data_6NRI # _model_server_result.job_id qVto7Ge7JP6KvsZYvMEg5g _model_server_result.datetime_utc '2025-01-25 11:06:30' _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 6nri # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1101}' # _entry.id 6NRI # _exptl.entry_id 6NRI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 455.465 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2Z)-2-{[4-(3-cyclopropyl-5,6-dihydro[1,2,4]triazolo[4,3-a]pyrazine-7(8H)-carbonyl)phenyl]methylidene}-3-oxo-2,3-dihydro-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 6NRI _cell.length_a 92.616 _cell.length_b 92.616 _cell.length_c 142.072 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6NRI _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 _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 2 _struct_asym.id B _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 2.034 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C25 H21 N5 O4' _chem_comp.formula_weight 455.465 _chem_comp.id KYM _chem_comp.mon_nstd_flag . _chem_comp.name (2Z)-2-{[4-(3-cyclopropyl-5,6-dihydro[1,2,4]triazolo[4,3-a]pyrazine-7(8H)-carbonyl)phenyl]methylidene}-3-oxo-2,3-dihydro-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 C14 N1 KYM sing 202 n n C14 C15 KYM sing 203 n n C11 C10 KYM doub 204 n y C11 C12 KYM sing 205 n y O2 C13 KYM doub 206 n n N1 C13 KYM sing 207 n n N1 C17 KYM sing 208 n n C10 C9 KYM sing 209 n y C15 N2 KYM sing 210 n n C13 C12 KYM sing 211 n n C17 C16 KYM sing 212 n n C12 C22 KYM doub 213 n y C9 C8 KYM sing 214 n n C9 C23 KYM doub 215 n y N2 C16 KYM sing 216 n y N2 C18 KYM sing 217 n y O1 C6 KYM doub 218 n n C8 C7 KYM doub 219 z n C16 N3 KYM doub 220 n y C22 C23 KYM sing 221 n y C21 C19 KYM sing 222 n n C21 C20 KYM sing 223 n n C6 C7 KYM sing 224 n n C6 C5 KYM sing 225 n n C7 O3 KYM sing 226 n n C18 C19 KYM sing 227 n n C18 N4 KYM doub 228 n y N3 N4 KYM sing 229 n y C19 C20 KYM sing 230 n n C5 C4 KYM doub 231 n y C5 C24 KYM sing 232 n y O3 C24 KYM sing 233 n n C4 C3 KYM sing 234 n y C24 C1 KYM doub 235 n y C3 C2 KYM doub 236 n y C1 C2 KYM sing 237 n y C1 C KYM sing 238 n n N C KYM sing 239 n n C O KYM doub 240 n n C17 H1 KYM sing 241 n n C17 H2 KYM sing 242 n n C19 H3 KYM sing 243 n n C21 H4 KYM sing 244 n n C21 H5 KYM sing 245 n n C20 H6 KYM sing 246 n n C20 H7 KYM sing 247 n n C15 H8 KYM sing 248 n n C15 H9 KYM sing 249 n n C14 H10 KYM sing 250 n n C14 H11 KYM sing 251 n n C11 H12 KYM sing 252 n n C10 H13 KYM sing 253 n n C22 H14 KYM sing 254 n n C23 H15 KYM sing 255 n n C8 H16 KYM sing 256 n n N H17 KYM sing 257 n n N H18 KYM sing 258 n n C4 H19 KYM sing 259 n n C3 H20 KYM sing 260 n n C2 H21 KYM sing 261 n n # _atom_sites.entry_id 6NRI _atom_sites.fract_transf_matrix[1][1] 0.010797 _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] 0.010797 _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] 0.007039 _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 KYM A 1 1101 1 KYM T71 . C 3 CIT A 1 1102 2 CIT CIT . D 4 DMS A 1 1103 1101 DMS DMS . E 5 CL A 1 1104 1 CL CL . F 6 HOH A 1 1201 18 HOH HOH . F 6 HOH A 2 1202 22 HOH HOH . F 6 HOH A 3 1203 24 HOH HOH . F 6 HOH A 4 1204 35 HOH HOH . F 6 HOH A 5 1205 55 HOH HOH . F 6 HOH A 6 1206 37 HOH HOH . F 6 HOH A 7 1207 9 HOH HOH . F 6 HOH A 8 1208 48 HOH HOH . F 6 HOH A 9 1209 54 HOH HOH . F 6 HOH A 10 1210 13 HOH HOH . F 6 HOH A 11 1211 12 HOH HOH . F 6 HOH A 12 1212 28 HOH HOH . F 6 HOH A 13 1213 41 HOH HOH . F 6 HOH A 14 1214 42 HOH HOH . F 6 HOH A 15 1215 6 HOH HOH . F 6 HOH A 16 1216 5 HOH HOH . F 6 HOH A 17 1217 11 HOH HOH . F 6 HOH A 18 1218 8 HOH HOH . F 6 HOH A 19 1219 17 HOH HOH . F 6 HOH A 20 1220 14 HOH HOH . F 6 HOH A 21 1221 21 HOH HOH . F 6 HOH A 22 1222 1 HOH HOH . F 6 HOH A 23 1223 25 HOH HOH . F 6 HOH A 24 1224 32 HOH HOH . F 6 HOH A 25 1225 31 HOH HOH . F 6 HOH A 26 1226 4 HOH HOH . F 6 HOH A 27 1227 47 HOH HOH . F 6 HOH A 28 1228 2 HOH HOH . F 6 HOH A 29 1229 7 HOH HOH . F 6 HOH A 30 1230 33 HOH HOH . F 6 HOH A 31 1231 16 HOH HOH . F 6 HOH A 32 1232 57 HOH HOH . F 6 HOH A 33 1233 43 HOH HOH . F 6 HOH A 34 1234 10 HOH HOH . F 6 HOH A 35 1235 56 HOH HOH . F 6 HOH A 36 1236 40 HOH HOH . F 6 HOH A 37 1237 19 HOH HOH . F 6 HOH A 38 1238 51 HOH HOH . F 6 HOH A 39 1239 29 HOH HOH . F 6 HOH A 40 1240 15 HOH HOH . F 6 HOH A 41 1241 30 HOH HOH . F 6 HOH A 42 1242 20 HOH HOH . F 6 HOH A 43 1243 53 HOH HOH . F 6 HOH A 44 1244 38 HOH HOH . F 6 HOH A 45 1245 39 HOH HOH . F 6 HOH A 46 1246 26 HOH HOH . F 6 HOH A 47 1247 58 HOH HOH . F 6 HOH A 48 1248 27 HOH HOH . F 6 HOH A 49 1249 23 HOH HOH . F 6 HOH A 50 1250 36 HOH HOH . F 6 HOH A 51 1251 46 HOH HOH . F 6 HOH A 52 1252 44 HOH HOH . F 6 HOH A 53 1253 50 HOH HOH . F 6 HOH A 54 1254 52 HOH HOH . F 6 HOH A 55 1255 34 HOH HOH . F 6 HOH A 56 1256 49 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 O2 KYM . . . B 2 21.165 -9.711 6.774 1 81.77 ? O2 KYM 1101 A 1 HETATM 2 C C13 KYM . . . B 2 22.174 -10.325 7.06 1 84.77 ? C13 KYM 1101 A 1 HETATM 3 N N1 KYM . . . B 2 22.282 -11.654 6.852 1 104.67 ? N1 KYM 1101 A 1 HETATM 4 C C17 KYM . . . B 2 23.354 -12.469 7.421 1 105.93 ? C17 KYM 1101 A 1 HETATM 5 C C16 KYM . . . B 2 22.569 -13.093 8.539 1 111.66 ? C16 KYM 1101 A 1 HETATM 6 N N3 KYM . . . B 2 22.934 -13.284 9.783 1 113.51 ? N3 KYM 1101 A 1 HETATM 7 N N4 KYM . . . B 2 21.853 -13.873 10.439 1 113.97 ? N4 KYM 1101 A 1 HETATM 8 C C18 KYM . . . B 2 20.888 -14.013 9.556 1 113.5 ? C18 KYM 1101 A 1 HETATM 9 C C19 KYM . . . B 2 19.547 -14.633 9.809 1 105.21 ? C19 KYM 1101 A 1 HETATM 10 C C21 KYM . . . B 2 19.063 -15.745 8.916 1 103.2 ? C21 KYM 1101 A 1 HETATM 11 C C20 KYM . . . B 2 19.423 -16.044 10.319 1 101.24 ? C20 KYM 1101 A 1 HETATM 12 N N2 KYM . . . B 2 21.282 -13.526 8.331 1 118.3 ? N2 KYM 1101 A 1 HETATM 13 C C15 KYM . . . B 2 20.558 -13.418 7.046 1 112.98 ? C15 KYM 1101 A 1 HETATM 14 C C14 KYM . . . B 2 21.282 -12.442 6.116 1 109.83 ? C14 KYM 1101 A 1 HETATM 15 C C12 KYM . . . B 2 23.38 -9.565 7.511 1 74.74 ? C12 KYM 1101 A 1 HETATM 16 C C11 KYM . . . B 2 24.494 -9.519 6.677 1 69.04 ? C11 KYM 1101 A 1 HETATM 17 C C10 KYM . . . B 2 25.605 -8.774 7.023 1 61.81 ? C10 KYM 1101 A 1 HETATM 18 C C22 KYM . . . B 2 23.415 -8.851 8.706 1 65.03 ? C22 KYM 1101 A 1 HETATM 19 C C23 KYM . . . B 2 24.521 -8.088 9.041 1 59.16 ? C23 KYM 1101 A 1 HETATM 20 C C9 KYM . . . B 2 25.636 -8.021 8.198 1 57.83 ? C9 KYM 1101 A 1 HETATM 21 C C8 KYM . . . B 2 26.836 -7.216 8.387 1 55.84 ? C8 KYM 1101 A 1 HETATM 22 C C7 KYM . . . B 2 27.169 -6.32 9.319 1 54.45 ? C7 KYM 1101 A 1 HETATM 23 C C6 KYM . . . B 2 28.286 -5.378 9.248 1 52 ? C6 KYM 1101 A 1 HETATM 24 O O1 KYM . . . B 2 29.125 -5.302 8.351 1 54.91 ? O1 KYM 1101 A 1 HETATM 25 O O3 KYM . . . B 2 26.437 -6.07 10.464 1 47.4 ? O3 KYM 1101 A 1 HETATM 26 C C24 KYM . . . B 2 27.019 -5.017 11.144 1 45.57 ? C24 KYM 1101 A 1 HETATM 27 C C1 KYM . . . B 2 26.663 -4.474 12.383 1 43.17 ? C1 KYM 1101 A 1 HETATM 28 C C KYM . . . B 2 25.504 -4.928 13.207 1 45.57 ? C KYM 1101 A 1 HETATM 29 O O KYM . . . B 2 25.167 -4.269 14.205 1 43.16 ? O KYM 1101 A 1 HETATM 30 N N KYM . . . B 2 24.87 -6.042 12.831 1 43.91 ? N KYM 1101 A 1 HETATM 31 C C5 KYM . . . B 2 28.136 -4.549 10.463 1 47.98 ? C5 KYM 1101 A 1 HETATM 32 C C4 KYM . . . B 2 28.923 -3.546 11.02 1 46.36 ? C4 KYM 1101 A 1 HETATM 33 C C3 KYM . . . B 2 28.578 -3.011 12.25 1 44.45 ? C3 KYM 1101 A 1 HETATM 34 C C2 KYM . . . B 2 27.457 -3.46 12.921 1 43.76 ? C2 KYM 1101 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 34 #