data_5CGD # _model_server_result.job_id utB8mnlY20fs5RmwJ6C8SQ _model_server_result.datetime_utc '2025-08-16 06:52:12' _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 5cgd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":4005}' # _entry.id 5CGD # _exptl.entry_id 5CGD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 310.713 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-chloro-5-[6-(5-fluoropyridin-2-yl)pyrimidin-4-yl]benzonitrile _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 98.97 _cell.angle_gamma 90 _cell.entry_id 5CGD _cell.length_a 143.574 _cell.length_b 43.727 _cell.length_c 81.862 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CGD _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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 3 _struct_asym.id F _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 79 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 644 _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 328 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 733 _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 'C16 H8 Cl F N4' _chem_comp.formula_weight 310.713 _chem_comp.id 51E _chem_comp.mon_nstd_flag . _chem_comp.name 3-chloro-5-[6-(5-fluoropyridin-2-yl)pyrimidin-4-yl]benzonitrile _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 F1 C1 51E sing 1 n n C1 C5 51E doub 2 n y C1 C2 51E sing 3 n y C5 N1 51E sing 4 n y C2 C3 51E doub 5 n y N1 C4 51E doub 6 n y C3 C4 51E sing 7 n y C4 C10 51E sing 8 n n C10 C9 51E doub 9 n y C10 N11 51E sing 10 n y C9 C8 51E sing 11 n y N11 C12 51E doub 12 n y C8 C7 51E sing 13 n n C8 N13 51E doub 14 n y C01 C7 51E doub 15 n y C01 C02 51E sing 16 n y CL C02 51E sing 17 n n C12 N13 51E sing 18 n y C7 C6 51E sing 19 n y C02 C03 51E doub 20 n y C6 C04 51E doub 21 n y C03 C04 51E sing 22 n y C04 C19 51E sing 23 n n C19 N20 51E trip 24 n n C01 H1 51E sing 25 n n C03 H2 51E sing 26 n n C6 H3 51E sing 27 n n C9 H4 51E sing 28 n n C12 H5 51E sing 29 n n C2 H6 51E sing 30 n n C3 H7 51E sing 31 n n C5 H8 51E sing 32 n n # _atom_sites.entry_id 5CGD _atom_sites.fract_transf_matrix[1][1] 0.006965 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001099 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022869 _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] 0.012367 _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 OLA A 1 4001 4001 OLA OLA . C 2 OLA A 1 4002 4002 OLA OLA . D 2 OLA A 1 4003 4003 OLA OLA . E 2 OLA A 1 4004 4004 OLA OLA . F 3 51E A 1 4005 911 51E 142 . G 4 HOH A 1 4101 15 HOH HOH . G 4 HOH A 2 4102 4141 HOH HOH . G 4 HOH A 3 4103 4120 HOH HOH . G 4 HOH A 4 4104 4132 HOH HOH . G 4 HOH A 5 4105 4121 HOH HOH . G 4 HOH A 6 4106 4135 HOH HOH . G 4 HOH A 7 4107 4140 HOH HOH . G 4 HOH A 8 4108 4109 HOH HOH . G 4 HOH A 9 4109 14 HOH HOH . G 4 HOH A 10 4110 2 HOH HOH . G 4 HOH A 11 4111 4 HOH HOH . G 4 HOH A 12 4112 4131 HOH HOH . G 4 HOH A 13 4113 4107 HOH HOH . G 4 HOH A 14 4114 13 HOH HOH . G 4 HOH A 15 4115 1 HOH HOH . G 4 HOH A 16 4116 6 HOH HOH . G 4 HOH A 17 4117 4125 HOH HOH . G 4 HOH A 18 4118 4124 HOH HOH . G 4 HOH A 19 4119 21 HOH HOH . G 4 HOH A 20 4120 4138 HOH HOH . G 4 HOH A 21 4121 5 HOH HOH . G 4 HOH A 22 4122 4122 HOH HOH . G 4 HOH A 23 4123 7 HOH HOH . G 4 HOH A 24 4124 22 HOH HOH . G 4 HOH A 25 4125 4123 HOH HOH . G 4 HOH A 26 4126 4137 HOH HOH . G 4 HOH A 27 4127 30 HOH HOH . G 4 HOH A 28 4128 4112 HOH HOH . G 4 HOH A 29 4129 17 HOH HOH . G 4 HOH A 30 4130 16 HOH HOH . G 4 HOH A 31 4131 4106 HOH HOH . G 4 HOH A 32 4132 4134 HOH HOH . G 4 HOH A 33 4133 28 HOH HOH . G 4 HOH A 34 4134 19 HOH HOH . G 4 HOH A 35 4135 12 HOH HOH . G 4 HOH A 36 4136 4145 HOH HOH . G 4 HOH A 37 4137 4133 HOH HOH . G 4 HOH A 38 4138 29 HOH HOH . G 4 HOH A 39 4139 4104 HOH HOH . G 4 HOH A 40 4140 4103 HOH HOH . G 4 HOH A 41 4141 4108 HOH HOH . G 4 HOH A 42 4142 4128 HOH HOH . G 4 HOH A 43 4143 26 HOH HOH . G 4 HOH A 44 4144 9 HOH HOH . G 4 HOH A 45 4145 25 HOH HOH . G 4 HOH A 46 4146 4127 HOH HOH . G 4 HOH A 47 4147 4146 HOH HOH . G 4 HOH A 48 4148 4114 HOH HOH . G 4 HOH A 49 4149 4110 HOH HOH . G 4 HOH A 50 4150 4115 HOH HOH . G 4 HOH A 51 4151 4111 HOH HOH . G 4 HOH A 52 4152 4129 HOH HOH . G 4 HOH A 53 4153 18 HOH HOH . G 4 HOH A 54 4154 3 HOH HOH . G 4 HOH A 55 4155 4130 HOH HOH . G 4 HOH A 56 4156 4118 HOH HOH . G 4 HOH A 57 4157 4105 HOH HOH . G 4 HOH A 58 4158 24 HOH HOH . G 4 HOH A 59 4159 20 HOH HOH . G 4 HOH A 60 4160 23 HOH HOH . G 4 HOH A 61 4161 27 HOH HOH . G 4 HOH A 62 4162 11 HOH HOH . G 4 HOH A 63 4163 10 HOH HOH . G 4 HOH A 64 4164 4139 HOH HOH . G 4 HOH A 65 4165 8 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 C C01 51E . . . F 3 -24.014 17.911 44.231 1 22.23 ? C01 51E 4005 A 1 HETATM 2 C C02 51E . . . F 3 -23.617 19.134 44.801 1 21.81 ? C02 51E 4005 A 1 HETATM 3 C C03 51E . . . F 3 -22.643 19.157 45.811 1 23.81 ? C03 51E 4005 A 1 HETATM 4 C C04 51E . . . F 3 -22.063 17.951 46.251 1 25.04 ? C04 51E 4005 A 1 HETATM 5 C C6 51E . . . F 3 -22.465 16.728 45.675 1 24.9 ? C6 51E 4005 A 1 HETATM 6 C C7 51E . . . F 3 -23.451 16.689 44.66 1 23.61 ? C7 51E 4005 A 1 HETATM 7 C C8 51E . . . F 3 -23.871 15.412 44.047 1 22.89 ? C8 51E 4005 A 1 HETATM 8 C C9 51E . . . F 3 -24.222 15.32 42.701 1 21.85 ? C9 51E 4005 A 1 HETATM 9 C C10 51E . . . F 3 -24.606 14.064 42.216 1 25.41 ? C10 51E 4005 A 1 HETATM 10 N N11 51E . . . F 3 -24.621 12.994 43.033 1 26.71 ? N11 51E 4005 A 1 HETATM 11 C C12 51E . . . F 3 -24.271 13.183 44.292 1 25.44 ? C12 51E 4005 A 1 HETATM 12 N N13 51E . . . F 3 -23.898 14.329 44.839 1 24.22 ? N13 51E 4005 A 1 HETATM 13 C C19 51E . . . F 3 -21.053 17.971 47.296 1 25.34 ? C19 51E 4005 A 1 HETATM 14 N N20 51E . . . F 3 -20.251 17.988 48.127 1 31.34 ? N20 51E 4005 A 1 HETATM 15 CL CL 51E . . . F 3 -24.333 20.607 44.256 1 19.88 ? CL 51E 4005 A 1 HETATM 16 C C1 51E . . . F 3 -25.697 13.679 38.125 1 26.64 ? C1 51E 4005 A 1 HETATM 17 C C2 51E . . . F 3 -25.492 12.498 38.86 1 26.54 ? C2 51E 4005 A 1 HETATM 18 C C3 51E . . . F 3 -25.131 12.583 40.213 1 24.93 ? C3 51E 4005 A 1 HETATM 19 C C4 51E . . . F 3 -24.991 13.861 40.796 1 24.83 ? C4 51E 4005 A 1 HETATM 20 N N1 51E . . . F 3 -25.186 14.994 40.08 1 24.73 ? N1 51E 4005 A 1 HETATM 21 C C5 51E . . . F 3 -25.532 14.908 38.781 1 22.85 ? C5 51E 4005 A 1 HETATM 22 F F1 51E . . . F 3 -26.045 13.638 36.817 1 28.94 ? F1 51E 4005 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 498 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 22 #