data_5OX6 # _model_server_result.job_id NcU6sIEOPCF2LDpt4qIkmQ _model_server_result.datetime_utc '2024-12-09 16:08:02' _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 5ox6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 5OX6 # _exptl.entry_id 5OX6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 306.701 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description Vadadustat _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 5OX6 _cell.length_a 111.088 _cell.length_b 111.088 _cell.length_c 39.971 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OX6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _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 _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 3 _struct_asym.id C _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 covale ? covale1 A NZ LYS 185 A LYS 359 1_555 E O3 SO4 . A SO4 504 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.297 ? covale ? covale2 A NH2 ARG 222 A ARG 396 1_555 D O1 SO4 . A SO4 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? metalc ? metalc1 A NE2 HIS 139 A HIS 313 1_555 B MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc2 A OD1 ASP 141 A ASP 315 1_555 B MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc3 A NE2 HIS 200 A HIS 374 1_555 B MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc4 B MN MN . A MN 501 1_555 C O10 A1Z . A A1Z 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc5 B MN MN . A MN 501 1_555 C N11 A1Z . A A1Z 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc6 B MN MN . A MN 501 1_555 H O HOH . A HOH 616 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? # _chem_comp.formula 'C14 H11 Cl N2 O4' _chem_comp.formula_weight 306.701 _chem_comp.id A1Z _chem_comp.mon_nstd_flag . _chem_comp.name Vadadustat _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GSK128863 # 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 O09 C07 A1Z doub 1 n n O08 C07 A1Z sing 2 n n C07 C06 A1Z sing 3 n n O10 C04 A1Z doub 4 n n C06 N05 A1Z sing 5 n n C04 N05 A1Z sing 6 n n C04 C03 A1Z sing 7 n n N11 C03 A1Z doub 8 n y N11 C12 A1Z sing 9 n y C03 C02 A1Z sing 10 n y C12 C13 A1Z doub 11 n y C02 O01 A1Z sing 12 n n C02 C21 A1Z doub 13 n y C13 C21 A1Z sing 14 n y C13 C14 A1Z sing 15 n n C20 C14 A1Z doub 16 n y C20 C19 A1Z sing 17 n y C14 C15 A1Z sing 18 n y C19 C18 A1Z doub 19 n y C15 C16 A1Z doub 20 n y C18 C16 A1Z sing 21 n y C16 CL A1Z sing 22 n n O01 H011 A1Z sing 23 n n N05 H051 A1Z sing 24 n n C06 H061 A1Z sing 25 n n C06 H062 A1Z sing 26 n n O08 H1 A1Z sing 27 n n C12 H121 A1Z sing 28 n n C21 H211 A1Z sing 29 n n C15 H151 A1Z sing 30 n n C18 H181 A1Z sing 31 n n C19 H191 A1Z sing 32 n n C20 H201 A1Z sing 33 n n # _atom_sites.entry_id 5OX6 _atom_sites.fract_transf_matrix[1][1] 0.009002 _atom_sites.fract_transf_matrix[1][2] 0.005197 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010394 _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] 0.025018 _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 MN A 1 501 501 MN MN . C 3 A1Z A 1 502 601 A1Z VAD . D 4 SO4 A 1 503 701 SO4 SO4 . E 4 SO4 A 1 504 702 SO4 SO4 . F 5 GOL A 1 505 801 GOL GOL . G 5 GOL A 1 506 802 GOL GOL . H 6 HOH A 1 601 1107 HOH HOH . H 6 HOH A 2 602 1106 HOH HOH . H 6 HOH A 3 603 1047 HOH HOH . H 6 HOH A 4 604 1095 HOH HOH . H 6 HOH A 5 605 1012 HOH HOH . H 6 HOH A 6 606 1116 HOH HOH . H 6 HOH A 7 607 1026 HOH HOH . H 6 HOH A 8 608 1018 HOH HOH . H 6 HOH A 9 609 1013 HOH HOH . H 6 HOH A 10 610 1010 HOH HOH . H 6 HOH A 11 611 1031 HOH HOH . H 6 HOH A 12 612 1011 HOH HOH . H 6 HOH A 13 613 1022 HOH HOH . H 6 HOH A 14 614 1058 HOH HOH . H 6 HOH A 15 615 1101 HOH HOH . H 6 HOH A 16 616 1001 HOH HOH . H 6 HOH A 17 617 1008 HOH HOH . H 6 HOH A 18 618 1019 HOH HOH . H 6 HOH A 19 619 1054 HOH HOH . H 6 HOH A 20 620 1053 HOH HOH . H 6 HOH A 21 621 1007 HOH HOH . H 6 HOH A 22 622 1037 HOH HOH . H 6 HOH A 23 623 1027 HOH HOH . H 6 HOH A 24 624 1004 HOH HOH . H 6 HOH A 25 625 1039 HOH HOH . H 6 HOH A 26 626 1048 HOH HOH . H 6 HOH A 27 627 1020 HOH HOH . H 6 HOH A 28 628 1077 HOH HOH . H 6 HOH A 29 629 1080 HOH HOH . H 6 HOH A 30 630 1100 HOH HOH . H 6 HOH A 31 631 1075 HOH HOH . H 6 HOH A 32 632 1118 HOH HOH . H 6 HOH A 33 633 1005 HOH HOH . H 6 HOH A 34 634 1112 HOH HOH . H 6 HOH A 35 635 1040 HOH HOH . H 6 HOH A 36 636 1050 HOH HOH . H 6 HOH A 37 637 1006 HOH HOH . H 6 HOH A 38 638 1009 HOH HOH . H 6 HOH A 39 639 1055 HOH HOH . H 6 HOH A 40 640 1002 HOH HOH . H 6 HOH A 41 641 1034 HOH HOH . H 6 HOH A 42 642 1086 HOH HOH . H 6 HOH A 43 643 1057 HOH HOH . H 6 HOH A 44 644 1063 HOH HOH . H 6 HOH A 45 645 1064 HOH HOH . H 6 HOH A 46 646 1056 HOH HOH . H 6 HOH A 47 647 1003 HOH HOH . H 6 HOH A 48 648 1052 HOH HOH . H 6 HOH A 49 649 1139 HOH HOH . H 6 HOH A 50 650 1016 HOH HOH . H 6 HOH A 51 651 1017 HOH HOH . H 6 HOH A 52 652 1033 HOH HOH . H 6 HOH A 53 653 1049 HOH HOH . H 6 HOH A 54 654 1081 HOH HOH . H 6 HOH A 55 655 1029 HOH HOH . H 6 HOH A 56 656 1204 HOH HOH . H 6 HOH A 57 657 1028 HOH HOH . H 6 HOH A 58 658 1060 HOH HOH . H 6 HOH A 59 659 1059 HOH HOH . H 6 HOH A 60 660 1085 HOH HOH . H 6 HOH A 61 661 1045 HOH HOH . H 6 HOH A 62 662 1207 HOH HOH . H 6 HOH A 63 663 1051 HOH HOH . H 6 HOH A 64 664 1014 HOH HOH . H 6 HOH A 65 665 1025 HOH HOH . H 6 HOH A 66 666 1076 HOH HOH . H 6 HOH A 67 667 1015 HOH HOH . H 6 HOH A 68 668 1102 HOH HOH . H 6 HOH A 69 669 1205 HOH HOH . H 6 HOH A 70 670 1035 HOH HOH . H 6 HOH A 71 671 1036 HOH HOH . H 6 HOH A 72 672 1138 HOH HOH . H 6 HOH A 73 673 1066 HOH HOH . H 6 HOH A 74 674 1062 HOH HOH . H 6 HOH A 75 675 1127 HOH HOH . H 6 HOH A 76 676 1021 HOH HOH . H 6 HOH A 77 677 1038 HOH HOH . H 6 HOH A 78 678 1208 HOH HOH . H 6 HOH A 79 679 1117 HOH HOH . H 6 HOH A 80 680 1089 HOH HOH . H 6 HOH A 81 681 1042 HOH HOH . H 6 HOH A 82 682 1061 HOH HOH . H 6 HOH A 83 683 1132 HOH HOH . H 6 HOH A 84 684 1065 HOH HOH . H 6 HOH A 85 685 1032 HOH HOH . H 6 HOH A 86 686 1043 HOH HOH . H 6 HOH A 87 687 1119 HOH HOH . H 6 HOH A 88 688 1067 HOH HOH . H 6 HOH A 89 689 1087 HOH HOH . H 6 HOH A 90 690 1206 HOH HOH . H 6 HOH A 91 691 1131 HOH HOH . H 6 HOH A 92 692 1109 HOH HOH . H 6 HOH A 93 693 1091 HOH HOH . H 6 HOH A 94 694 1121 HOH HOH . H 6 HOH A 95 695 1105 HOH HOH . H 6 HOH A 96 696 1202 HOH HOH . H 6 HOH A 97 697 1123 HOH HOH . H 6 HOH A 98 698 1079 HOH HOH . H 6 HOH A 99 699 1201 HOH HOH . H 6 HOH A 100 700 1082 HOH HOH . H 6 HOH A 101 701 1136 HOH HOH . H 6 HOH A 102 702 1088 HOH HOH . H 6 HOH A 103 703 1023 HOH HOH . H 6 HOH A 104 704 1024 HOH HOH . H 6 HOH A 105 705 1203 HOH HOH . H 6 HOH A 106 706 1044 HOH HOH . H 6 HOH A 107 707 1110 HOH HOH . H 6 HOH A 108 708 1093 HOH HOH . H 6 HOH A 109 709 1070 HOH HOH . H 6 HOH A 110 710 1092 HOH HOH . H 6 HOH A 111 711 1122 HOH HOH . H 6 HOH A 112 712 1108 HOH HOH . H 6 HOH A 113 713 1068 HOH HOH . H 6 HOH A 114 714 1097 HOH HOH . H 6 HOH A 115 715 1103 HOH HOH . H 6 HOH A 116 716 1113 HOH HOH . H 6 HOH A 117 717 1096 HOH HOH . H 6 HOH A 118 718 1135 HOH HOH . H 6 HOH A 119 719 1133 HOH HOH . H 6 HOH A 120 720 1099 HOH HOH . H 6 HOH A 121 721 1071 HOH HOH . H 6 HOH A 122 722 1090 HOH HOH . H 6 HOH A 123 723 1069 HOH HOH . H 6 HOH A 124 724 1098 HOH HOH . H 6 HOH A 125 725 1041 HOH HOH . H 6 HOH A 126 726 1104 HOH HOH . H 6 HOH A 127 727 1140 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 O01 A1Z . . . C 3 14.416 114.188 -5.13 1 29.71 ? O01 A1Z 502 A 1 HETATM 2 C C02 A1Z . . . C 3 13.998 115.451 -5.464 1 26.94 ? C02 A1Z 502 A 1 HETATM 3 C C03 A1Z . . . C 3 14.761 116.312 -6.237 1 26.31 ? C03 A1Z 502 A 1 HETATM 4 C C04 A1Z . . . C 3 16.117 116.009 -6.754 1 24.18 ? C04 A1Z 502 A 1 HETATM 5 N N05 A1Z . . . C 3 16.89 114.879 -6.283 1 22.96 ? N05 A1Z 502 A 1 HETATM 6 C C06 A1Z . . . C 3 18.227 114.745 -6.804 1 23.19 ? C06 A1Z 502 A 1 HETATM 7 C C07 A1Z . . . C 3 18.867 113.588 -6.057 1 25.49 ? C07 A1Z 502 A 1 HETATM 8 O O08 A1Z . . . C 3 18.097 112.864 -5.385 1 24.29 ? O08 A1Z 502 A 1 HETATM 9 O O09 A1Z . . . C 3 20.09 113.372 -6.19 1 27.05 ? O09 A1Z 502 A 1 HETATM 10 O O10 A1Z . . . C 3 16.523 116.782 -7.559 1 23.32 ? O10 A1Z 502 A 1 HETATM 11 N N11 A1Z . . . C 3 14.399 117.529 -6.539 1 23.24 ? N11 A1Z 502 A 1 HETATM 12 C C12 A1Z . . . C 3 13.222 117.964 -6.152 1 26.07 ? C12 A1Z 502 A 1 HETATM 13 C C13 A1Z . . . C 3 12.374 117.148 -5.399 1 27.9 ? C13 A1Z 502 A 1 HETATM 14 C C21 A1Z . . . C 3 12.756 115.878 -5.039 1 27.05 ? C21 A1Z 502 A 1 HETATM 15 C C14 A1Z . . . C 3 10.992 117.653 -4.981 1 39.54 ? C14 A1Z 502 A 1 HETATM 16 C C15 A1Z . . . C 3 10.483 117.392 -3.73 1 45.93 ? C15 A1Z 502 A 1 HETATM 17 C C16 A1Z . . . C 3 9.217 117.847 -3.394 1 52.67 ? C16 A1Z 502 A 1 HETATM 18 CL CL A1Z . . . C 3 8.627 117.507 -1.742 1 58.45 ? CL A1Z 502 A 1 HETATM 19 C C18 A1Z . . . C 3 8.443 118.547 -4.307 1 49.51 ? C18 A1Z 502 A 1 HETATM 20 C C19 A1Z . . . C 3 8.937 118.8 -5.577 1 47.41 ? C19 A1Z 502 A 1 HETATM 21 C C20 A1Z . . . C 3 10.222 118.35 -5.907 1 42.46 ? C20 A1Z 502 A 1 HETATM 22 H H011 A1Z . . . C 3 13.8 113.789 -4.702 1 35.7 ? H011 A1Z 502 A 1 HETATM 23 H H051 A1Z . . . C 3 16.59 114.351 -5.674 1 27.59 ? H051 A1Z 502 A 1 HETATM 24 H H061 A1Z . . . C 3 18.196 114.552 -7.754 1 27.87 ? H061 A1Z 502 A 1 HETATM 25 H H062 A1Z . . . C 3 18.728 115.561 -6.646 1 27.87 ? H062 A1Z 502 A 1 HETATM 26 H H121 A1Z . . . C 3 12.942 118.816 -6.398 1 31.33 ? H121 A1Z 502 A 1 HETATM 27 H H211 A1Z . . . C 3 12.196 115.325 -4.542 1 32.51 ? H211 A1Z 502 A 1 HETATM 28 H H151 A1Z . . . C 3 10.993 116.928 -3.106 1 55.17 ? H151 A1Z 502 A 1 HETATM 29 H H181 A1Z . . . C 3 7.598 118.851 -4.067 1 59.46 ? H181 A1Z 502 A 1 HETATM 30 H H191 A1Z . . . C 3 8.429 119.273 -6.196 1 56.94 ? H191 A1Z 502 A 1 HETATM 31 H H201 A1Z . . . C 3 10.559 118.507 -6.76 1 51 ? H201 A1Z 502 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #