data_8HDO # _model_server_result.job_id dTigDODLrCQAFd6y4wKzCw _model_server_result.datetime_utc '2025-07-02 09:49:09' _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 8hdo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":408}' # _entry.id 8HDO # _exptl.entry_id 8HDO _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 379.436 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-[6-azanyl-3,5-dicyano-4-[4-(cyclopropylmethoxy)phenyl]pyridin-2-yl]sulfanylethanamide _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 8HDO _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8HDO _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,H,I,J,K,L,M _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 ? _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 7 _struct_asym.id M _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 E _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 78 _struct_conn.ptnr1_auth_asym_id R _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 78 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id E _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 171 _struct_conn.ptnr2_auth_asym_id R _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 171 _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 2.033 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C19 H17 N5 O2 S' _chem_comp.formula_weight 379.436 _chem_comp.id I5D _chem_comp.mon_nstd_flag . _chem_comp.name 2-[6-azanyl-3,5-dicyano-4-[4-(cyclopropylmethoxy)phenyl]pyridin-2-yl]sulfanylethanamide _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 C15 I5D sing 227 n n C14 C13 I5D sing 228 n n C15 C13 I5D sing 229 n n C13 C12 I5D sing 230 n n OP3 C12 I5D sing 231 n n OP3 C11 I5D sing 232 n n C16 C11 I5D doub 233 n y C16 C17 I5D sing 234 n y C11 C10 I5D sing 235 n y N2 CAA I5D trip 236 n n C17 C4' I5D doub 237 n y C10 C5' I5D doub 238 n y CAA C2' I5D sing 239 n n C4' C5' I5D sing 240 n y C4' C3' I5D sing 241 n n C2' C3' I5D doub 242 n y C2' C1' I5D sing 243 n y C3' C18 I5D sing 244 n y S1 C1' I5D sing 245 n n S1 C5 I5D sing 246 n n C1' N9 I5D doub 247 n y C18 C19 I5D sing 248 n n C18 C8 I5D doub 249 n y C19 N3 I5D trip 250 n n N1 C6 I5D sing 251 n n N9 C8 I5D sing 252 n y C5 C6 I5D sing 253 n n C6 O6 I5D doub 254 n n C8 NAA I5D sing 255 n n N1 H1 I5D sing 256 n n N1 H2 I5D sing 257 n n C5 H3 I5D sing 258 n n C5 H4 I5D sing 259 n n C10 H5 I5D sing 260 n n C13 H6 I5D sing 261 n n C15 H7 I5D sing 262 n n C15 H8 I5D sing 263 n n C17 H9 I5D sing 264 n n C12 H10 I5D sing 265 n n C12 H11 I5D sing 266 n n C14 H12 I5D sing 267 n n C14 H13 I5D sing 268 n n C16 H14 I5D sing 269 n n C5' H15 I5D sing 270 n n NAA H16 I5D sing 271 n n NAA H17 I5D sing 272 n n # _atom_sites.entry_id 8HDO _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 F 6 CLR R 1 401 401 CLR CLR . G 6 CLR R 1 402 402 CLR CLR . H 6 CLR R 1 403 403 CLR CLR . I 6 CLR R 1 404 404 CLR CLR . J 6 CLR R 1 405 405 CLR CLR . K 6 CLR R 1 406 406 CLR CLR . L 6 CLR R 1 407 407 CLR CLR . M 7 I5D R 1 408 396 I5D BAY . # 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 I5D . . . M 7 136.094 131.883 111.492 1 58.1 ? N1 I5D 408 R 1 HETATM 2 N N3 I5D . . . M 7 140.665 129.08 103.825 1 58.1 ? N3 I5D 408 R 1 HETATM 3 C C5 I5D . . . M 7 138.322 130.551 111.355 1 58.1 ? C5 I5D 408 R 1 HETATM 4 C C6 I5D . . . M 7 137.372 131.509 112.095 1 58.1 ? C6 I5D 408 R 1 HETATM 5 C C8 I5D . . . M 7 139.788 130.193 107.104 1 58.1 ? C8 I5D 408 R 1 HETATM 6 C C10 I5D . . . M 7 138.483 125.091 104.262 1 58.1 ? C10 I5D 408 R 1 HETATM 7 C C13 I5D . . . M 7 138.813 123.039 101.47 1 58.1 ? C13 I5D 408 R 1 HETATM 8 C C15 I5D . . . M 7 139.677 122.894 100.207 1 58.1 ? C15 I5D 408 R 1 HETATM 9 C C17 I5D . . . M 7 136.744 127.316 104.689 1 58.1 ? C17 I5D 408 R 1 HETATM 10 C C1' I5D . . . M 7 138.188 129.367 108.624 1 58.1 ? C1' I5D 408 R 1 HETATM 11 C C11 I5D . . . M 7 137.348 125.177 103.582 1 58.1 ? C11 I5D 408 R 1 HETATM 12 C C12 I5D . . . M 7 137.784 124.195 101.464 1 58.1 ? C12 I5D 408 R 1 HETATM 13 C C14 I5D . . . M 7 140.289 123.47 101.491 1 58.1 ? C14 I5D 408 R 1 HETATM 14 C C16 I5D . . . M 7 136.412 126.375 103.811 1 58.1 ? C16 I5D 408 R 1 HETATM 15 C C18 I5D . . . M 7 139.432 129.206 106.187 1 58.1 ? C18 I5D 408 R 1 HETATM 16 C C19 I5D . . . M 7 140.144 129.137 104.832 1 58.1 ? C19 I5D 408 R 1 HETATM 17 C C2' I5D . . . M 7 137.827 128.375 107.71 1 58.1 ? C2' I5D 408 R 1 HETATM 18 C C3' I5D . . . M 7 138.453 128.306 106.498 1 58.1 ? C3' I5D 408 R 1 HETATM 19 C C4' I5D . . . M 7 138.062 127.211 105.477 1 58.1 ? C4' I5D 408 R 1 HETATM 20 C C5' I5D . . . M 7 138.868 126.177 105.278 1 58.1 ? C5' I5D 408 R 1 HETATM 21 C CAA I5D . . . M 7 136.729 127.369 108.067 1 58.1 ? CAA I5D 408 R 1 HETATM 22 N N2 I5D . . . M 7 135.915 126.619 108.324 1 58.1 ? N2 I5D 408 R 1 HETATM 23 N N9 I5D . . . M 7 139.162 130.261 108.31 1 58.1 ? N9 I5D 408 R 1 HETATM 24 N NAA I5D . . . M 7 140.835 131.155 106.768 1 58.1 ? NAA I5D 408 R 1 HETATM 25 O O6 I5D . . . M 7 137.678 131.946 113.157 1 58.1 ? O6 I5D 408 R 1 HETATM 26 O OP3 I5D . . . M 7 137.011 124.165 102.649 1 58.1 ? OP3 I5D 408 R 1 HETATM 27 S S1 I5D . . . M 7 137.355 129.467 110.246 1 58.1 ? S1 I5D 408 R 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 364 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #