data_6DBK # _model_server_result.job_id lH_HSJBIW5clg6WBIZ_EXA _model_server_result.datetime_utc '2024-10-20 01:32:03' _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 6dbk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":4000}' # _entry.id 6DBK # _exptl.entry_id 6DBK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 405.453 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-({4-[(1S,4S)-5-(cyanoacetyl)-2,5-diazabicyclo[2.2.1]heptan-2-yl]pyrimidin-2-yl}amino)-N-ethylbenzamide _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 6DBK _cell.length_a 36.483 _cell.length_b 73.139 _cell.length_c 103.026 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DBK _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order covale ? covale1 A C GLU 189 A GLU 1053 1_555 A N PTR 190 A PTR 1054 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C PTR 190 A PTR 1054 1_555 A N TYR 191 A TYR 1055 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? # _chem_comp.formula 'C21 H23 N7 O2' _chem_comp.formula_weight 405.453 _chem_comp.id G5D _chem_comp.mon_nstd_flag . _chem_comp.name 4-({4-[(1S,4S)-5-(cyanoacetyl)-2,5-diazabicyclo[2.2.1]heptan-2-yl]pyrimidin-2-yl}amino)-N-ethylbenzamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 6DBK _atom_sites.fract_transf_matrix[1][1] 0.02741 _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] 0.013673 _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] 0.009706 _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 G5D A 1 4000 4000 G5D PFE . C 3 HOH A 1 4101 132 HOH HOH . C 3 HOH A 2 4102 192 HOH HOH . C 3 HOH A 3 4103 138 HOH HOH . C 3 HOH A 4 4104 186 HOH HOH . C 3 HOH A 5 4105 185 HOH HOH . C 3 HOH A 6 4106 204 HOH HOH . C 3 HOH A 7 4107 116 HOH HOH . C 3 HOH A 8 4108 154 HOH HOH . C 3 HOH A 9 4109 131 HOH HOH . C 3 HOH A 10 4110 15 HOH HOH . C 3 HOH A 11 4111 76 HOH HOH . C 3 HOH A 12 4112 177 HOH HOH . C 3 HOH A 13 4113 42 HOH HOH . C 3 HOH A 14 4114 113 HOH HOH . C 3 HOH A 15 4115 24 HOH HOH . C 3 HOH A 16 4116 41 HOH HOH . C 3 HOH A 17 4117 3 HOH HOH . C 3 HOH A 18 4118 189 HOH HOH . C 3 HOH A 19 4119 25 HOH HOH . C 3 HOH A 20 4120 127 HOH HOH . C 3 HOH A 21 4121 180 HOH HOH . C 3 HOH A 22 4122 46 HOH HOH . C 3 HOH A 23 4123 36 HOH HOH . C 3 HOH A 24 4124 9 HOH HOH . C 3 HOH A 25 4125 187 HOH HOH . C 3 HOH A 26 4126 206 HOH HOH . C 3 HOH A 27 4127 164 HOH HOH . C 3 HOH A 28 4128 194 HOH HOH . C 3 HOH A 29 4129 115 HOH HOH . C 3 HOH A 30 4130 18 HOH HOH . C 3 HOH A 31 4131 12 HOH HOH . C 3 HOH A 32 4132 198 HOH HOH . C 3 HOH A 33 4133 80 HOH HOH . C 3 HOH A 34 4134 53 HOH HOH . C 3 HOH A 35 4135 38 HOH HOH . C 3 HOH A 36 4136 168 HOH HOH . C 3 HOH A 37 4137 193 HOH HOH . C 3 HOH A 38 4138 141 HOH HOH . C 3 HOH A 39 4139 124 HOH HOH . C 3 HOH A 40 4140 66 HOH HOH . C 3 HOH A 41 4141 157 HOH HOH . C 3 HOH A 42 4142 83 HOH HOH . C 3 HOH A 43 4143 196 HOH HOH . C 3 HOH A 44 4144 60 HOH HOH . C 3 HOH A 45 4145 71 HOH HOH . C 3 HOH A 46 4146 191 HOH HOH . C 3 HOH A 47 4147 72 HOH HOH . C 3 HOH A 48 4148 202 HOH HOH . C 3 HOH A 49 4149 50 HOH HOH . C 3 HOH A 50 4150 149 HOH HOH . C 3 HOH A 51 4151 34 HOH HOH . C 3 HOH A 52 4152 55 HOH HOH . C 3 HOH A 53 4153 32 HOH HOH . C 3 HOH A 54 4154 78 HOH HOH . C 3 HOH A 55 4155 20 HOH HOH . C 3 HOH A 56 4156 122 HOH HOH . C 3 HOH A 57 4157 99 HOH HOH . C 3 HOH A 58 4158 8 HOH HOH . C 3 HOH A 59 4159 197 HOH HOH . C 3 HOH A 60 4160 7 HOH HOH . C 3 HOH A 61 4161 179 HOH HOH . C 3 HOH A 62 4162 23 HOH HOH . C 3 HOH A 63 4163 91 HOH HOH . C 3 HOH A 64 4164 146 HOH HOH . C 3 HOH A 65 4165 111 HOH HOH . C 3 HOH A 66 4166 62 HOH HOH . C 3 HOH A 67 4167 26 HOH HOH . C 3 HOH A 68 4168 205 HOH HOH . C 3 HOH A 69 4169 37 HOH HOH . C 3 HOH A 70 4170 117 HOH HOH . C 3 HOH A 71 4171 112 HOH HOH . C 3 HOH A 72 4172 190 HOH HOH . C 3 HOH A 73 4173 74 HOH HOH . C 3 HOH A 74 4174 31 HOH HOH . C 3 HOH A 75 4175 101 HOH HOH . C 3 HOH A 76 4176 28 HOH HOH . C 3 HOH A 77 4177 134 HOH HOH . C 3 HOH A 78 4178 2 HOH HOH . C 3 HOH A 79 4179 169 HOH HOH . C 3 HOH A 80 4180 5 HOH HOH . C 3 HOH A 81 4181 184 HOH HOH . C 3 HOH A 82 4182 173 HOH HOH . C 3 HOH A 83 4183 47 HOH HOH . C 3 HOH A 84 4184 188 HOH HOH . C 3 HOH A 85 4185 22 HOH HOH . C 3 HOH A 86 4186 52 HOH HOH . C 3 HOH A 87 4187 68 HOH HOH . C 3 HOH A 88 4188 199 HOH HOH . C 3 HOH A 89 4189 200 HOH HOH . C 3 HOH A 90 4190 51 HOH HOH . C 3 HOH A 91 4191 208 HOH HOH . C 3 HOH A 92 4192 209 HOH HOH . C 3 HOH A 93 4193 33 HOH HOH . C 3 HOH A 94 4194 10 HOH HOH . C 3 HOH A 95 4195 45 HOH HOH . C 3 HOH A 96 4196 73 HOH HOH . C 3 HOH A 97 4197 183 HOH HOH . C 3 HOH A 98 4198 58 HOH HOH . C 3 HOH A 99 4199 114 HOH HOH . C 3 HOH A 100 4200 109 HOH HOH . C 3 HOH A 101 4201 16 HOH HOH . C 3 HOH A 102 4202 100 HOH HOH . C 3 HOH A 103 4203 121 HOH HOH . C 3 HOH A 104 4204 106 HOH HOH . C 3 HOH A 105 4205 181 HOH HOH . C 3 HOH A 106 4206 11 HOH HOH . C 3 HOH A 107 4207 88 HOH HOH . C 3 HOH A 108 4208 162 HOH HOH . C 3 HOH A 109 4209 79 HOH HOH . C 3 HOH A 110 4210 176 HOH HOH . C 3 HOH A 111 4211 172 HOH HOH . C 3 HOH A 112 4212 65 HOH HOH . C 3 HOH A 113 4213 19 HOH HOH . C 3 HOH A 114 4214 178 HOH HOH . C 3 HOH A 115 4215 98 HOH HOH . C 3 HOH A 116 4216 85 HOH HOH . C 3 HOH A 117 4217 64 HOH HOH . C 3 HOH A 118 4218 57 HOH HOH . C 3 HOH A 119 4219 93 HOH HOH . C 3 HOH A 120 4220 105 HOH HOH . C 3 HOH A 121 4221 165 HOH HOH . C 3 HOH A 122 4222 84 HOH HOH . C 3 HOH A 123 4223 145 HOH HOH . C 3 HOH A 124 4224 159 HOH HOH . C 3 HOH A 125 4225 110 HOH HOH . C 3 HOH A 126 4226 87 HOH HOH . C 3 HOH A 127 4227 156 HOH HOH . C 3 HOH A 128 4228 54 HOH HOH . C 3 HOH A 129 4229 43 HOH HOH . C 3 HOH A 130 4230 94 HOH HOH . C 3 HOH A 131 4231 108 HOH HOH . C 3 HOH A 132 4232 21 HOH HOH . C 3 HOH A 133 4233 174 HOH HOH . C 3 HOH A 134 4234 175 HOH HOH . C 3 HOH A 135 4235 201 HOH HOH . C 3 HOH A 136 4236 81 HOH HOH . C 3 HOH A 137 4237 29 HOH HOH . C 3 HOH A 138 4238 61 HOH HOH . C 3 HOH A 139 4239 6 HOH HOH . C 3 HOH A 140 4240 82 HOH HOH . C 3 HOH A 141 4241 120 HOH HOH . C 3 HOH A 142 4242 77 HOH HOH . C 3 HOH A 143 4243 195 HOH HOH . C 3 HOH A 144 4244 96 HOH HOH . C 3 HOH A 145 4245 210 HOH HOH . C 3 HOH A 146 4246 86 HOH HOH . C 3 HOH A 147 4247 119 HOH HOH . C 3 HOH A 148 4248 207 HOH HOH . C 3 HOH A 149 4249 123 HOH HOH . C 3 HOH A 150 4250 203 HOH HOH . C 3 HOH A 151 4251 39 HOH HOH . C 3 HOH A 152 4252 92 HOH HOH . C 3 HOH A 153 4253 182 HOH HOH . C 3 HOH A 154 4254 160 HOH HOH . C 3 HOH A 155 4255 56 HOH HOH . C 3 HOH A 156 4256 63 HOH HOH . C 3 HOH A 157 4257 107 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 N3 G5D . . . B 2 7.908 -8.468 15.107 1 31.13 ? N3 G5D 4000 A 1 HETATM 2 C C4 G5D . . . B 2 10.168 -11.278 14.491 1 28.29 ? C4 G5D 4000 A 1 HETATM 3 N N2 G5D . . . B 2 10.004 -12.015 15.604 1 29.1 ? N2 G5D 4000 A 1 HETATM 4 C C7 G5D . . . B 2 5.727 -7.662 15.749 1 28.41 ? C7 G5D 4000 A 1 HETATM 5 C C6 G5D . . . B 2 7.279 -6.266 14.555 1 29.34 ? C6 G5D 4000 A 1 HETATM 6 C C9 G5D . . . B 2 8.047 -12.142 18.729 1 33.43 ? C9 G5D 4000 A 1 HETATM 7 C C13 G5D . . . B 2 6.332 -11.01 19.982 1 38.3 ? C13 G5D 4000 A 1 HETATM 8 C C20 G5D . . . B 2 3.849 -10.982 23.624 1 51.75 ? C20 G5D 4000 A 1 HETATM 9 C C21 G5D . . . B 2 2.545 -11.781 23.657 1 52.55 ? C21 G5D 4000 A 1 HETATM 10 C C8 G5D . . . B 2 7.203 -7.789 16.222 1 30.15 ? C8 G5D 4000 A 1 HETATM 11 N N5 G5D . . . B 2 8.91 -12.325 17.633 1 34.46 ? N5 G5D 4000 A 1 HETATM 12 C C18 G5D . . . B 2 5.106 -5.411 12.658 1 27.17 ? C18 G5D 4000 A 1 HETATM 13 C C16 G5D . . . B 2 7.699 -6.328 16.051 1 30.34 ? C16 G5D 4000 A 1 HETATM 14 C C19 G5D . . . B 2 3.949 -5.314 11.796 1 31.8 ? C19 G5D 4000 A 1 HETATM 15 C C1 G5D . . . B 2 9.074 -11.513 16.516 1 30.62 ? C1 G5D 4000 A 1 HETATM 16 N N1 G5D . . . B 2 8.368 -10.344 16.397 1 30.63 ? N1 G5D 4000 A 1 HETATM 17 C C2 G5D . . . B 2 8.612 -9.642 15.233 1 28.91 ? C2 G5D 4000 A 1 HETATM 18 C C3 G5D . . . B 2 9.496 -10.085 14.228 1 27.43 ? C3 G5D 4000 A 1 HETATM 19 C C5 G5D . . . B 2 8.063 -7.502 13.994 1 31.63 ? C5 G5D 4000 A 1 HETATM 20 N N4 G5D . . . B 2 5.859 -6.65 14.661 1 29.58 ? N4 G5D 4000 A 1 HETATM 21 C C10 G5D . . . B 2 8.218 -13.039 19.805 1 34.54 ? C10 G5D 4000 A 1 HETATM 22 C C11 G5D . . . B 2 7.484 -12.879 20.964 1 35.78 ? C11 G5D 4000 A 1 HETATM 23 C C12 G5D . . . B 2 6.565 -11.836 21.071 1 39.85 ? C12 G5D 4000 A 1 HETATM 24 C C14 G5D . . . B 2 7.057 -11.162 18.805 1 34.41 ? C14 G5D 4000 A 1 HETATM 25 C C15 G5D . . . B 2 5.932 -11.608 22.393 1 45.61 ? C15 G5D 4000 A 1 HETATM 26 O O1 G5D . . . B 2 6.571 -11.719 23.438 1 48.56 ? O1 G5D 4000 A 1 HETATM 27 N N6 G5D . . . B 2 4.594 -11.253 22.392 1 48.37 ? N6 G5D 4000 A 1 HETATM 28 C C17 G5D . . . B 2 4.82 -6.375 13.793 1 25.1 ? C17 G5D 4000 A 1 HETATM 29 O O2 G5D . . . B 2 3.724 -6.884 13.988 1 26.47 ? O2 G5D 4000 A 1 HETATM 30 N N7 G5D . . . B 2 3.029 -5.246 11.102 1 36.27 ? N7 G5D 4000 A 1 HETATM 31 H H2 G5D . . . B 2 10.893 -11.69 13.775 1 27.42 ? H2 G5D 4000 A 1 HETATM 32 H H6 G5D . . . B 2 5.284 -8.618 15.395 1 27.23 ? H6 G5D 4000 A 1 HETATM 33 H H7 G5D . . . B 2 5.055 -7.297 16.556 1 28.31 ? H7 G5D 4000 A 1 HETATM 34 H H5 G5D . . . B 2 7.475 -5.315 14.023 1 28.61 ? H5 G5D 4000 A 1 HETATM 35 H H12 G5D . . . B 2 5.593 -10.203 20.04 1 38.62 ? H12 G5D 4000 A 1 HETATM 36 H H19 G5D . . . B 2 3.633 -9.888 23.689 1 51.46 ? H19 G5D 4000 A 1 HETATM 37 H H20 G5D . . . B 2 4.459 -11.208 24.531 1 51.41 ? H20 G5D 4000 A 1 HETATM 38 H H23 G5D . . . B 2 1.873 -11.534 22.822 1 52.6 ? H23 G5D 4000 A 1 HETATM 39 H H21 G5D . . . B 2 1.983 -11.582 24.581 1 52.27 ? H21 G5D 4000 A 1 HETATM 40 H H22 G5D . . . B 2 2.718 -12.866 23.618 1 52.01 ? H22 G5D 4000 A 1 HETATM 41 H H8 G5D . . . B 2 7.341 -8.244 17.224 1 30.29 ? H8 G5D 4000 A 1 HETATM 42 H H9 G5D . . . B 2 9.515 -13.149 17.661 1 36.09 ? H9 G5D 4000 A 1 HETATM 43 H H18 G5D . . . B 2 5.371 -4.403 13.046 1 26.43 ? H18 G5D 4000 A 1 HETATM 44 H H17 G5D . . . B 2 5.977 -5.755 12.058 1 27.72 ? H17 G5D 4000 A 1 HETATM 45 H H15 G5D . . . B 2 7.19 -5.6 16.706 1 30.66 ? H15 G5D 4000 A 1 HETATM 46 H H16 G5D . . . B 2 8.778 -6.179 16.226 1 30.9 ? H16 G5D 4000 A 1 HETATM 47 H H1 G5D . . . B 2 9.659 -9.547 13.297 1 26.03 ? H1 G5D 4000 A 1 HETATM 48 H H4 G5D . . . B 2 9.124 -7.247 13.779 1 31.75 ? H4 G5D 4000 A 1 HETATM 49 H H3 G5D . . . B 2 7.642 -7.899 13.046 1 32.01 ? H3 G5D 4000 A 1 HETATM 50 H H10 G5D . . . B 2 8.939 -13.862 19.755 1 34.48 ? H10 G5D 4000 A 1 HETATM 51 H H11 G5D . . . B 2 7.642 -13.556 21.812 1 36.13 ? H11 G5D 4000 A 1 HETATM 52 H H13 G5D . . . B 2 6.829 -10.5 17.964 1 34.29 ? H13 G5D 4000 A 1 HETATM 53 H H14 G5D . . . B 2 4.063 -11.264 21.529 1 48.53 ? H14 G5D 4000 A 1 # _model_server_stats.io_time_ms 140 _model_server_stats.parse_time_ms 143 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 53 #