data_8CG9 # _model_server_result.job_id gtQqhCq5A-hMYgQL-N0Pcg _model_server_result.datetime_utc '2025-01-10 17:49:01' _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 8cg9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1102}' # _entry.id 8CG9 # _exptl.entry_id 8CG9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 332.331 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-[[(3~{R})-2,3-dihydro-1,4-benzodioxin-3-yl]methyl]-3-oxidanyl-thieno[3,2-d]pyrimidine-2,4-dione _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 8CG9 _cell.length_a 51.522 _cell.length_b 57.148 _cell.length_c 113.903 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CG9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _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,F,G _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 37 A HIS 732 1_555 B NI NI . A NI 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc2 A ND1 HIS 39 A HIS 734 1_555 B NI NI . A NI 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc3 A NE2 HIS 42 A HIS 737 1_555 E ZN ZN . A ZN 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc4 A NE2 HIS 98 A HIS 793 1_555 B NI NI . A NI 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc5 A OD2 ASP 120 A ASP 815 1_555 B NI NI . A NI 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc6 A OD2 ASP 120 A ASP 815 1_555 E ZN ZN . A ZN 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc7 B NI NI . A NI 1101 1_555 D O19 R3Z . A R3Z 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc8 B NI NI . A NI 1101 1_555 D N20 R3Z . A R3Z 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.776 ? metalc ? metalc9 B NI NI . A NI 1101 1_555 D O23 R3Z . A R3Z 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc10 C O19 XOB . A XOB 1102 1_555 E ZN ZN . A ZN 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc11 C O23 XOB . A XOB 1102 1_555 E ZN ZN . A ZN 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc12 D O23 R3Z . A R3Z 1103 1_555 E ZN ZN . A ZN 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc13 E ZN ZN . A ZN 1104 1_555 G O HOH . A HOH 1234 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? # _chem_comp.formula 'C15 H12 N2 O5 S' _chem_comp.formula_weight 332.331 _chem_comp.id XOB _chem_comp.mon_nstd_flag . _chem_comp.name 1-[[(3~{R})-2,3-dihydro-1,4-benzodioxin-3-yl]methyl]-3-oxidanyl-thieno[3,2-d]pyrimidine-2,4-dione _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 C2 C1 XOB doub 418 n y C2 C3 XOB sing 419 n y C1 C6 XOB sing 420 n y C3 C4 XOB doub 421 n y C6 C5 XOB doub 422 n y C4 C5 XOB sing 423 n y C4 O10 XOB sing 424 n n C5 O7 XOB sing 425 n n O10 C9 XOB sing 426 n n O7 C8 XOB sing 427 n n C9 C8 XOB sing 428 n n C9 C11 XOB sing 429 n n C11 N12 XOB sing 430 n n N12 C13 XOB sing 431 n n N12 C21 XOB sing 432 n n C14 C13 XOB sing 433 n y C14 C15 XOB doub 434 n y O22 C21 XOB doub 435 n n C13 C17 XOB doub 436 n y C21 N20 XOB sing 437 n n C15 S16 XOB sing 438 n y C17 S16 XOB sing 439 n y C17 C18 XOB sing 440 n n N20 C18 XOB sing 441 n n N20 O23 XOB sing 442 n n C18 O19 XOB doub 443 n n C1 H1 XOB sing 444 n n C2 H2 XOB sing 445 n n C3 H3 XOB sing 446 n n C6 H4 XOB sing 447 n n C8 H5 XOB sing 448 n n C8 H6 XOB sing 449 n n C9 H7 XOB sing 450 n n C11 H8 XOB sing 451 n n C11 H9 XOB sing 452 n n C14 H10 XOB sing 453 n n C15 H11 XOB sing 454 n n O23 H12 XOB sing 455 n n # _atom_sites.entry_id 8CG9 _atom_sites.fract_transf_matrix[1][1] 0.019409 _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] 0.017498 _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] 0.008779 _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 NI A 1 1101 1102 NI NI . C 3 XOB A 1 1102 1508 XOB UNL . D 4 R3Z A 1 1103 1509 R3Z ABZ . E 5 ZN A 1 1104 1 ZN ZN . F 6 SO4 A 1 1105 1 SO4 SO4 . G 7 HOH A 1 1201 93 HOH HOH . G 7 HOH A 2 1202 119 HOH HOH . G 7 HOH A 3 1203 97 HOH HOH . G 7 HOH A 4 1204 135 HOH HOH . G 7 HOH A 5 1205 2 HOH HOH . G 7 HOH A 6 1206 131 HOH HOH . G 7 HOH A 7 1207 110 HOH HOH . G 7 HOH A 8 1208 133 HOH HOH . G 7 HOH A 9 1209 128 HOH HOH . G 7 HOH A 10 1210 80 HOH HOH . G 7 HOH A 11 1211 14 HOH HOH . G 7 HOH A 12 1212 8 HOH HOH . G 7 HOH A 13 1213 117 HOH HOH . G 7 HOH A 14 1214 87 HOH HOH . G 7 HOH A 15 1215 1 HOH HOH . G 7 HOH A 16 1216 50 HOH HOH . G 7 HOH A 17 1217 56 HOH HOH . G 7 HOH A 18 1218 81 HOH HOH . G 7 HOH A 19 1219 140 HOH HOH . G 7 HOH A 20 1220 67 HOH HOH . G 7 HOH A 21 1221 94 HOH HOH . G 7 HOH A 22 1222 10 HOH HOH . G 7 HOH A 23 1223 5 HOH HOH . G 7 HOH A 24 1224 102 HOH HOH . G 7 HOH A 25 1225 113 HOH HOH . G 7 HOH A 26 1226 11 HOH HOH . G 7 HOH A 27 1227 6 HOH HOH . G 7 HOH A 28 1228 24 HOH HOH . G 7 HOH A 29 1229 83 HOH HOH . G 7 HOH A 30 1230 30 HOH HOH . G 7 HOH A 31 1231 103 HOH HOH . G 7 HOH A 32 1232 18 HOH HOH . G 7 HOH A 33 1233 36 HOH HOH . G 7 HOH A 34 1234 69 HOH HOH . G 7 HOH A 35 1235 20 HOH HOH . G 7 HOH A 36 1236 75 HOH HOH . G 7 HOH A 37 1237 70 HOH HOH . G 7 HOH A 38 1238 9 HOH HOH . G 7 HOH A 39 1239 51 HOH HOH . G 7 HOH A 40 1240 101 HOH HOH . G 7 HOH A 41 1241 33 HOH HOH . G 7 HOH A 42 1242 19 HOH HOH . G 7 HOH A 43 1243 73 HOH HOH . G 7 HOH A 44 1244 29 HOH HOH . G 7 HOH A 45 1245 35 HOH HOH . G 7 HOH A 46 1246 125 HOH HOH . G 7 HOH A 47 1247 26 HOH HOH . G 7 HOH A 48 1248 45 HOH HOH . G 7 HOH A 49 1249 4 HOH HOH . G 7 HOH A 50 1250 105 HOH HOH . G 7 HOH A 51 1251 7 HOH HOH . G 7 HOH A 52 1252 12 HOH HOH . G 7 HOH A 53 1253 22 HOH HOH . G 7 HOH A 54 1254 78 HOH HOH . G 7 HOH A 55 1255 46 HOH HOH . G 7 HOH A 56 1256 77 HOH HOH . G 7 HOH A 57 1257 44 HOH HOH . G 7 HOH A 58 1258 34 HOH HOH . G 7 HOH A 59 1259 38 HOH HOH . G 7 HOH A 60 1260 17 HOH HOH . G 7 HOH A 61 1261 71 HOH HOH . G 7 HOH A 62 1262 49 HOH HOH . G 7 HOH A 63 1263 52 HOH HOH . G 7 HOH A 64 1264 130 HOH HOH . G 7 HOH A 65 1265 25 HOH HOH . G 7 HOH A 66 1266 48 HOH HOH . G 7 HOH A 67 1267 74 HOH HOH . G 7 HOH A 68 1268 16 HOH HOH . G 7 HOH A 69 1269 41 HOH HOH . G 7 HOH A 70 1270 68 HOH HOH . G 7 HOH A 71 1271 82 HOH HOH . G 7 HOH A 72 1272 143 HOH HOH . G 7 HOH A 73 1273 111 HOH HOH . G 7 HOH A 74 1274 15 HOH HOH . G 7 HOH A 75 1275 47 HOH HOH . G 7 HOH A 76 1276 31 HOH HOH . G 7 HOH A 77 1277 37 HOH HOH . G 7 HOH A 78 1278 58 HOH HOH . G 7 HOH A 79 1279 136 HOH HOH . G 7 HOH A 80 1280 92 HOH HOH . G 7 HOH A 81 1281 32 HOH HOH . G 7 HOH A 82 1282 54 HOH HOH . G 7 HOH A 83 1283 91 HOH HOH . G 7 HOH A 84 1284 55 HOH HOH . G 7 HOH A 85 1285 59 HOH HOH . G 7 HOH A 86 1286 89 HOH HOH . G 7 HOH A 87 1287 42 HOH HOH . G 7 HOH A 88 1288 28 HOH HOH . G 7 HOH A 89 1289 88 HOH HOH . G 7 HOH A 90 1290 84 HOH HOH . G 7 HOH A 91 1291 85 HOH HOH . G 7 HOH A 92 1292 141 HOH HOH . G 7 HOH A 93 1293 126 HOH HOH . G 7 HOH A 94 1294 39 HOH HOH . G 7 HOH A 95 1295 124 HOH HOH . G 7 HOH A 96 1296 23 HOH HOH . G 7 HOH A 97 1297 21 HOH HOH . G 7 HOH A 98 1298 53 HOH HOH . G 7 HOH A 99 1299 95 HOH HOH . G 7 HOH A 100 1300 104 HOH HOH . G 7 HOH A 101 1301 72 HOH HOH . G 7 HOH A 102 1302 43 HOH HOH . G 7 HOH A 103 1303 138 HOH HOH . G 7 HOH A 104 1304 123 HOH HOH . G 7 HOH A 105 1305 3 HOH HOH . G 7 HOH A 106 1306 90 HOH HOH . G 7 HOH A 107 1307 134 HOH HOH . G 7 HOH A 108 1308 60 HOH HOH . G 7 HOH A 109 1309 76 HOH HOH . G 7 HOH A 110 1310 132 HOH HOH . G 7 HOH A 111 1311 96 HOH HOH . G 7 HOH A 112 1312 13 HOH HOH . G 7 HOH A 113 1313 121 HOH HOH . G 7 HOH A 114 1314 98 HOH HOH . G 7 HOH A 115 1315 86 HOH HOH . G 7 HOH A 116 1316 108 HOH HOH . G 7 HOH A 117 1317 27 HOH HOH . G 7 HOH A 118 1318 40 HOH HOH . G 7 HOH A 119 1319 107 HOH HOH . G 7 HOH A 120 1320 122 HOH HOH . G 7 HOH A 121 1321 120 HOH HOH . G 7 HOH A 122 1322 99 HOH HOH . G 7 HOH A 123 1323 100 HOH HOH . G 7 HOH A 124 1324 57 HOH HOH . G 7 HOH A 125 1325 109 HOH HOH . G 7 HOH A 126 1326 106 HOH HOH . G 7 HOH A 127 1327 129 HOH HOH . G 7 HOH A 128 1328 61 HOH HOH . G 7 HOH A 129 1329 64 HOH HOH . G 7 HOH A 130 1330 62 HOH HOH . G 7 HOH A 131 1331 114 HOH HOH . G 7 HOH A 132 1332 116 HOH HOH . G 7 HOH A 133 1333 127 HOH HOH . G 7 HOH A 134 1334 115 HOH HOH . G 7 HOH A 135 1335 139 HOH HOH . G 7 HOH A 136 1336 63 HOH HOH . G 7 HOH A 137 1337 142 HOH HOH . G 7 HOH A 138 1338 65 HOH HOH . G 7 HOH A 139 1339 66 HOH HOH . G 7 HOH A 140 1340 79 HOH HOH . G 7 HOH A 141 1341 137 HOH HOH . G 7 HOH A 142 1342 112 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 C1 XOB . . . C 3 0.898 18.568 20.211 1 47.69 ? C1 XOB 1102 A 1 HETATM 2 C C2 XOB . . . C 3 2.104 18.816 19.587 1 53.62 ? C2 XOB 1102 A 1 HETATM 3 C C3 XOB . . . C 3 3.283 18.765 20.309 1 53.76 ? C3 XOB 1102 A 1 HETATM 4 C C4 XOB . . . C 3 3.244 18.476 21.666 1 48.1 ? C4 XOB 1102 A 1 HETATM 5 C C5 XOB . . . C 3 2.035 18.208 22.291 1 49.91 ? C5 XOB 1102 A 1 HETATM 6 C C6 XOB . . . C 3 0.858 18.274 21.564 1 52.06 ? C6 XOB 1102 A 1 HETATM 7 O O7 XOB . . . C 3 1.967 17.912 23.636 1 46.27 ? O7 XOB 1102 A 1 HETATM 8 C C8 XOB . . . C 3 3.237 17.527 24.2 1 45.27 ? C8 XOB 1102 A 1 HETATM 9 C C9 XOB . . . C 3 4.324 18.478 23.771 1 47.9 ? C9 XOB 1102 A 1 HETATM 10 O O10 XOB . . . C 3 4.444 18.439 22.341 1 47.6 ? O10 XOB 1102 A 1 HETATM 11 C C11 XOB . . . C 3 5.715 18.12 24.316 1 43.34 ? C11 XOB 1102 A 1 HETATM 12 N N12 XOB . . . C 3 5.867 18.208 25.783 1 42.83 ? N12 XOB 1102 A 1 HETATM 13 C C13 XOB . . . C 3 6.086 19.4 26.428 1 41.16 ? C13 XOB 1102 A 1 HETATM 14 C C14 XOB . . . C 3 6.182 20.752 25.85 1 44.99 ? C14 XOB 1102 A 1 HETATM 15 C C15 XOB . . . C 3 6.403 21.696 26.804 1 44.24 ? C15 XOB 1102 A 1 HETATM 16 S S16 XOB . . . C 3 6.501 21.061 28.402 1 45.1 ? S16 XOB 1102 A 1 HETATM 17 C C17 XOB . . . C 3 6.242 19.442 27.812 1 41.34 ? C17 XOB 1102 A 1 HETATM 18 C C18 XOB . . . C 3 6.183 18.274 28.559 1 37.28 ? C18 XOB 1102 A 1 HETATM 19 O O19 XOB . . . C 3 6.316 18.238 29.779 1 34.3 ? O19 XOB 1102 A 1 HETATM 20 N N20 XOB . . . C 3 5.968 17.105 27.876 1 33.54 ? N20 XOB 1102 A 1 HETATM 21 C C21 XOB . . . C 3 5.809 17.049 26.511 1 38.8 ? C21 XOB 1102 A 1 HETATM 22 O O22 XOB . . . C 3 5.621 15.987 25.939 1 36.93 ? O22 XOB 1102 A 1 HETATM 23 O O23 XOB . . . C 3 5.9 15.916 28.579 1 35.5 ? O23 XOB 1102 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #