_result.job_id XSdZAyJ0b7rX1szcYnuyTg _model_server_result.datetime_utc '2025-06-25 09:07:19' _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 8gd3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":512}' # _entry.id 8GD3 # _exptl.entry_id 8GD3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 455.911 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3S,5R)-N-(4-chloro-3-fluorophenyl)-1-(4-glycylpiperazine-1-carbonyl)-5-(hydroxymethyl)piperidine-3-carboxamide _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 8GD3 _cell.length_a 62.73 _cell.length_b 66.948 _cell.length_c 92.175 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GD3 _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,O _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 A SG CYS 78 A CYS 119 1_555 A SG CYS 91 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 104 A CYS 218 1_555 A SG CYS 133 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf4 A SG CYS 114 A CYS 228 1_555 A SG CYS 125 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf5 A SG CYS 182 A CYS 296 1_555 A SG CYS 201 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf6 A SG CYS 247 A CYS 378 1_555 A SG CYS 308 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf7 A SG CYS 254 A CYS 385 1_555 A SG CYS 281 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf8 A SG CYS 264 A CYS 395 1_555 A SG CYS 273 A CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 120 A ASN 234 1_555 B C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 A ND2 ASN 127 A ASN 241 1_555 C C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 A ND2 ASN 148 A ASN 262 1_555 D C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale4 A ND2 ASN 162 A ASN 276 1_555 E C1 NAG . A NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale5 A ND2 ASN 175 A ASN 289 1_555 F C1 NAG . A NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 A ND2 ASN 181 A ASN 295 1_555 G C1 NAG . A NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale7 A ND2 ASN 204 A ASN 334 1_555 H C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale8 A ND2 ASN 255 A ASN 386 1_555 I C1 NAG . A NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale9 A ND2 ASN 311 A ASN 448 1_555 J C1 NAG . A NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale10 A ND2 ASN 324 A ASN 461 1_555 K C1 NAG . A NAG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? # _chem_comp.formula 'C20 H27 Cl F N5 O4' _chem_comp.formula_weight 455.911 _chem_comp.id Z1Z _chem_comp.mon_nstd_flag . _chem_comp.name (3S,5R)-N-(4-chloro-3-fluorophenyl)-1-(4-glycylpiperazine-1-carbonyl)-5-(hydroxymethyl)piperidine-3-carboxamide _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 Z1Z sing 455 n n C21 C19 Z1Z doub 456 n y C21 C22 Z1Z sing 457 n y C19 C17 Z1Z sing 458 n y C22 C15 Z1Z doub 459 n y C17 F18 Z1Z sing 460 n n C17 C16 Z1Z doub 461 n y C15 C16 Z1Z sing 462 n y C15 N14 Z1Z sing 463 n n N14 C12 Z1Z sing 464 n n C12 O13 Z1Z doub 465 n n C12 C11 Z1Z sing 466 n n C23 C11 Z1Z sing 467 n n C23 C24 Z1Z sing 468 n n C11 C10 Z1Z sing 469 n n C24 C25 Z1Z sing 470 n n C24 C27 Z1Z sing 471 n n C25 O26 Z1Z sing 472 n n C10 N09 Z1Z sing 473 n n C27 N09 Z1Z sing 474 n n N09 C08 Z1Z sing 475 n n C29 N07 Z1Z sing 476 n n C29 C30 Z1Z sing 477 n n C08 N07 Z1Z sing 478 n n C08 O28 Z1Z doub 479 n n N07 C06 Z1Z sing 480 n n C06 C05 Z1Z sing 481 n n C05 N04 Z1Z sing 482 n n C30 N04 Z1Z sing 483 n n N04 C03 Z1Z sing 484 n n C03 C02 Z1Z sing 485 n n C03 O31 Z1Z doub 486 n n N01 C02 Z1Z sing 487 n n C10 H1 Z1Z sing 488 n n C10 H2 Z1Z sing 489 n n C11 H3 Z1Z sing 490 n n C16 H4 Z1Z sing 491 n n C21 H5 Z1Z sing 492 n n C22 H6 Z1Z sing 493 n n C23 H7 Z1Z sing 494 n n C23 H8 Z1Z sing 495 n n C24 H9 Z1Z sing 496 n n C25 H10 Z1Z sing 497 n n C25 H11 Z1Z sing 498 n n C27 H12 Z1Z sing 499 n n C27 H13 Z1Z sing 500 n n C29 H14 Z1Z sing 501 n n C29 H15 Z1Z sing 502 n n C30 H16 Z1Z sing 503 n n C30 H17 Z1Z sing 504 n n C02 H18 Z1Z sing 505 n n C02 H19 Z1Z sing 506 n n C05 H20 Z1Z sing 507 n n C05 H21 Z1Z sing 508 n n C06 H22 Z1Z sing 509 n n C06 H23 Z1Z sing 510 n n N01 H24 Z1Z sing 511 n n N01 H25 Z1Z sing 512 n n N14 H27 Z1Z sing 513 n n O26 H28 Z1Z sing 514 n n # _atom_sites.entry_id 8GD3 _atom_sites.fract_transf_matrix[1][1] 0.015941 _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] 0.014937 _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] 0.010849 _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 Z1Z A 1 512 1 Z1Z MW9 . N 5 PEG A 1 513 1 PEG PEG . O 6 HOH A 1 601 30 HOH HOH . O 6 HOH A 2 602 11 HOH HOH . O 6 HOH A 3 603 38 HOH HOH . O 6 HOH A 4 604 20 HOH HOH . O 6 HOH A 5 605 43 HOH HOH . O 6 HOH A 6 606 46 HOH HOH . O 6 HOH A 7 607 4 HOH HOH . O 6 HOH A 8 608 27 HOH HOH . O 6 HOH A 9 609 58 HOH HOH . O 6 HOH A 10 610 63 HOH HOH . O 6 HOH A 11 611 9 HOH HOH . O 6 HOH A 12 612 5 HOH HOH . O 6 HOH A 13 613 22 HOH HOH . O 6 HOH A 14 614 10 HOH HOH . O 6 HOH A 15 615 21 HOH HOH . O 6 HOH A 16 616 47 HOH HOH . O 6 HOH A 17 617 59 HOH HOH . O 6 HOH A 18 618 16 HOH HOH . O 6 HOH A 19 619 51 HOH HOH . O 6 HOH A 20 620 7 HOH HOH . O 6 HOH A 21 621 50 HOH HOH . O 6 HOH A 22 622 25 HOH HOH . O 6 HOH A 23 623 29 HOH HOH . O 6 HOH A 24 624 33 HOH HOH . O 6 HOH A 25 625 32 HOH HOH . O 6 HOH A 26 626 15 HOH HOH . O 6 HOH A 27 627 13 HOH HOH . O 6 HOH A 28 628 14 HOH HOH . O 6 HOH A 29 629 61 HOH HOH . O 6 HOH A 30 630 67 HOH HOH . O 6 HOH A 31 631 1 HOH HOH . O 6 HOH A 32 632 8 HOH HOH . O 6 HOH A 33 633 26 HOH HOH . O 6 HOH A 34 634 24 HOH HOH . O 6 HOH A 35 635 6 HOH HOH . O 6 HOH A 36 636 2 HOH HOH . O 6 HOH A 37 637 40 HOH HOH . O 6 HOH A 38 638 17 HOH HOH . O 6 HOH A 39 639 36 HOH HOH . O 6 HOH A 40 640 48 HOH HOH . O 6 HOH A 41 641 52 HOH HOH . O 6 HOH A 42 642 39 HOH HOH . O 6 HOH A 43 643 23 HOH HOH . O 6 HOH A 44 644 57 HOH HOH . O 6 HOH A 45 645 12 HOH HOH . O 6 HOH A 46 646 18 HOH HOH . O 6 HOH A 47 647 41 HOH HOH . O 6 HOH A 48 648 19 HOH HOH . O 6 HOH A 49 649 60 HOH HOH . O 6 HOH A 50 650 31 HOH HOH . O 6 HOH A 51 651 37 HOH HOH . O 6 HOH A 52 652 34 HOH HOH . O 6 HOH A 53 653 28 HOH HOH . O 6 HOH A 54 654 49 HOH HOH . O 6 HOH A 55 655 56 HOH HOH . O 6 HOH A 56 656 62 HOH HOH . O 6 HOH A 57 657 3 HOH HOH . O 6 HOH A 58 658 69 HOH HOH . O 6 HOH A 59 659 55 HOH HOH . O 6 HOH A 60 660 71 HOH HOH . O 6 HOH A 61 661 42 HOH HOH . O 6 HOH A 62 662 70 HOH HOH . O 6 HOH A 63 663 66 HOH HOH . O 6 HOH A 64 664 73 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 Z1Z . . . M 4 -2.067 17.519 -12.43 1 50.1 ? C10 Z1Z 512 A 1 HETATM 2 C C11 Z1Z . . . M 4 -1.901 17.844 -13.954 1 47.08 ? C11 Z1Z 512 A 1 HETATM 3 C C12 Z1Z . . . M 4 -3.044 17.533 -14.972 1 47.42 ? C12 Z1Z 512 A 1 HETATM 4 C C15 Z1Z . . . M 4 -3.33 17.273 -17.527 1 46.64 ? C15 Z1Z 512 A 1 HETATM 5 C C16 Z1Z . . . M 4 -4.72 17.258 -17.508 1 44.62 ? C16 Z1Z 512 A 1 HETATM 6 C C17 Z1Z . . . M 4 -5.418 17.044 -18.683 1 45.98 ? C17 Z1Z 512 A 1 HETATM 7 C C19 Z1Z . . . M 4 -4.737 16.862 -19.879 1 45.19 ? C19 Z1Z 512 A 1 HETATM 8 C C21 Z1Z . . . M 4 -3.35 16.898 -19.9 1 47.69 ? C21 Z1Z 512 A 1 HETATM 9 C C22 Z1Z . . . M 4 -2.644 17.101 -18.719 1 46.32 ? C22 Z1Z 512 A 1 HETATM 10 C C23 Z1Z . . . M 4 -1.622 19.277 -14.182 1 45.63 ? C23 Z1Z 512 A 1 HETATM 11 C C24 Z1Z . . . M 4 -0.349 19.664 -13.509 1 49.27 ? C24 Z1Z 512 A 1 HETATM 12 C C25 Z1Z . . . M 4 -0.212 21.196 -13.384 1 49.67 ? C25 Z1Z 512 A 1 HETATM 13 C C27 Z1Z . . . M 4 -0.318 19.153 -12.068 1 50.62 ? C27 Z1Z 512 A 1 HETATM 14 C C29 Z1Z . . . M 4 -0.925 14.538 -11.872 1 54.33 ? C29 Z1Z 512 A 1 HETATM 15 C C30 Z1Z . . . M 4 -1.259 14.032 -10.474 1 59.19 ? C30 Z1Z 512 A 1 HETATM 16 C C02 Z1Z . . . M 4 0.297 10.912 -8.54 1 73.08 ? C02 Z1Z 512 A 1 HETATM 17 C C03 Z1Z . . . M 4 -0.642 12.036 -8.998 1 68.75 ? C03 Z1Z 512 A 1 HETATM 18 C C05 Z1Z . . . M 4 0.929 13.026 -10.794 1 60.76 ? C05 Z1Z 512 A 1 HETATM 19 C C06 Z1Z . . . M 4 1.379 14.385 -11.328 1 58.46 ? C06 Z1Z 512 A 1 HETATM 20 C C08 Z1Z . . . M 4 0.446 16.732 -11.729 1 52.25 ? C08 Z1Z 512 A 1 HETATM 21 F F18 Z1Z . . . M 4 -6.782 17.008 -18.653 1 44.94 ? F18 Z1Z 512 A 1 HETATM 22 N N01 Z1Z . . . M 4 1.725 11.176 -8.629 1 79.33 ? N01 Z1Z 512 A 1 HETATM 23 N N04 Z1Z . . . M 4 -0.323 12.996 -10.051 1 61.65 ? N04 Z1Z 512 A 1 HETATM 24 N N07 Z1Z . . . M 4 0.288 15.282 -11.668 1 54.94 ? N07 Z1Z 512 A 1 HETATM 25 N N09 Z1Z . . . M 4 -0.625 17.699 -12.022 1 52.86 ? N09 Z1Z 512 A 1 HETATM 26 N N14 Z1Z . . . M 4 -2.557 17.5 -16.333 1 44.44 ? N14 Z1Z 512 A 1 HETATM 27 O O13 Z1Z . . . M 4 -4.186 17.371 -14.693 1 47.85 ? O13 Z1Z 512 A 1 HETATM 28 O O26 Z1Z . . . M 4 0.806 21.419 -12.447 1 52.26 ? O26 Z1Z 512 A 1 HETATM 29 O O28 Z1Z . . . M 4 1.525 17.163 -11.504 1 52.99 ? O28 Z1Z 512 A 1 HETATM 30 O O31 Z1Z . . . M 4 -1.702 12.12 -8.471 1 78.58 ? O31 Z1Z 512 A 1 HETATM 31 CL CL1 Z1Z . . . M 4 -5.644 16.587 -21.392 1 83.82 ? CL1 Z1Z 512 A 1 # _model_server_stats.io_time_ms 89 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 411 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #