data_5OPC # _model_server_result.job_id YgsDiTYOEOiSIT-zsWTUAg _model_server_result.datetime_utc '2024-11-27 22:18:10' _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 5opc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":412}' # _entry.id 5OPC # _exptl.entry_id 5OPC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 306.701 _entity.id 5 _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 90 _cell.entry_id 5OPC _cell.length_a 86.799 _cell.length_b 86.799 _cell.length_c 149.52 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OPC _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_465 y-1,x+1,-z 0 1 0 1 0 0 0 0 -1 -86.799 86.799 0 # _struct_asym.details ? _struct_asym.entity_id 5 _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 metalc ? metalc1 A NE2 HIS 200 A HIS 199 1_555 G ZN ZN . A ZN 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc2 A OD2 ASP 202 A ASP 201 1_555 G ZN ZN . A ZN 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc3 A NE2 HIS 280 A HIS 279 1_555 G ZN ZN . A ZN 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc4 G ZN ZN . A ZN 406 1_555 M O10 A1Z . A A1Z 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc5 G ZN ZN . A ZN 406 1_555 M N11 A1Z . A A1Z 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? # _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 5OPC _atom_sites.fract_transf_matrix[1][1] 0.011521 _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] 0.011521 _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] 0.006688 _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 SO4 A 1 401 1 SO4 SO4 . C 2 SO4 A 1 402 2 SO4 SO4 . D 2 SO4 A 1 403 3 SO4 SO4 . E 2 SO4 A 1 404 4 SO4 SO4 . F 2 SO4 A 1 405 5 SO4 SO4 . G 3 ZN A 1 406 1 ZN ZN . H 4 GOL A 1 407 1 GOL GOL . I 4 GOL A 1 408 2 GOL GOL . J 4 GOL A 1 409 5 GOL GOL . K 4 GOL A 1 410 7 GOL GOL . L 4 GOL A 1 411 8 GOL GOL . M 5 A1Z A 1 412 1 A1Z AKB . N 6 HOH A 1 501 143 HOH HOH . N 6 HOH A 2 502 24 HOH HOH . N 6 HOH A 3 503 50 HOH HOH . N 6 HOH A 4 504 6 HOH HOH . N 6 HOH A 5 505 71 HOH HOH . N 6 HOH A 6 506 11 HOH HOH . N 6 HOH A 7 507 94 HOH HOH . N 6 HOH A 8 508 128 HOH HOH . N 6 HOH A 9 509 138 HOH HOH . N 6 HOH A 10 510 46 HOH HOH . N 6 HOH A 11 511 139 HOH HOH . N 6 HOH A 12 512 5 HOH HOH . N 6 HOH A 13 513 96 HOH HOH . N 6 HOH A 14 514 23 HOH HOH . N 6 HOH A 15 515 1 HOH HOH . N 6 HOH A 16 516 47 HOH HOH . N 6 HOH A 17 517 61 HOH HOH . N 6 HOH A 18 518 134 HOH HOH . N 6 HOH A 19 519 79 HOH HOH . N 6 HOH A 20 520 98 HOH HOH . N 6 HOH A 21 521 21 HOH HOH . N 6 HOH A 22 522 100 HOH HOH . N 6 HOH A 23 523 34 HOH HOH . N 6 HOH A 24 524 45 HOH HOH . N 6 HOH A 25 525 8 HOH HOH . N 6 HOH A 26 526 102 HOH HOH . N 6 HOH A 27 527 9 HOH HOH . N 6 HOH A 28 528 75 HOH HOH . N 6 HOH A 29 529 137 HOH HOH . N 6 HOH A 30 530 32 HOH HOH . N 6 HOH A 31 531 31 HOH HOH . N 6 HOH A 32 532 17 HOH HOH . N 6 HOH A 33 533 13 HOH HOH . N 6 HOH A 34 534 2 HOH HOH . N 6 HOH A 35 535 4 HOH HOH . N 6 HOH A 36 536 33 HOH HOH . N 6 HOH A 37 537 25 HOH HOH . N 6 HOH A 38 538 41 HOH HOH . N 6 HOH A 39 539 12 HOH HOH . N 6 HOH A 40 540 106 HOH HOH . N 6 HOH A 41 541 90 HOH HOH . N 6 HOH A 42 542 14 HOH HOH . N 6 HOH A 43 543 140 HOH HOH . N 6 HOH A 44 544 10 HOH HOH . N 6 HOH A 45 545 54 HOH HOH . N 6 HOH A 46 546 15 HOH HOH . N 6 HOH A 47 547 19 HOH HOH . N 6 HOH A 48 548 118 HOH HOH . N 6 HOH A 49 549 95 HOH HOH . N 6 HOH A 50 550 87 HOH HOH . N 6 HOH A 51 551 112 HOH HOH . N 6 HOH A 52 552 16 HOH HOH . N 6 HOH A 53 553 52 HOH HOH . N 6 HOH A 54 554 88 HOH HOH . N 6 HOH A 55 555 63 HOH HOH . N 6 HOH A 56 556 84 HOH HOH . N 6 HOH A 57 557 29 HOH HOH . N 6 HOH A 58 558 125 HOH HOH . N 6 HOH A 59 559 58 HOH HOH . N 6 HOH A 60 560 39 HOH HOH . N 6 HOH A 61 561 53 HOH HOH . N 6 HOH A 62 562 99 HOH HOH . N 6 HOH A 63 563 72 HOH HOH . N 6 HOH A 64 564 105 HOH HOH . N 6 HOH A 65 565 18 HOH HOH . N 6 HOH A 66 566 124 HOH HOH . N 6 HOH A 67 567 142 HOH HOH . N 6 HOH A 68 568 93 HOH HOH . N 6 HOH A 69 569 68 HOH HOH . N 6 HOH A 70 570 121 HOH HOH . N 6 HOH A 71 571 114 HOH HOH . N 6 HOH A 72 572 126 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 . . . M 5 -24.02 20.903 -5.667 1 90.21 ? O01 A1Z 412 A 1 HETATM 2 C C02 A1Z . . . M 5 -24.571 22.22 -5.886 1 91.06 ? C02 A1Z 412 A 1 HETATM 3 C C03 A1Z . . . M 5 -25.605 22.409 -6.762 1 80.89 ? C03 A1Z 412 A 1 HETATM 4 C C04 A1Z . . . M 5 -26.188 21.221 -7.524 1 75.63 ? C04 A1Z 412 A 1 HETATM 5 N N05 A1Z . . . M 5 -25.695 19.925 -7.322 1 83.14 ? N05 A1Z 412 A 1 HETATM 6 C C06 A1Z . . . M 5 -26.288 18.775 -8.094 1 74.19 ? C06 A1Z 412 A 1 HETATM 7 C C07 A1Z . . . M 5 -25.425 18.419 -9.234 1 94.54 ? C07 A1Z 412 A 1 HETATM 8 O O08 A1Z . . . M 5 -25.259 17.261 -9.517 1 70.97 -1 O08 A1Z 412 A 1 HETATM 9 O O09 A1Z . . . M 5 -24.822 19.383 -9.926 1 97.63 ? O09 A1Z 412 A 1 HETATM 10 O O10 A1Z . . . M 5 -27.052 21.393 -8.309 1 70.28 ? O10 A1Z 412 A 1 HETATM 11 N N11 A1Z . . . M 5 -26.122 23.619 -6.972 1 101.42 ? N11 A1Z 412 A 1 HETATM 12 C C12 A1Z . . . M 5 -25.652 24.683 -6.337 1 101.71 ? C12 A1Z 412 A 1 HETATM 13 C C13 A1Z . . . M 5 -24.616 24.578 -5.442 1 109.84 ? C13 A1Z 412 A 1 HETATM 14 C C21 A1Z . . . M 5 -24.048 23.327 -5.198 1 102.01 ? C21 A1Z 412 A 1 HETATM 15 C C14 A1Z . E . M 5 -24.105 25.852 -4.729 0.16 96.74 ? C14 A1Z 412 A 1 HETATM 16 C C14 A1Z . F . M 5 -24.069 25.834 -4.723 0.5 95.72 ? C14 A1Z 412 A 1 HETATM 17 C C15 A1Z . E . M 5 -24.978 26.595 -3.981 0.16 94.28 ? C15 A1Z 412 A 1 HETATM 18 C C15 A1Z . F . M 5 -24.112 27.04 -5.371 0.5 97.38 ? C15 A1Z 412 A 1 HETATM 19 C C16 A1Z . E . M 5 -24.534 27.749 -3.336 0.16 94.99 ? C16 A1Z 412 A 1 HETATM 20 C C16 A1Z . F . M 5 -23.615 28.184 -4.752 0.5 101.26 ? C16 A1Z 412 A 1 HETATM 21 CL CL A1Z . E . M 5 -25.683 28.715 -2.353 0.16 87.73 ? CL A1Z 412 A 1 HETATM 22 CL CL A1Z . F . M 5 -23.691 29.757 -5.612 0.5 116.47 ? CL A1Z 412 A 1 HETATM 23 C C18 A1Z . E . M 5 -23.207 28.145 -3.459 0.16 97.94 ? C18 A1Z 412 A 1 HETATM 24 C C18 A1Z . F . M 5 -23.066 28.099 -3.478 0.5 99.59 ? C18 A1Z 412 A 1 HETATM 25 C C19 A1Z . E . M 5 -22.34 27.401 -4.211 0.16 96.79 ? C19 A1Z 412 A 1 HETATM 26 C C19 A1Z . F . M 5 -23.015 26.891 -2.837 0.5 95.34 ? C19 A1Z 412 A 1 HETATM 27 C C20 A1Z . E . M 5 -22.788 26.246 -4.855 0.16 93.69 ? C20 A1Z 412 A 1 HETATM 28 C C20 A1Z . F . M 5 -23.514 25.746 -3.461 0.5 95.87 ? C20 A1Z 412 A 1 HETATM 29 H H011 A1Z . . . M 5 -23.509 20.918 -4.989 1 108.25 ? H011 A1Z 412 A 1 HETATM 30 H H051 A1Z . . . M 5 -25.063 19.787 -6.755 1 99.77 ? H051 A1Z 412 A 1 HETATM 31 H H061 A1Z . . . M 5 -26.373 18.006 -7.508 1 89.03 ? H061 A1Z 412 A 1 HETATM 32 H H062 A1Z . . . M 5 -27.164 19.028 -8.423 1 89.03 ? H062 A1Z 412 A 1 HETATM 33 H H121 A1Z . . . M 5 -26.028 25.517 -6.503 1 122.05 ? H121 A1Z 412 A 1 HETATM 34 H H211 A1Z . . . M 5 -23.345 23.23 -4.596 1 122.41 ? H211 A1Z 412 A 1 HETATM 35 H H151 A1Z . E . M 5 -25.865 26.329 -3.9 0.16 113.14 ? H151 A1Z 412 A 1 HETATM 36 H H151 A1Z . F . M 5 -24.48 27.095 -6.223 0.5 116.86 ? H151 A1Z 412 A 1 HETATM 37 H H181 A1Z . E . M 5 -22.909 28.914 -3.029 0.16 117.53 ? H181 A1Z 412 A 1 HETATM 38 H H181 A1Z . F . M 5 -22.733 28.861 -3.061 0.5 119.51 ? H181 A1Z 412 A 1 HETATM 39 H H191 A1Z . E . M 5 -21.452 27.665 -4.292 0.16 116.15 ? H191 A1Z 412 A 1 HETATM 40 H H191 A1Z . F . M 5 -22.649 26.833 -1.984 0.5 114.41 ? H191 A1Z 412 A 1 HETATM 41 H H201 A1Z . E . M 5 -22.199 25.739 -5.366 0.16 112.43 ? H201 A1Z 412 A 1 HETATM 42 H H201 A1Z . F . M 5 -23.482 24.925 -3.025 0.5 115.04 ? H201 A1Z 412 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 42 #