data_6NRF # _model_server_result.job_id NKKhjTbpyX-lh_XTAVUMtA _model_server_result.datetime_utc '2025-02-26 21:34:08' _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 6nrf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1103}' # _entry.id 6NRF # _exptl.entry_id 6NRF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 495.529 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-({4-[4-(1H-benzimidazol-2-yl)piperazine-1-carbonyl]phenyl}methyl)-3-hydroxy-1-benzofuran-7-carboxamide _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 6NRF _cell.length_a 93.39 _cell.length_b 93.39 _cell.length_c 138.213 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6NRF _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 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 _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 104 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 845 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 104 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 845 _struct_conn.ptnr2_symmetry 7_545 _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 2.042 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C28 H25 N5 O4' _chem_comp.formula_weight 495.529 _chem_comp.id KYV _chem_comp.mon_nstd_flag . _chem_comp.name 2-({4-[4-(1H-benzimidazol-2-yl)piperazine-1-carbonyl]phenyl}methyl)-3-hydroxy-1-benzofuran-7-carboxamide _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 O2 C13 KYV doub 202 n n C25 C26 KYV doub 203 n y C25 C12 KYV sing 204 n y C26 C9 KYV sing 205 n y C13 C12 KYV sing 206 n n C13 N1 KYV sing 207 n n C12 C11 KYV doub 208 n y C14 N1 KYV sing 209 n n C14 C15 KYV sing 210 n n N1 C24 KYV sing 211 n n C9 C8 KYV sing 212 n n C9 C10 KYV doub 213 n y O1 C6 KYV sing 214 n n C8 C7 KYV sing 215 n n C11 C10 KYV sing 216 n y C15 N2 KYV sing 217 n n C24 C23 KYV sing 218 n n C6 C7 KYV doub 219 n y C6 C5 KYV sing 220 n y C7 O3 KYV sing 221 n y N2 C23 KYV sing 222 n n N2 C16 KYV sing 223 n n O3 C27 KYV sing 224 n y C5 C4 KYV doub 225 n y C5 C27 KYV sing 226 n y N3 C16 KYV sing 227 n y N3 C17 KYV sing 228 n y C16 N4 KYV doub 229 n y C4 C3 KYV sing 230 n y C27 C1 KYV doub 231 n y C17 C18 KYV doub 232 n y C17 C22 KYV sing 233 n y N4 C22 KYV sing 234 n y C18 C19 KYV sing 235 n y C1 C2 KYV sing 236 n y C1 C KYV sing 237 n n C3 C2 KYV doub 238 n y N C KYV sing 239 n n C22 C21 KYV doub 240 n y C O KYV doub 241 n n C19 C20 KYV doub 242 n y C21 C20 KYV sing 243 n y N3 H1 KYV sing 244 n n C3 H2 KYV sing 245 n n C8 H4 KYV sing 246 n n C8 H5 KYV sing 247 n n C2 H6 KYV sing 248 n n C10 H7 KYV sing 249 n n C4 H8 KYV sing 250 n n C11 H10 KYV sing 251 n n C24 H11 KYV sing 252 n n C24 H12 KYV sing 253 n n C23 H13 KYV sing 254 n n C23 H14 KYV sing 255 n n C21 H15 KYV sing 256 n n C20 H16 KYV sing 257 n n C19 H17 KYV sing 258 n n C18 H18 KYV sing 259 n n C15 H19 KYV sing 260 n n C15 H20 KYV sing 261 n n C14 H21 KYV sing 262 n n C14 H22 KYV sing 263 n n C25 H23 KYV sing 264 n n C26 H24 KYV sing 265 n n N H25 KYV sing 266 n n N H26 KYV sing 267 n n O1 H3 KYV sing 268 n n # _atom_sites.entry_id 6NRF _atom_sites.fract_transf_matrix[1][1] 0.010708 _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] 0.010708 _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] 0.007235 _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 CIT A 1 1101 1101 CIT CIT . C 3 DMS A 1 1102 1 DMS DMS . D 4 KYV A 1 1103 1 KYV 100 . E 5 CL A 1 1104 1 CL CL . F 5 CL A 1 1105 2 CL CL . G 6 HOH A 1 1201 18 HOH HOH . G 6 HOH A 2 1202 25 HOH HOH . G 6 HOH A 3 1203 57 HOH HOH . G 6 HOH A 4 1204 123 HOH HOH . G 6 HOH A 5 1205 145 HOH HOH . G 6 HOH A 6 1206 154 HOH HOH . G 6 HOH A 7 1207 14 HOH HOH . G 6 HOH A 8 1208 158 HOH HOH . G 6 HOH A 9 1209 125 HOH HOH . G 6 HOH A 10 1210 37 HOH HOH . G 6 HOH A 11 1211 12 HOH HOH . G 6 HOH A 12 1212 67 HOH HOH . G 6 HOH A 13 1213 126 HOH HOH . G 6 HOH A 14 1214 101 HOH HOH . G 6 HOH A 15 1215 124 HOH HOH . G 6 HOH A 16 1216 24 HOH HOH . G 6 HOH A 17 1217 53 HOH HOH . G 6 HOH A 18 1218 28 HOH HOH . G 6 HOH A 19 1219 167 HOH HOH . G 6 HOH A 20 1220 82 HOH HOH . G 6 HOH A 21 1221 55 HOH HOH . G 6 HOH A 22 1222 7 HOH HOH . G 6 HOH A 23 1223 6 HOH HOH . G 6 HOH A 24 1224 10 HOH HOH . G 6 HOH A 25 1225 142 HOH HOH . G 6 HOH A 26 1226 17 HOH HOH . G 6 HOH A 27 1227 77 HOH HOH . G 6 HOH A 28 1228 51 HOH HOH . G 6 HOH A 29 1229 81 HOH HOH . G 6 HOH A 30 1230 5 HOH HOH . G 6 HOH A 31 1231 118 HOH HOH . G 6 HOH A 32 1232 22 HOH HOH . G 6 HOH A 33 1233 23 HOH HOH . G 6 HOH A 34 1234 11 HOH HOH . G 6 HOH A 35 1235 36 HOH HOH . G 6 HOH A 36 1236 9 HOH HOH . G 6 HOH A 37 1237 120 HOH HOH . G 6 HOH A 38 1238 122 HOH HOH . G 6 HOH A 39 1239 63 HOH HOH . G 6 HOH A 40 1240 42 HOH HOH . G 6 HOH A 41 1241 131 HOH HOH . G 6 HOH A 42 1242 137 HOH HOH . G 6 HOH A 43 1243 144 HOH HOH . G 6 HOH A 44 1244 147 HOH HOH . G 6 HOH A 45 1245 15 HOH HOH . G 6 HOH A 46 1246 149 HOH HOH . G 6 HOH A 47 1247 4 HOH HOH . G 6 HOH A 48 1248 140 HOH HOH . G 6 HOH A 49 1249 35 HOH HOH . G 6 HOH A 50 1250 54 HOH HOH . G 6 HOH A 51 1251 2 HOH HOH . G 6 HOH A 52 1252 139 HOH HOH . G 6 HOH A 53 1253 45 HOH HOH . G 6 HOH A 54 1254 161 HOH HOH . G 6 HOH A 55 1255 155 HOH HOH . G 6 HOH A 56 1256 60 HOH HOH . G 6 HOH A 57 1257 44 HOH HOH . G 6 HOH A 58 1258 119 HOH HOH . G 6 HOH A 59 1259 46 HOH HOH . G 6 HOH A 60 1260 61 HOH HOH . G 6 HOH A 61 1261 62 HOH HOH . G 6 HOH A 62 1262 1 HOH HOH . G 6 HOH A 63 1263 30 HOH HOH . G 6 HOH A 64 1264 157 HOH HOH . G 6 HOH A 65 1265 163 HOH HOH . G 6 HOH A 66 1266 165 HOH HOH . G 6 HOH A 67 1267 130 HOH HOH . G 6 HOH A 68 1268 65 HOH HOH . G 6 HOH A 69 1269 27 HOH HOH . G 6 HOH A 70 1270 48 HOH HOH . G 6 HOH A 71 1271 16 HOH HOH . G 6 HOH A 72 1272 107 HOH HOH . G 6 HOH A 73 1273 78 HOH HOH . G 6 HOH A 74 1274 84 HOH HOH . G 6 HOH A 75 1275 8 HOH HOH . G 6 HOH A 76 1276 156 HOH HOH . G 6 HOH A 77 1277 64 HOH HOH . G 6 HOH A 78 1278 20 HOH HOH . G 6 HOH A 79 1279 87 HOH HOH . G 6 HOH A 80 1280 88 HOH HOH . G 6 HOH A 81 1281 85 HOH HOH . G 6 HOH A 82 1282 168 HOH HOH . G 6 HOH A 83 1283 132 HOH HOH . G 6 HOH A 84 1284 97 HOH HOH . G 6 HOH A 85 1285 26 HOH HOH . G 6 HOH A 86 1286 141 HOH HOH . G 6 HOH A 87 1287 71 HOH HOH . G 6 HOH A 88 1288 151 HOH HOH . G 6 HOH A 89 1289 127 HOH HOH . G 6 HOH A 90 1290 164 HOH HOH . G 6 HOH A 91 1291 128 HOH HOH . G 6 HOH A 92 1292 136 HOH HOH . G 6 HOH A 93 1293 19 HOH HOH . G 6 HOH A 94 1294 110 HOH HOH . G 6 HOH A 95 1295 146 HOH HOH . G 6 HOH A 96 1296 160 HOH HOH . G 6 HOH A 97 1297 129 HOH HOH . G 6 HOH A 98 1298 152 HOH HOH . G 6 HOH A 99 1299 117 HOH HOH . G 6 HOH A 100 1300 162 HOH HOH . G 6 HOH A 101 1301 159 HOH HOH . G 6 HOH A 102 1302 109 HOH HOH . G 6 HOH A 103 1303 138 HOH HOH . G 6 HOH A 104 1304 106 HOH HOH . G 6 HOH A 105 1305 153 HOH HOH . G 6 HOH A 106 1306 143 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 N N1 KYV . . . D 4 23.133 -11.642 6.669 1 63.83 ? N1 KYV 1103 A 1 HETATM 2 N N3 KYV . . . D 4 20.104 -14.636 9.493 1 84.89 ? N3 KYV 1103 A 1 HETATM 3 C C3 KYV . . . D 4 28.891 -2.678 11.214 1 33.89 ? C3 KYV 1103 A 1 HETATM 4 N N4 KYV . . . D 4 21.801 -14.186 10.878 1 89.61 ? N4 KYV 1103 A 1 HETATM 5 N N2 KYV . . . D 4 21.85 -13.199 8.689 1 76.59 ? N2 KYV 1103 A 1 HETATM 6 C C8 KYV . . . D 4 27.59 -6.897 7.214 1 41.48 ? C8 KYV 1103 A 1 HETATM 7 C C9 KYV . . . D 4 26.477 -7.801 6.942 1 43.56 ? C9 KYV 1103 A 1 HETATM 8 O O1 KYV . . . D 4 29.574 -4.661 7.147 1 38.45 ? O1 KYV 1103 A 1 HETATM 9 C C1 KYV . . . D 4 27.032 -4.231 11.209 1 32.44 ? C1 KYV 1103 A 1 HETATM 10 C C2 KYV . . . D 4 27.784 -3.237 11.84 1 32.06 ? C2 KYV 1103 A 1 HETATM 11 C C10 KYV . . . D 4 25.289 -7.882 7.674 1 44.9 ? C10 KYV 1103 A 1 HETATM 12 C C4 KYV . . . D 4 29.267 -3.089 9.941 1 34.32 ? C4 KYV 1103 A 1 HETATM 13 C C5 KYV . . . D 4 28.531 -4.086 9.301 1 34.74 ? C5 KYV 1103 A 1 HETATM 14 C C6 KYV . . . D 4 28.759 -4.856 8.059 1 35.9 ? C6 KYV 1103 A 1 HETATM 15 C C7 KYV . . . D 4 27.741 -5.91 8.101 1 37.39 ? C7 KYV 1103 A 1 HETATM 16 C C12 KYV . . . D 4 24.442 -9.613 6.22 1 48.53 ? C12 KYV 1103 A 1 HETATM 17 C C11 KYV . . . D 4 24.289 -8.772 7.319 1 44.58 ? C11 KYV 1103 A 1 HETATM 18 O O2 KYV . . . D 4 22.858 -10.514 4.757 1 49.67 ? O2 KYV 1103 A 1 HETATM 19 C C13 KYV . . . D 4 23.402 -10.617 5.834 1 51.68 ? C13 KYV 1103 A 1 HETATM 20 C C24 KYV . . . D 4 23.777 -11.878 7.971 1 65.4 ? C24 KYV 1103 A 1 HETATM 21 C C23 KYV . . . D 4 22.732 -12.082 9.05 1 70.6 ? C23 KYV 1103 A 1 HETATM 22 C C16 KYV . . . D 4 21.25 -14.004 9.649 1 84.16 ? C16 KYV 1103 A 1 HETATM 23 C C22 KYV . . . D 4 20.937 -14.995 11.59 1 86.71 ? C22 KYV 1103 A 1 HETATM 24 C C21 KYV . . . D 4 20.963 -15.489 12.889 1 79.51 ? C21 KYV 1103 A 1 HETATM 25 C C20 KYV . . . D 4 19.907 -16.285 13.31 1 74.07 ? C20 KYV 1103 A 1 HETATM 26 C C19 KYV . . . D 4 18.849 -16.575 12.454 1 79.55 ? C19 KYV 1103 A 1 HETATM 27 C C18 KYV . . . D 4 18.826 -16.076 11.155 1 84.05 ? C18 KYV 1103 A 1 HETATM 28 C C17 KYV . . . D 4 19.884 -15.276 10.72 1 88.57 ? C17 KYV 1103 A 1 HETATM 29 C C15 KYV . . . D 4 21.164 -12.918 7.421 1 73.98 ? C15 KYV 1103 A 1 HETATM 30 C C14 KYV . . . D 4 22.18 -12.701 6.306 1 68.52 ? C14 KYV 1103 A 1 HETATM 31 C C25 KYV . . . D 4 25.613 -9.526 5.476 1 45.63 ? C25 KYV 1103 A 1 HETATM 32 C C26 KYV . . . D 4 26.613 -8.638 5.832 1 44.92 ? C26 KYV 1103 A 1 HETATM 33 O O3 KYV . . . D 4 26.972 -5.752 9.238 1 34.84 ? O3 KYV 1103 A 1 HETATM 34 C C27 KYV . . . D 4 27.449 -4.669 9.953 1 32.91 ? C27 KYV 1103 A 1 HETATM 35 C C KYV . . . D 4 25.785 -4.714 11.886 1 32.11 ? C KYV 1103 A 1 HETATM 36 O O KYV . . . D 4 25.33 -4.095 12.857 1 30.77 ? O KYV 1103 A 1 HETATM 37 N N KYV . . . D 4 25.191 -5.795 11.387 1 30.39 ? N KYV 1103 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 37 #