data_6NTU # _model_server_result.job_id YX-fKlqcyH3-7LYg3HO0vQ _model_server_result.datetime_utc '2024-11-05 14:46:21' _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 6ntu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1105}' # _entry.id 6NTU # _exptl.entry_id 6NTU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 485.495 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'methyl 2-{4-[4-(7-carbamoyl-1H-benzimidazol-2-yl)benzene-1-carbonyl]piperazin-1-yl}pyrimidine-5-carboxylate' _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 6NTU _cell.length_a 92.662 _cell.length_b 92.662 _cell.length_c 135.341 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6NTU _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _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 _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 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 1 _pdbx_entity_branch_link.entity_branch_list_num_2 2 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 FRU _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B GLC 1 B 1 GLC A 1101 SUC 2 n B FRU 2 B 2 FRU A 1101 SUC # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id C1 _struct_conn.ptnr1_label_comp_id GLC _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id GLC _struct_conn.ptnr1_auth_seq_id 1 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id O2 _struct_conn.ptnr2_label_comp_id FRU _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id FRU _struct_conn.ptnr2_auth_seq_id 2 _struct_conn.ptnr2_symmetry 1_555 _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 1.433 _struct_conn.pdbx_value_order sing # _chem_comp.formula 'C25 H23 N7 O4' _chem_comp.formula_weight 485.495 _chem_comp.id L1S _chem_comp.mon_nstd_flag . _chem_comp.name 'methyl 2-{4-[4-(7-carbamoyl-1H-benzimidazol-2-yl)benzene-1-carbonyl]piperazin-1-yl}pyrimidine-5-carboxylate' _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 C17 C16 L1S doub 267 n y C17 C18 L1S sing 268 n y C16 C14 L1S sing 269 n y C18 C19 L1S doub 270 n y O3 C15 L1S doub 271 n n C14 C15 L1S sing 272 n n C14 C13 L1S doub 273 n y C15 N4 L1S sing 274 n n C19 C13 L1S sing 275 n y C19 N5 L1S sing 276 n y C13 N3 L1S sing 277 n y N5 C12 L1S doub 278 n y N3 C12 L1S sing 279 n y C12 C11 L1S sing 280 n n C11 C20 L1S doub 281 n y C11 C10 L1S sing 282 n y C20 C21 L1S sing 283 n y C10 C9 L1S doub 284 n y C3 N L1S doub 285 n y C3 C2 L1S sing 286 n y O1 C1 L1S doub 287 n n N C4 L1S sing 288 n y C21 C8 L1S doub 289 n y C5 C6 L1S sing 290 n n C5 N1 L1S sing 291 n n C9 C8 L1S sing 292 n y C6 N2 L1S sing 293 n n C8 C7 L1S sing 294 n n C1 C2 L1S sing 295 n n C1 O L1S sing 296 n n C2 C24 L1S doub 297 n y C4 N1 L1S sing 298 n n C4 N6 L1S doub 299 n y N1 C23 L1S sing 300 n n C7 N2 L1S sing 301 n n C7 O2 L1S doub 302 n n N2 C22 L1S sing 303 n n O C L1S sing 304 n n C24 N6 L1S sing 305 n y C23 C22 L1S sing 306 n n C5 H1 L1S sing 307 n n C5 H2 L1S sing 308 n n C6 H3 L1S sing 309 n n C6 H4 L1S sing 310 n n C9 H5 L1S sing 311 n n C10 H6 L1S sing 312 n n N3 H7 L1S sing 313 n n N4 H8 L1S sing 314 n n N4 H9 L1S sing 315 n n C16 H10 L1S sing 316 n n C17 H11 L1S sing 317 n n C18 H12 L1S sing 318 n n C20 H14 L1S sing 319 n n C21 H15 L1S sing 320 n n C22 H16 L1S sing 321 n n C22 H17 L1S sing 322 n n C23 H18 L1S sing 323 n n C23 H19 L1S sing 324 n n C3 H20 L1S sing 325 n n C24 H21 L1S sing 326 n n C H22 L1S sing 327 n n C H23 L1S sing 328 n n C H24 L1S sing 329 n n # _atom_sites.entry_id 6NTU _atom_sites.fract_transf_matrix[1][1] 0.010792 _atom_sites.fract_transf_matrix[1][2] 0.006231 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012461 _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] 0.007389 _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 C 3 DMS A 1 1102 1201 DMS DMS . D 3 DMS A 1 1103 1301 DMS DMS . E 4 1PE A 1 1104 1401 1PE 1PE . F 5 L1S A 1 1105 2000 L1S XXX . G 6 SO4 A 1 1106 1 SO4 SO4 . H 6 SO4 A 1 1107 2 SO4 SO4 . I 7 HOH A 1 1201 88 HOH HOH . I 7 HOH A 2 1202 48 HOH HOH . I 7 HOH A 3 1203 77 HOH HOH . I 7 HOH A 4 1204 54 HOH HOH . I 7 HOH A 5 1205 101 HOH HOH . I 7 HOH A 6 1206 106 HOH HOH . I 7 HOH A 7 1207 9 HOH HOH . I 7 HOH A 8 1208 79 HOH HOH . I 7 HOH A 9 1209 35 HOH HOH . I 7 HOH A 10 1210 80 HOH HOH . I 7 HOH A 11 1211 45 HOH HOH . I 7 HOH A 12 1212 73 HOH HOH . I 7 HOH A 13 1213 92 HOH HOH . I 7 HOH A 14 1214 84 HOH HOH . I 7 HOH A 15 1215 74 HOH HOH . I 7 HOH A 16 1216 36 HOH HOH . I 7 HOH A 17 1217 95 HOH HOH . I 7 HOH A 18 1218 11 HOH HOH . I 7 HOH A 19 1219 56 HOH HOH . I 7 HOH A 20 1220 23 HOH HOH . I 7 HOH A 21 1221 3 HOH HOH . I 7 HOH A 22 1222 14 HOH HOH . I 7 HOH A 23 1223 5 HOH HOH . I 7 HOH A 24 1224 10 HOH HOH . I 7 HOH A 25 1225 70 HOH HOH . I 7 HOH A 26 1226 105 HOH HOH . I 7 HOH A 27 1227 53 HOH HOH . I 7 HOH A 28 1228 15 HOH HOH . I 7 HOH A 29 1229 57 HOH HOH . I 7 HOH A 30 1230 40 HOH HOH . I 7 HOH A 31 1231 61 HOH HOH . I 7 HOH A 32 1232 39 HOH HOH . I 7 HOH A 33 1233 76 HOH HOH . I 7 HOH A 34 1234 7 HOH HOH . I 7 HOH A 35 1235 114 HOH HOH . I 7 HOH A 36 1236 99 HOH HOH . I 7 HOH A 37 1237 62 HOH HOH . I 7 HOH A 38 1238 18 HOH HOH . I 7 HOH A 39 1239 41 HOH HOH . I 7 HOH A 40 1240 113 HOH HOH . I 7 HOH A 41 1241 27 HOH HOH . I 7 HOH A 42 1242 109 HOH HOH . I 7 HOH A 43 1243 50 HOH HOH . I 7 HOH A 44 1244 108 HOH HOH . I 7 HOH A 45 1245 58 HOH HOH . I 7 HOH A 46 1246 112 HOH HOH . I 7 HOH A 47 1247 19 HOH HOH . I 7 HOH A 48 1248 60 HOH HOH . I 7 HOH A 49 1249 102 HOH HOH . I 7 HOH A 50 1250 20 HOH HOH . I 7 HOH A 51 1251 71 HOH HOH . I 7 HOH A 52 1252 49 HOH HOH . I 7 HOH A 53 1253 75 HOH HOH . I 7 HOH A 54 1254 34 HOH HOH . I 7 HOH A 55 1255 16 HOH HOH . I 7 HOH A 56 1256 13 HOH HOH . I 7 HOH A 57 1257 89 HOH HOH . I 7 HOH A 58 1258 22 HOH HOH . I 7 HOH A 59 1259 90 HOH HOH . I 7 HOH A 60 1260 8 HOH HOH . I 7 HOH A 61 1261 2 HOH HOH . I 7 HOH A 62 1262 66 HOH HOH . I 7 HOH A 63 1263 33 HOH HOH . I 7 HOH A 64 1264 94 HOH HOH . I 7 HOH A 65 1265 30 HOH HOH . I 7 HOH A 66 1266 52 HOH HOH . I 7 HOH A 67 1267 12 HOH HOH . I 7 HOH A 68 1268 32 HOH HOH . I 7 HOH A 69 1269 72 HOH HOH . I 7 HOH A 70 1270 28 HOH HOH . I 7 HOH A 71 1271 69 HOH HOH . I 7 HOH A 72 1272 91 HOH HOH . I 7 HOH A 73 1273 37 HOH HOH . I 7 HOH A 74 1274 67 HOH HOH . I 7 HOH A 75 1275 65 HOH HOH . I 7 HOH A 76 1276 4 HOH HOH . I 7 HOH A 77 1277 1 HOH HOH . I 7 HOH A 78 1278 107 HOH HOH . I 7 HOH A 79 1279 24 HOH HOH . I 7 HOH A 80 1280 100 HOH HOH . I 7 HOH A 81 1281 42 HOH HOH . I 7 HOH A 82 1282 63 HOH HOH . I 7 HOH A 83 1283 17 HOH HOH . I 7 HOH A 84 1284 51 HOH HOH . I 7 HOH A 85 1285 64 HOH HOH . I 7 HOH A 86 1286 68 HOH HOH . I 7 HOH A 87 1287 93 HOH HOH . I 7 HOH A 88 1288 38 HOH HOH . I 7 HOH A 89 1289 21 HOH HOH . I 7 HOH A 90 1290 26 HOH HOH . I 7 HOH A 91 1291 98 HOH HOH . I 7 HOH A 92 1292 46 HOH HOH . I 7 HOH A 93 1293 97 HOH HOH . I 7 HOH A 94 1294 25 HOH HOH . I 7 HOH A 95 1295 104 HOH HOH . I 7 HOH A 96 1296 103 HOH HOH . I 7 HOH A 97 1297 96 HOH HOH . I 7 HOH A 98 1298 59 HOH HOH . I 7 HOH A 99 1299 47 HOH HOH . I 7 HOH A 100 1300 110 HOH HOH . I 7 HOH A 101 1301 111 HOH HOH . I 7 HOH A 102 1302 78 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 O3 L1S . . . F 5 0.51 38.252 8.61 1 24.06 ? O3 L1S 1105 A 1 HETATM 2 C C4 L1S . . . F 5 -12.458 43.762 14.005 1 33.14 ? C4 L1S 1105 A 1 HETATM 3 C C5 L1S . . . F 5 -10.503 42.622 12.986 1 35.32 ? C5 L1S 1105 A 1 HETATM 4 C C6 L1S . . . F 5 -9.741 41.423 13.526 1 29.5 ? C6 L1S 1105 A 1 HETATM 5 N N1 L1S . . . F 5 -11.173 43.347 14.071 1 34.36 ? N1 L1S 1105 A 1 HETATM 6 C C7 L1S . . . F 5 -7.521 41.769 14.608 1 27.96 ? C7 L1S 1105 A 1 HETATM 7 C C8 L1S . . . F 5 -6.846 40.894 13.604 1 24.28 ? C8 L1S 1105 A 1 HETATM 8 N N2 L1S . . . F 5 -8.852 41.839 14.61 1 29.55 ? N2 L1S 1105 A 1 HETATM 9 C C9 L1S . . . F 5 -7.213 39.58 13.333 1 23.47 ? C9 L1S 1105 A 1 HETATM 10 C C10 L1S . . . F 5 -6.501 38.831 12.407 1 24.06 ? C10 L1S 1105 A 1 HETATM 11 C C11 L1S . . . F 5 -5.416 39.389 11.734 1 21.82 ? C11 L1S 1105 A 1 HETATM 12 C C12 L1S . . . F 5 -4.605 38.603 10.809 1 22.31 ? C12 L1S 1105 A 1 HETATM 13 N N3 L1S . . . F 5 -3.327 38.847 10.563 1 21.35 ? N3 L1S 1105 A 1 HETATM 14 C C13 L1S . . . F 5 -2.954 37.867 9.656 1 21.86 ? C13 L1S 1105 A 1 HETATM 15 C C14 L1S . . . F 5 -1.716 37.568 9.074 1 21.86 ? C14 L1S 1105 A 1 HETATM 16 C C15 L1S . . . F 5 -0.548 38.488 9.234 1 22.92 ? C15 L1S 1105 A 1 HETATM 17 N N4 L1S . . . F 5 -0.663 39.528 10.071 1 22.29 ? N4 L1S 1105 A 1 HETATM 18 C C16 L1S . . . F 5 -1.608 36.431 8.269 1 23.56 ? C16 L1S 1105 A 1 HETATM 19 C C17 L1S . . . F 5 -2.71 35.627 8.011 1 23.98 ? C17 L1S 1105 A 1 HETATM 20 C C18 L1S . . . F 5 -3.948 35.923 8.554 1 23.71 ? C18 L1S 1105 A 1 HETATM 21 C C19 L1S . . . F 5 -4.038 37.039 9.368 1 23.01 ? C19 L1S 1105 A 1 HETATM 22 N N5 L1S . . . F 5 -5.084 37.539 10.116 1 24.12 ? N5 L1S 1105 A 1 HETATM 23 C C20 L1S . . . F 5 -5.064 40.702 12 1 26.01 ? C20 L1S 1105 A 1 HETATM 24 C C21 L1S . . . F 5 -5.77 41.448 12.92 1 28.46 ? C21 L1S 1105 A 1 HETATM 25 O O2 L1S . . . F 5 -6.852 42.349 15.426 1 28.39 ? O2 L1S 1105 A 1 HETATM 26 C C22 L1S . . . F 5 -9.585 42.479 15.708 1 36.26 ? C22 L1S 1105 A 1 HETATM 27 C C23 L1S . . . F 5 -10.305 43.696 15.199 1 34.17 ? C23 L1S 1105 A 1 HETATM 28 N N L1S . . . F 5 -13.152 43.418 12.911 1 36.96 ? N L1S 1105 A 1 HETATM 29 C C3 L1S . . . F 5 -14.423 43.838 12.874 1 42.31 ? C3 L1S 1105 A 1 HETATM 30 N N6 L1S . . . F 5 -12.92 44.459 15.057 1 40.6 ? N6 L1S 1105 A 1 HETATM 31 C C24 L1S . . . F 5 -14.198 44.84 14.982 1 37.82 ? C24 L1S 1105 A 1 HETATM 32 C C2 L1S . . . F 5 -15.013 44.574 13.893 1 39.5 ? C2 L1S 1105 A 1 HETATM 33 C C1 L1S . . . F 5 -16.433 45.021 13.83 1 44.35 ? C1 L1S 1105 A 1 HETATM 34 O O1 L1S . . . F 5 -17.139 44.863 12.875 1 45.31 ? O1 L1S 1105 A 1 HETATM 35 O O L1S . . . F 5 -16.835 45.608 14.957 1 53 ? O L1S 1105 A 1 HETATM 36 C C L1S . . . F 5 -16.628 47.039 15.054 1 72.77 ? C L1S 1105 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 231 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 36 #