data_7UMP # _model_server_result.job_id aCovxwun9ML9boZPBm87Jw _model_server_result.datetime_utc '2024-11-13 21:15:50' _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 7ump # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1002}' # _entry.id 7UMP # _exptl.entry_id 7UMP _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 7UMP _cell.length_a 111.4 _cell.length_b 111.4 _cell.length_c 40.42 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7UMP _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 metalc ? metalc1 A NE2 HIS 126 A HIS 313 1_555 B FE FE2 . A FE2 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc2 A OD2 ASP 128 A ASP 315 1_555 B FE FE2 . A FE2 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc3 A NE2 HIS 187 A HIS 374 1_555 B FE FE2 . A FE2 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc4 B FE FE2 . A FE2 1001 1_555 C O10 A1Z . A A1Z 1002 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.148 ? metalc ? metalc5 B FE FE2 . A FE2 1001 1_555 C O10 A1Z . A A1Z 1002 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.282 ? metalc ? metalc6 B FE FE2 . A FE2 1001 1_555 C N11 A1Z . A A1Z 1002 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.211 ? metalc ? metalc7 B FE FE2 . A FE2 1001 1_555 C N11 A1Z . A A1Z 1002 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.299 ? metalc ? metalc8 B FE FE2 . A FE2 1001 1_555 E O HOH . A HOH 1108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? # _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 7UMP _atom_sites.fract_transf_matrix[1][1] 0.008977 _atom_sites.fract_transf_matrix[1][2] 0.005183 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010365 _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] 0.02474 _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 FE2 A 1 1001 1001 FE2 FE2 . C 3 A1Z A 1 1002 1 A1Z LIG . D 4 EDO A 1 1003 1 EDO EDO . E 5 HOH A 1 1101 108 HOH HOH . E 5 HOH A 2 1102 102 HOH HOH . E 5 HOH A 3 1103 120 HOH HOH . E 5 HOH A 4 1104 116 HOH HOH . E 5 HOH A 5 1105 49 HOH HOH . E 5 HOH A 6 1106 55 HOH HOH . E 5 HOH A 7 1107 100 HOH HOH . E 5 HOH A 8 1108 2 HOH HOH . E 5 HOH A 9 1109 53 HOH HOH . E 5 HOH A 10 1110 16 HOH HOH . E 5 HOH A 11 1111 126 HOH HOH . E 5 HOH A 12 1112 122 HOH HOH . E 5 HOH A 13 1113 47 HOH HOH . E 5 HOH A 14 1114 7 HOH HOH . E 5 HOH A 15 1115 69 HOH HOH . E 5 HOH A 16 1116 128 HOH HOH . E 5 HOH A 17 1117 112 HOH HOH . E 5 HOH A 18 1118 56 HOH HOH . E 5 HOH A 19 1119 88 HOH HOH . E 5 HOH A 20 1120 91 HOH HOH . E 5 HOH A 21 1121 77 HOH HOH . E 5 HOH A 22 1122 11 HOH HOH . E 5 HOH A 23 1123 17 HOH HOH . E 5 HOH A 24 1124 89 HOH HOH . E 5 HOH A 25 1125 94 HOH HOH . E 5 HOH A 26 1126 117 HOH HOH . E 5 HOH A 27 1127 41 HOH HOH . E 5 HOH A 28 1128 65 HOH HOH . E 5 HOH A 29 1129 95 HOH HOH . E 5 HOH A 30 1130 32 HOH HOH . E 5 HOH A 31 1131 8 HOH HOH . E 5 HOH A 32 1132 99 HOH HOH . E 5 HOH A 33 1133 34 HOH HOH . E 5 HOH A 34 1134 119 HOH HOH . E 5 HOH A 35 1135 59 HOH HOH . E 5 HOH A 36 1136 3 HOH HOH . E 5 HOH A 37 1137 36 HOH HOH . E 5 HOH A 38 1138 22 HOH HOH . E 5 HOH A 39 1139 44 HOH HOH . E 5 HOH A 40 1140 45 HOH HOH . E 5 HOH A 41 1141 23 HOH HOH . E 5 HOH A 42 1142 13 HOH HOH . E 5 HOH A 43 1143 28 HOH HOH . E 5 HOH A 44 1144 12 HOH HOH . E 5 HOH A 45 1145 90 HOH HOH . E 5 HOH A 46 1146 62 HOH HOH . E 5 HOH A 47 1147 38 HOH HOH . E 5 HOH A 48 1148 42 HOH HOH . E 5 HOH A 49 1149 87 HOH HOH . E 5 HOH A 50 1150 9 HOH HOH . E 5 HOH A 51 1151 123 HOH HOH . E 5 HOH A 52 1152 97 HOH HOH . E 5 HOH A 53 1153 58 HOH HOH . E 5 HOH A 54 1154 4 HOH HOH . E 5 HOH A 55 1155 111 HOH HOH . E 5 HOH A 56 1156 86 HOH HOH . E 5 HOH A 57 1157 1 HOH HOH . E 5 HOH A 58 1158 129 HOH HOH . E 5 HOH A 59 1159 51 HOH HOH . E 5 HOH A 60 1160 71 HOH HOH . E 5 HOH A 61 1161 5 HOH HOH . E 5 HOH A 62 1162 26 HOH HOH . E 5 HOH A 63 1163 109 HOH HOH . E 5 HOH A 64 1164 18 HOH HOH . E 5 HOH A 65 1165 115 HOH HOH . E 5 HOH A 66 1166 21 HOH HOH . E 5 HOH A 67 1167 30 HOH HOH . E 5 HOH A 68 1168 57 HOH HOH . E 5 HOH A 69 1169 39 HOH HOH . E 5 HOH A 70 1170 27 HOH HOH . E 5 HOH A 71 1171 104 HOH HOH . E 5 HOH A 72 1172 6 HOH HOH . E 5 HOH A 73 1173 54 HOH HOH . E 5 HOH A 74 1174 72 HOH HOH . E 5 HOH A 75 1175 114 HOH HOH . E 5 HOH A 76 1176 70 HOH HOH . E 5 HOH A 77 1177 92 HOH HOH . E 5 HOH A 78 1178 103 HOH HOH . E 5 HOH A 79 1179 64 HOH HOH . E 5 HOH A 80 1180 15 HOH HOH . E 5 HOH A 81 1181 33 HOH HOH . E 5 HOH A 82 1182 20 HOH HOH . E 5 HOH A 83 1183 78 HOH HOH . E 5 HOH A 84 1184 14 HOH HOH . E 5 HOH A 85 1185 67 HOH HOH . E 5 HOH A 86 1186 81 HOH HOH . E 5 HOH A 87 1187 29 HOH HOH . E 5 HOH A 88 1188 113 HOH HOH . E 5 HOH A 89 1189 10 HOH HOH . E 5 HOH A 90 1190 74 HOH HOH . E 5 HOH A 91 1191 101 HOH HOH . E 5 HOH A 92 1192 98 HOH HOH . E 5 HOH A 93 1193 50 HOH HOH . E 5 HOH A 94 1194 66 HOH HOH . E 5 HOH A 95 1195 96 HOH HOH . E 5 HOH A 96 1196 19 HOH HOH . E 5 HOH A 97 1197 24 HOH HOH . E 5 HOH A 98 1198 68 HOH HOH . E 5 HOH A 99 1199 83 HOH HOH . E 5 HOH A 100 1200 25 HOH HOH . E 5 HOH A 101 1201 48 HOH HOH . E 5 HOH A 102 1202 79 HOH HOH . E 5 HOH A 103 1203 76 HOH HOH . E 5 HOH A 104 1204 31 HOH HOH . E 5 HOH A 105 1205 93 HOH HOH . E 5 HOH A 106 1206 121 HOH HOH . E 5 HOH A 107 1207 106 HOH HOH . E 5 HOH A 108 1208 105 HOH HOH . E 5 HOH A 109 1209 35 HOH HOH . E 5 HOH A 110 1210 46 HOH HOH . E 5 HOH A 111 1211 127 HOH HOH . E 5 HOH A 112 1212 43 HOH HOH . E 5 HOH A 113 1213 40 HOH HOH . E 5 HOH A 114 1214 82 HOH HOH . E 5 HOH A 115 1215 73 HOH HOH . E 5 HOH A 116 1216 124 HOH HOH . E 5 HOH A 117 1217 85 HOH HOH . E 5 HOH A 118 1218 80 HOH HOH . E 5 HOH A 119 1219 75 HOH HOH . E 5 HOH A 120 1220 118 HOH HOH . E 5 HOH A 121 1221 52 HOH HOH . E 5 HOH A 122 1222 37 HOH HOH . E 5 HOH A 123 1223 61 HOH HOH . E 5 HOH A 124 1224 63 HOH HOH . E 5 HOH A 125 1225 107 HOH HOH . E 5 HOH A 126 1226 110 HOH HOH . E 5 HOH A 127 1227 125 HOH HOH . E 5 HOH A 128 1228 84 HOH HOH . E 5 HOH A 129 1229 60 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 . A . C 3 41.216 -18.109 -13.359 0.66 22.78 ? O01 A1Z 1002 A 1 HETATM 2 O O01 A1Z . B . C 3 41.259 -18.116 -13.244 0.34 22.64 ? O01 A1Z 1002 A 1 HETATM 3 C C02 A1Z . A . C 3 41.722 -19.372 -13.665 0.66 22.58 ? C02 A1Z 1002 A 1 HETATM 4 C C02 A1Z . B . C 3 41.79 -19.362 -13.579 0.34 20.63 ? C02 A1Z 1002 A 1 HETATM 5 C C03 A1Z . A . C 3 40.979 -20.269 -14.431 0.66 14.14 ? C03 A1Z 1002 A 1 HETATM 6 C C03 A1Z . B . C 3 41.06 -20.236 -14.369 0.34 18.11 ? C03 A1Z 1002 A 1 HETATM 7 C C04 A1Z . A . C 3 39.594 -19.947 -14.974 0.66 17.06 ? C04 A1Z 1002 A 1 HETATM 8 C C04 A1Z . B . C 3 39.672 -19.864 -14.892 0.34 13.46 ? C04 A1Z 1002 A 1 HETATM 9 N N05 A1Z . A . C 3 38.863 -18.815 -14.526 0.66 16.04 ? N05 A1Z 1002 A 1 HETATM 10 N N05 A1Z . B . C 3 38.862 -18.842 -14.296 0.34 22.2 ? N05 A1Z 1002 A 1 HETATM 11 C C06 A1Z . A . C 3 37.547 -18.639 -15.08 0.66 18.38 ? C06 A1Z 1002 A 1 HETATM 12 C C06 A1Z . B . C 3 37.565 -18.631 -14.901 0.34 18.11 ? C06 A1Z 1002 A 1 HETATM 13 C C07 A1Z . A . C 3 36.866 -17.511 -14.321 0.66 20.14 ? C07 A1Z 1002 A 1 HETATM 14 C C07 A1Z . B . C 3 36.882 -17.447 -14.236 0.34 19.22 ? C07 A1Z 1002 A 1 HETATM 15 O O08 A1Z . A . C 3 37.566 -16.742 -13.62 0.66 21.34 ? O08 A1Z 1002 A 1 HETATM 16 O O08 A1Z . B . C 3 37.569 -16.653 -13.548 0.34 22.28 ? O08 A1Z 1002 A 1 HETATM 17 O O09 A1Z . A . C 3 35.627 -17.358 -14.45 0.66 21.52 -1 O09 A1Z 1002 A 1 HETATM 18 O O09 A1Z . B . C 3 35.65 -17.268 -14.405 0.34 21.89 -1 O09 A1Z 1002 A 1 HETATM 19 O O10 A1Z . A . C 3 39.069 -20.603 -15.833 0.66 14.34 ? O10 A1Z 1002 A 1 HETATM 20 O O10 A1Z . B . C 3 39.202 -20.403 -15.841 0.34 20.63 ? O10 A1Z 1002 A 1 HETATM 21 N N11 A1Z . A . C 3 41.467 -21.462 -14.673 0.66 19.06 ? N11 A1Z 1002 A 1 HETATM 22 N N11 A1Z . B . C 3 41.559 -21.417 -14.667 0.34 20.93 ? N11 A1Z 1002 A 1 HETATM 23 C C12 A1Z . A . C 3 42.643 -21.907 -14.307 0.66 20.82 ? C12 A1Z 1002 A 1 HETATM 24 C C12 A1Z . B . C 3 42.741 -21.852 -14.293 0.34 22.1 ? C12 A1Z 1002 A 1 HETATM 25 C C13 A1Z . A . C 3 43.435 -21.065 -13.558 0.66 25.07 ? C13 A1Z 1002 A 1 HETATM 26 C C13 A1Z . B . C 3 43.521 -21.028 -13.507 0.34 23.93 ? C13 A1Z 1002 A 1 HETATM 27 C C21 A1Z . A . C 3 42.974 -19.795 -13.222 0.66 21.22 ? C21 A1Z 1002 A 1 HETATM 28 C C21 A1Z . B . C 3 43.046 -19.774 -13.142 0.34 22.44 ? C21 A1Z 1002 A 1 HETATM 29 C C14 A1Z . A . C 3 44.681 -21.552 -13.164 0.66 22.5 ? C14 A1Z 1002 A 1 HETATM 30 C C14 A1Z . B . C 3 44.772 -21.488 -13.112 0.34 24.47 ? C14 A1Z 1002 A 1 HETATM 31 C C15 A1Z . A . C 3 45.16 -21.284 -11.902 0.66 30.09 ? C15 A1Z 1002 A 1 HETATM 32 C C15 A1Z . B . C 3 45.543 -22.21 -14.01 0.34 28.13 ? C15 A1Z 1002 A 1 HETATM 33 C C16 A1Z . A . C 3 46.397 -21.781 -11.527 0.66 32.28 ? C16 A1Z 1002 A 1 HETATM 34 C C16 A1Z . B . C 3 46.802 -22.671 -13.645 0.34 32.7 ? C16 A1Z 1002 A 1 HETATM 35 CL CL A1Z . A . C 3 46.959 -21.419 -9.883 0.66 32.22 ? CL A1Z 1002 A 1 HETATM 36 CL CL A1Z . B . C 3 47.798 -23.597 -14.798 0.34 42.08 ? CL A1Z 1002 A 1 HETATM 37 C C18 A1Z . A . C 3 47.172 -22.532 -12.4 0.66 31.68 ? C18 A1Z 1002 A 1 HETATM 38 C C18 A1Z . B . C 3 47.283 -22.417 -12.372 0.34 32.18 ? C18 A1Z 1002 A 1 HETATM 39 C C19 A1Z . A . C 3 46.694 -22.795 -13.675 0.66 32.99 ? C19 A1Z 1002 A 1 HETATM 40 C C19 A1Z . B . C 3 46.511 -21.697 -11.474 0.34 31.63 ? C19 A1Z 1002 A 1 HETATM 41 C C20 A1Z . A . C 3 45.441 -22.309 -14.043 0.66 26.34 ? C20 A1Z 1002 A 1 HETATM 42 C C20 A1Z . B . C 3 45.257 -21.227 -11.841 0.34 28.88 ? C20 A1Z 1002 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 42 #