data_5YJB # _model_server_result.job_id 2BHDax_XadORzLx7daSGBg _model_server_result.datetime_utc '2025-04-09 05:00:28' _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 5yjb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":902}' # _entry.id 5YJB # _exptl.entry_id 5YJB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 383.486 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-[2-(4-methylphenyl)-5-(piperidin-4-ylmethoxy)pyridin-3-yl]benzenecarbonitrile _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 5YJB _cell.length_a 121.144 _cell.length_b 179.624 _cell.length_c 234.953 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YJB _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C25 H25 N3 O' _chem_comp.formula_weight 383.486 _chem_comp.id 8WC _chem_comp.mon_nstd_flag . _chem_comp.name 4-[2-(4-methylphenyl)-5-(piperidin-4-ylmethoxy)pyridin-3-yl]benzenecarbonitrile _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 C C1 8WC sing 1 n n C1 C4 8WC doub 2 n y C1 C2 8WC sing 3 n y C4 C5 8WC sing 4 n y N C13 8WC trip 5 n n C13 C12 8WC sing 6 n n C2 C3 8WC doub 7 n y C5 C6 8WC doub 8 n y C12 C14 8WC doub 9 n y C12 C11 8WC sing 10 n y C14 C15 8WC sing 11 n y C11 C10 8WC doub 12 n y C3 C6 8WC sing 13 n y C6 C7 8WC sing 14 n n C15 C9 8WC doub 15 n y C10 C9 8WC sing 16 n y C9 C8 8WC sing 17 n n C7 C8 8WC doub 18 n y C7 N2 8WC sing 19 n y C8 C16 8WC sing 20 n y N2 C24 8WC doub 21 n y C16 C17 8WC doub 22 n y C24 C17 8WC sing 23 n y C17 O 8WC sing 24 n n O C18 8WC sing 25 n n C19 C18 8WC sing 26 n n C19 C23 8WC sing 27 n n C19 C20 8WC sing 28 n n C21 C20 8WC sing 29 n n C21 N1 8WC sing 30 n n C22 C23 8WC sing 31 n n C22 N1 8WC sing 32 n n C4 H1 8WC sing 33 n n C5 H2 8WC sing 34 n n N1 H3 8WC sing 35 n n C10 H5 8WC sing 36 n n C11 H6 8WC sing 37 n n C14 H7 8WC sing 38 n n C15 H8 8WC sing 39 n n C H9 8WC sing 40 n n C H10 8WC sing 41 n n C H11 8WC sing 42 n n C16 H12 8WC sing 43 n n C18 H13 8WC sing 44 n n C18 H14 8WC sing 45 n n C19 H15 8WC sing 46 n n C2 H16 8WC sing 47 n n C20 H17 8WC sing 48 n n C20 H18 8WC sing 49 n n C21 H19 8WC sing 50 n n C21 H20 8WC sing 51 n n C22 H21 8WC sing 52 n n C22 H22 8WC sing 53 n n C23 H23 8WC sing 54 n n C23 H24 8WC sing 55 n n C24 H25 8WC sing 56 n n C3 H26 8WC sing 57 n n # _atom_sites.entry_id 5YJB _atom_sites.fract_transf_matrix[1][1] 0.008255 _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] 0.005567 _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] 0.004256 _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 FAD A 1 901 901 FAD FAD . D 4 8WC A 1 902 902 8WC XXX . E 5 GOL A 1 903 903 GOL GOL . F 5 GOL A 1 904 904 GOL GOL . # 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 C4 8WC . . . D 4 7.272 -51.226 -39.955 1 66.36 ? C4 8WC 902 A 1 HETATM 2 C C5 8WC . . . D 4 6.626 -51.432 -38.752 1 74.78 ? C5 8WC 902 A 1 HETATM 3 C C6 8WC . . . D 4 7.258 -51.149 -37.538 1 79.61 ? C6 8WC 902 A 1 HETATM 4 N N1 8WC . . . D 4 -0.078 -53.17 -31.102 1 75.02 ? N1 8WC 902 A 1 HETATM 5 C C7 8WC . . . D 4 6.633 -51.535 -36.241 1 83.85 ? C7 8WC 902 A 1 HETATM 6 C C8 8WC . . . D 4 6.307 -52.875 -35.913 1 70.58 ? C8 8WC 902 A 1 HETATM 7 N N2 8WC . . . D 4 6.325 -50.509 -35.431 1 91.93 ? N2 8WC 902 A 1 HETATM 8 C C9 8WC . . . D 4 6.689 -54.057 -36.734 1 59.03 ? C9 8WC 902 A 1 HETATM 9 C C10 8WC . . . D 4 5.728 -54.997 -37.114 1 56 ? C10 8WC 902 A 1 HETATM 10 C C11 8WC . . . D 4 6.071 -56.116 -37.853 1 55.86 ? C11 8WC 902 A 1 HETATM 11 C C12 8WC . . . D 4 7.395 -56.317 -38.246 1 49.24 ? C12 8WC 902 A 1 HETATM 12 C C13 8WC . . . D 4 7.736 -57.439 -39.086 1 53 ? C13 8WC 902 A 1 HETATM 13 C C14 8WC . . . D 4 8.368 -55.386 -37.874 1 47.32 ? C14 8WC 902 A 1 HETATM 14 C C15 8WC . . . D 4 8.014 -54.272 -37.127 1 48.53 ? C15 8WC 902 A 1 HETATM 15 N N 8WC . . . D 4 7.972 -58.332 -39.763 1 54.28 ? N 8WC 902 A 1 HETATM 16 C C 8WC . . . D 4 9.242 -50.447 -41.325 1 76.92 ? C 8WC 902 A 1 HETATM 17 O O 8WC . . . D 4 4.555 -52.067 -32.74 1 68.78 ? O 8WC 902 A 1 HETATM 18 C C1 8WC . . . D 4 8.558 -50.715 -40.005 1 73.85 ? C1 8WC 902 A 1 HETATM 19 C C16 8WC . . . D 4 5.59 -53.092 -34.737 1 73.46 ? C16 8WC 902 A 1 HETATM 20 C C17 8WC . . . D 4 5.26 -52.022 -33.925 1 76.05 ? C17 8WC 902 A 1 HETATM 21 C C18 8WC . . . D 4 4.076 -53.321 -32.238 1 60.5 ? C18 8WC 902 A 1 HETATM 22 C C19 8WC . . . D 4 2.568 -53.263 -32.252 1 55.28 ? C19 8WC 902 A 1 HETATM 23 C C2 8WC . . . D 4 9.182 -50.41 -38.803 1 67.71 ? C2 8WC 902 A 1 HETATM 24 C C20 8WC . . . D 4 1.958 -54.474 -31.566 1 64.42 ? C20 8WC 902 A 1 HETATM 25 C C21 8WC . . . D 4 0.449 -54.401 -31.714 1 77.34 ? C21 8WC 902 A 1 HETATM 26 C C22 8WC . . . D 4 0.532 -51.985 -31.71 1 65.36 ? C22 8WC 902 A 1 HETATM 27 C C23 8WC . . . D 4 2.043 -52.013 -31.572 1 49.03 ? C23 8WC 902 A 1 HETATM 28 C C24 8WC . . . D 4 5.655 -50.756 -34.298 1 87.94 ? C24 8WC 902 A 1 HETATM 29 C C3 8WC . . . D 4 8.541 -50.613 -37.593 1 69.84 ? C3 8WC 902 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 29 #