data_3JVX # _model_server_result.job_id Tl1o25YGAovdQXrMS427Fw _model_server_result.datetime_utc '2024-12-01 05:27:09' _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 3jvx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":208}' # _entry.id 3JVX # _exptl.entry_id 3JVX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 342.392 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 6-ethyl-5-[3-(3,4,5-trimethoxyphenyl)prop-1-yn-1-yl]pyrimidine-2,4-diamine _entity.pdbx_number_of_molecules 2 _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 3JVX _cell.length_a 78.241 _cell.length_b 78.241 _cell.length_c 66.79 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3JVX _symmetry.cell_setting ? _symmetry.Int_Tables_number 77 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H 1 1 A,B,C,D,E,F,G,H 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N N # _chem_comp.formula 'C18 H22 N4 O3' _chem_comp.formula_weight 342.392 _chem_comp.id EKB _chem_comp.mon_nstd_flag . _chem_comp.name 6-ethyl-5-[3-(3,4,5-trimethoxyphenyl)prop-1-yn-1-yl]pyrimidine-2,4-diamine _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 C2 N1 EKB doub 83 n y C6 N1 EKB sing 84 n y N3 C2 EKB sing 85 n y C2 N1E EKB sing 86 n n C4 N3 EKB doub 87 n y C1K C4 EKB sing 88 n n C4 C5 EKB sing 89 n y C1H C5 EKB sing 90 n n C5 C6 EKB doub 91 n y C6 N1F EKB sing 92 n n C1A C1K EKB sing 93 n n C1A H1A EKB sing 94 n n C1A H1AA EKB sing 95 n n C1A H1AB EKB sing 96 n n O1O C1B EKB sing 97 n n C1B H1B EKB sing 98 n n C1B H1BA EKB sing 99 n n C1B H1BB EKB sing 100 n n O1P C1C EKB sing 101 n n C1C H1C EKB sing 102 n n C1C H1CA EKB sing 103 n n C1C H1CB EKB sing 104 n n C1D O1Q EKB sing 105 n n C1D H1D EKB sing 106 n n C1D H1DA EKB sing 107 n n C1D H1DB EKB sing 108 n n N1E HN1E EKB sing 109 n n N1E HN1A EKB sing 110 n n N1F HN1F EKB sing 111 n n N1F HN1B EKB sing 112 n n C1L C1G EKB sing 113 n n C1G C1H EKB trip 114 n n C1V C1I EKB doub 115 n y C1I C1S EKB sing 116 n y C1I H1I EKB sing 117 n n C1W C1J EKB sing 118 n y C1J C1S EKB doub 119 n y C1J H1J EKB sing 120 n n C1K H1K EKB sing 121 n n C1K H1KA EKB sing 122 n n C1S C1L EKB sing 123 n n C1L H1L EKB sing 124 n n C1L H1LA EKB sing 125 n n O1O C1V EKB sing 126 n n O1P C1W EKB sing 127 n n O1Q C1Y EKB sing 128 n n C1Y C1V EKB sing 129 n y C1Y C1W EKB doub 130 n y # _atom_sites.entry_id 3JVX _atom_sites.fract_transf_matrix[1][1] 0.012781 _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] 0.012781 _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] 0.014972 _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 2 NDP A 1 207 207 NDP NAP . D 3 EKB A 1 208 1 EKB EKB . E 2 NDP B 1 207 207 NDP NAP . F 3 EKB B 1 208 1 EKB EKB . G 4 HOH A 1 163 1 HOH HOH . G 4 HOH A 2 164 3 HOH HOH . G 4 HOH A 3 165 4 HOH HOH . G 4 HOH A 4 166 10 HOH HOH . G 4 HOH A 5 167 15 HOH HOH . G 4 HOH A 6 168 168 HOH HOH . G 4 HOH A 7 169 17 HOH HOH . G 4 HOH A 8 170 18 HOH HOH . G 4 HOH A 9 171 19 HOH HOH . G 4 HOH A 10 172 172 HOH HOH . G 4 HOH A 11 173 20 HOH HOH . G 4 HOH A 12 174 174 HOH HOH . G 4 HOH A 13 175 21 HOH HOH . G 4 HOH A 14 176 22 HOH HOH . G 4 HOH A 15 177 177 HOH HOH . G 4 HOH A 16 178 178 HOH HOH . G 4 HOH A 17 179 179 HOH HOH . G 4 HOH A 18 180 180 HOH HOH . G 4 HOH A 19 181 181 HOH HOH . G 4 HOH A 20 182 23 HOH HOH . G 4 HOH A 21 183 25 HOH HOH . G 4 HOH A 22 184 26 HOH HOH . G 4 HOH A 23 185 30 HOH HOH . G 4 HOH A 24 186 186 HOH HOH . G 4 HOH A 25 187 187 HOH HOH . G 4 HOH A 26 188 188 HOH HOH . G 4 HOH A 27 189 189 HOH HOH . G 4 HOH A 28 190 31 HOH HOH . G 4 HOH A 29 191 191 HOH HOH . G 4 HOH A 30 192 33 HOH HOH . G 4 HOH A 31 193 193 HOH HOH . G 4 HOH A 32 194 34 HOH HOH . G 4 HOH A 33 195 35 HOH HOH . G 4 HOH A 34 196 36 HOH HOH . G 4 HOH A 35 197 197 HOH HOH . G 4 HOH A 36 198 198 HOH HOH . G 4 HOH A 37 199 199 HOH HOH . G 4 HOH A 38 200 200 HOH HOH . G 4 HOH A 39 201 39 HOH HOH . G 4 HOH A 40 202 40 HOH HOH . G 4 HOH A 41 203 41 HOH HOH . G 4 HOH A 42 204 204 HOH HOH . G 4 HOH A 43 205 205 HOH HOH . G 4 HOH A 44 206 206 HOH HOH . G 4 HOH A 45 209 209 HOH HOH . G 4 HOH A 46 210 42 HOH HOH . G 4 HOH A 47 211 44 HOH HOH . G 4 HOH A 48 212 45 HOH HOH . G 4 HOH A 49 213 47 HOH HOH . G 4 HOH A 50 214 214 HOH HOH . G 4 HOH A 51 215 215 HOH HOH . G 4 HOH A 52 216 48 HOH HOH . G 4 HOH A 53 217 53 HOH HOH . G 4 HOH A 54 218 218 HOH HOH . G 4 HOH A 55 219 219 HOH HOH . G 4 HOH A 56 220 220 HOH HOH . G 4 HOH A 57 221 57 HOH HOH . G 4 HOH A 58 222 222 HOH HOH . G 4 HOH A 59 223 223 HOH HOH . G 4 HOH A 60 224 59 HOH HOH . G 4 HOH A 61 225 60 HOH HOH . G 4 HOH A 62 226 61 HOH HOH . G 4 HOH A 63 227 227 HOH HOH . G 4 HOH A 64 228 228 HOH HOH . G 4 HOH A 65 229 65 HOH HOH . G 4 HOH A 66 230 68 HOH HOH . G 4 HOH A 67 231 69 HOH HOH . G 4 HOH A 68 232 70 HOH HOH . G 4 HOH A 69 233 72 HOH HOH . G 4 HOH A 70 234 73 HOH HOH . G 4 HOH A 71 235 74 HOH HOH . G 4 HOH A 72 236 76 HOH HOH . G 4 HOH A 73 237 80 HOH HOH . G 4 HOH A 74 238 238 HOH HOH . G 4 HOH A 75 239 239 HOH HOH . G 4 HOH A 76 240 81 HOH HOH . G 4 HOH A 77 241 83 HOH HOH . G 4 HOH A 78 242 242 HOH HOH . G 4 HOH A 79 243 84 HOH HOH . G 4 HOH A 80 244 90 HOH HOH . G 4 HOH A 81 245 245 HOH HOH . G 4 HOH A 82 246 96 HOH HOH . G 4 HOH A 83 247 98 HOH HOH . G 4 HOH A 84 248 248 HOH HOH . G 4 HOH A 85 249 99 HOH HOH . G 4 HOH A 86 250 250 HOH HOH . G 4 HOH A 87 251 100 HOH HOH . G 4 HOH A 88 252 252 HOH HOH . G 4 HOH A 89 253 102 HOH HOH . G 4 HOH A 90 254 254 HOH HOH . G 4 HOH A 91 255 103 HOH HOH . G 4 HOH A 92 256 256 HOH HOH . G 4 HOH A 93 257 257 HOH HOH . G 4 HOH A 94 258 258 HOH HOH . G 4 HOH A 95 259 259 HOH HOH . G 4 HOH A 96 260 106 HOH HOH . G 4 HOH A 97 261 261 HOH HOH . G 4 HOH A 98 262 108 HOH HOH . G 4 HOH A 99 263 263 HOH HOH . G 4 HOH A 100 264 113 HOH HOH . G 4 HOH A 101 265 115 HOH HOH . G 4 HOH A 102 266 118 HOH HOH . G 4 HOH A 103 267 267 HOH HOH . G 4 HOH A 104 268 121 HOH HOH . G 4 HOH A 105 269 125 HOH HOH . G 4 HOH A 106 270 270 HOH HOH . G 4 HOH A 107 271 128 HOH HOH . G 4 HOH A 108 272 131 HOH HOH . G 4 HOH A 109 273 132 HOH HOH . G 4 HOH A 110 274 133 HOH HOH . G 4 HOH A 111 275 136 HOH HOH . G 4 HOH A 112 276 147 HOH HOH . G 4 HOH A 113 277 149 HOH HOH . G 4 HOH A 114 278 150 HOH HOH . G 4 HOH A 115 279 151 HOH HOH . G 4 HOH A 116 280 152 HOH HOH . G 4 HOH A 117 281 153 HOH HOH . G 4 HOH A 118 282 154 HOH HOH . G 4 HOH A 119 283 155 HOH HOH . G 4 HOH A 120 284 156 HOH HOH . G 4 HOH A 121 285 157 HOH HOH . G 4 HOH A 122 286 207 HOH HOH . H 4 HOH B 1 163 163 HOH HOH . H 4 HOH B 2 164 164 HOH HOH . H 4 HOH B 3 165 2 HOH HOH . H 4 HOH B 4 166 166 HOH HOH . H 4 HOH B 5 167 167 HOH HOH . H 4 HOH B 6 168 5 HOH HOH . H 4 HOH B 7 169 6 HOH HOH . H 4 HOH B 8 170 170 HOH HOH . H 4 HOH B 9 171 7 HOH HOH . H 4 HOH B 10 172 8 HOH HOH . H 4 HOH B 11 173 173 HOH HOH . H 4 HOH B 12 174 9 HOH HOH . H 4 HOH B 13 175 175 HOH HOH . H 4 HOH B 14 176 176 HOH HOH . H 4 HOH B 15 177 11 HOH HOH . H 4 HOH B 16 178 12 HOH HOH . H 4 HOH B 17 179 13 HOH HOH . H 4 HOH B 18 180 14 HOH HOH . H 4 HOH B 19 181 16 HOH HOH . H 4 HOH B 20 182 182 HOH HOH . H 4 HOH B 21 183 183 HOH HOH . H 4 HOH B 22 184 184 HOH HOH . H 4 HOH B 23 185 185 HOH HOH . H 4 HOH B 24 186 24 HOH HOH . H 4 HOH B 25 187 27 HOH HOH . H 4 HOH B 26 188 28 HOH HOH . H 4 HOH B 27 189 29 HOH HOH . H 4 HOH B 28 190 190 HOH HOH . H 4 HOH B 29 191 32 HOH HOH . H 4 HOH B 30 192 37 HOH HOH . H 4 HOH B 31 193 38 HOH HOH . H 4 HOH B 32 194 194 HOH HOH . H 4 HOH B 33 195 43 HOH HOH . H 4 HOH B 34 196 46 HOH HOH . H 4 HOH B 35 197 50 HOH HOH . H 4 HOH B 36 198 51 HOH HOH . H 4 HOH B 37 199 52 HOH HOH . H 4 HOH B 38 200 54 HOH HOH . H 4 HOH B 39 201 201 HOH HOH . H 4 HOH B 40 202 202 HOH HOH . H 4 HOH B 41 203 203 HOH HOH . H 4 HOH B 42 204 55 HOH HOH . H 4 HOH B 43 205 56 HOH HOH . H 4 HOH B 44 206 58 HOH HOH . H 4 HOH B 45 209 62 HOH HOH . H 4 HOH B 46 210 63 HOH HOH . H 4 HOH B 47 211 64 HOH HOH . H 4 HOH B 48 212 212 HOH HOH . H 4 HOH B 49 213 213 HOH HOH . H 4 HOH B 50 214 66 HOH HOH . H 4 HOH B 51 215 67 HOH HOH . H 4 HOH B 52 216 216 HOH HOH . H 4 HOH B 53 217 71 HOH HOH . H 4 HOH B 54 218 75 HOH HOH . H 4 HOH B 55 219 79 HOH HOH . H 4 HOH B 56 220 82 HOH HOH . H 4 HOH B 57 221 85 HOH HOH . H 4 HOH B 58 222 86 HOH HOH . H 4 HOH B 59 223 87 HOH HOH . H 4 HOH B 60 224 88 HOH HOH . H 4 HOH B 61 225 89 HOH HOH . H 4 HOH B 62 226 91 HOH HOH . H 4 HOH B 63 227 92 HOH HOH . H 4 HOH B 64 228 94 HOH HOH . H 4 HOH B 65 229 229 HOH HOH . H 4 HOH B 66 230 95 HOH HOH . H 4 HOH B 67 231 97 HOH HOH . H 4 HOH B 68 232 101 HOH HOH . H 4 HOH B 69 233 104 HOH HOH . H 4 HOH B 70 234 105 HOH HOH . H 4 HOH B 71 235 235 HOH HOH . H 4 HOH B 72 236 107 HOH HOH . H 4 HOH B 73 237 237 HOH HOH . H 4 HOH B 74 238 109 HOH HOH . H 4 HOH B 75 239 110 HOH HOH . H 4 HOH B 76 240 240 HOH HOH . H 4 HOH B 77 241 111 HOH HOH . H 4 HOH B 78 242 112 HOH HOH . H 4 HOH B 79 243 114 HOH HOH . H 4 HOH B 80 244 244 HOH HOH . H 4 HOH B 81 245 116 HOH HOH . H 4 HOH B 82 246 246 HOH HOH . H 4 HOH B 83 247 247 HOH HOH . H 4 HOH B 84 248 117 HOH HOH . H 4 HOH B 85 249 119 HOH HOH . H 4 HOH B 86 250 122 HOH HOH . H 4 HOH B 87 251 251 HOH HOH . H 4 HOH B 88 252 124 HOH HOH . H 4 HOH B 89 253 253 HOH HOH . H 4 HOH B 90 254 126 HOH HOH . H 4 HOH B 91 255 255 HOH HOH . H 4 HOH B 92 256 127 HOH HOH . H 4 HOH B 93 257 129 HOH HOH . H 4 HOH B 94 258 130 HOH HOH . H 4 HOH B 95 259 134 HOH HOH . H 4 HOH B 96 260 135 HOH HOH . H 4 HOH B 97 261 137 HOH HOH . H 4 HOH B 98 262 262 HOH HOH . H 4 HOH B 99 263 140 HOH HOH . H 4 HOH B 100 264 264 HOH HOH . H 4 HOH B 101 265 265 HOH HOH . H 4 HOH B 102 266 266 HOH HOH . H 4 HOH B 103 267 146 HOH HOH . H 4 HOH B 104 268 268 HOH HOH . H 4 HOH B 105 269 269 HOH HOH . H 4 HOH B 106 270 158 HOH HOH . H 4 HOH B 107 271 271 HOH HOH . H 4 HOH B 108 272 272 HOH HOH . H 4 HOH B 109 273 159 HOH HOH . H 4 HOH B 110 274 160 HOH HOH . H 4 HOH B 111 275 161 HOH HOH . H 4 HOH B 112 276 162 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 N1 EKB . . . F 3 14.225 -9.6 8.626 1 21.35 ? N1 EKB 208 B 1 HETATM 2 C C2 EKB . . . F 3 15.078 -9.451 7.595 1 22.06 ? C2 EKB 208 B 1 HETATM 3 N N3 EKB . . . F 3 14.613 -9.334 6.349 1 21.85 ? N3 EKB 208 B 1 HETATM 4 C C4 EKB . . . F 3 13.297 -9.374 6.082 1 22.67 ? C4 EKB 208 B 1 HETATM 5 C C5 EKB . . . F 3 12.402 -9.529 7.139 1 22 ? C5 EKB 208 B 1 HETATM 6 C C6 EKB . . . F 3 12.892 -9.635 8.433 1 21.75 ? C6 EKB 208 B 1 HETATM 7 C C1A EKB . . . F 3 12.795 -7.738 4.287 1 22.62 ? C1A EKB 208 B 1 HETATM 8 C C1B EKB . . . F 3 5.253 -8.892 2.177 1 27.5 ? C1B EKB 208 B 1 HETATM 9 C C1C EKB . . . F 3 9.668 -14.272 3.908 1 25.3 ? C1C EKB 208 B 1 HETATM 10 C C1D EKB . . . F 3 8.339 -11.824 0.137 1 27.01 ? C1D EKB 208 B 1 HETATM 11 N N1E EKB . . . F 3 16.398 -9.407 7.783 1 21.39 ? N1E EKB 208 B 1 HETATM 12 N N1F EKB . . . F 3 12.055 -9.783 9.465 1 21.42 ? N1F EKB 208 B 1 HETATM 13 C C1G EKB . . . F 3 9.82 -9.591 6.544 1 22.16 ? C1G EKB 208 B 1 HETATM 14 C C1H EKB . . . F 3 11.002 -9.567 6.852 1 22.28 ? C1H EKB 208 B 1 HETATM 15 C C1I EKB . . . F 3 7.216 -9.834 3.923 1 25.17 ? C1I EKB 208 B 1 HETATM 16 C C1J EKB . . . F 3 8.863 -11.53 4.489 1 25.88 ? C1J EKB 208 B 1 HETATM 17 C C1K EKB . . . F 3 12.878 -9.235 4.617 1 21.66 ? C1K EKB 208 B 1 HETATM 18 C C1L EKB . . . F 3 8.413 -9.622 6.14 1 23.38 ? C1L EKB 208 B 1 HETATM 19 O O1O EKB . . . F 3 6.045 -10.048 1.795 1 26.4 ? O1O EKB 208 B 1 HETATM 20 O O1P EKB . . . F 3 9.267 -13.337 2.885 1 25.99 ? O1P EKB 208 B 1 HETATM 21 O O1Q EKB . . . F 3 7.432 -12.296 1.197 1 27.02 ? O1Q EKB 208 B 1 HETATM 22 C C1S EKB . . . F 3 8.166 -10.354 4.812 1 25.47 ? C1S EKB 208 B 1 HETATM 23 C C1V EKB . . . F 3 6.968 -10.492 2.706 1 26.03 ? C1V EKB 208 B 1 HETATM 24 C C1W EKB . . . F 3 8.613 -12.189 3.274 1 26 ? C1W EKB 208 B 1 HETATM 25 C C1Y EKB . . . F 3 7.672 -11.657 2.388 1 25.51 ? C1Y EKB 208 B 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #