data_3EEM # _model_server_result.job_id ig-IFTV8feofWPcp1oJVFA _model_server_result.datetime_utc '2024-11-05 16:21:45' _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 3eem # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":229}' # _entry.id 3EEM # _exptl.entry_id 3EEM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 386.489 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5-[(3R)-3-(5-methoxy-2',6'-dimethylbiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-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 3EEM _cell.length_a 42.822 _cell.length_b 42.822 _cell.length_c 231.532 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EEM _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,C,D,G 1 1 B,E,F,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 'C24 H26 N4 O' _chem_comp.formula_weight 386.489 _chem_comp.id 53V _chem_comp.mon_nstd_flag . _chem_comp.name "5-[(3R)-3-(5-methoxy-2',6'-dimethylbiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-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 C1 C6 53V doub 1 n y C1 N2 53V sing 2 n y C1 N9 53V sing 3 n n C2 O17 53V sing 4 n n C3 N4 53V sing 5 n y C3 N7 53V sing 6 n n C3 N2 53V doub 7 n y C6 C10 53V sing 8 n n C6 C5 53V sing 9 n y C12 C13 53V sing 10 n n C12 C14 53V sing 11 n n C12 C11 53V sing 12 n n C14 C15 53V doub 13 n y C14 C19 53V sing 14 n y C15 C16 53V sing 15 n y C16 C17 53V doub 16 n y C16 O17 53V sing 17 n n C17 C18 53V sing 18 n y C18 C25 53V sing 19 n y C18 C19 53V doub 20 n y C26 C20 53V sing 21 n n C20 C21 53V doub 22 n y C20 C25 53V sing 23 n y C21 C22 53V sing 24 n y C22 C23 53V doub 25 n y C23 C24 53V sing 26 n y C24 C27 53V sing 27 n n C24 C25 53V doub 28 n y C11 C10 53V trip 29 n n C5 C8 53V sing 30 n n C5 N4 53V doub 31 n y C2 H2 53V sing 32 n n C2 H2A 53V sing 33 n n C2 H2B 53V sing 34 n n C12 H12 53V sing 35 n n C13 H13 53V sing 36 n n C13 H13A 53V sing 37 n n C13 H13B 53V sing 38 n n C15 H15 53V sing 39 n n C17 H17 53V sing 40 n n C26 H26 53V sing 41 n n C26 H26A 53V sing 42 n n C26 H26B 53V sing 43 n n C21 H21 53V sing 44 n n C22 H22 53V sing 45 n n C23 H23 53V sing 46 n n C27 H27 53V sing 47 n n C27 H27A 53V sing 48 n n C27 H27B 53V sing 49 n n C19 H19 53V sing 50 n n C8 H8 53V sing 51 n n C8 H8A 53V sing 52 n n C8 H8B 53V sing 53 n n N7 HN7 53V sing 54 n n N7 HN7A 53V sing 55 n n N9 HN9 53V sing 56 n n N9 HN9A 53V sing 57 n n # _atom_sites.entry_id 3EEM _atom_sites.fract_transf_matrix[1][1] 0.023352 _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] 0.023352 _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] 0.004319 _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 1 228 207 NDP NAP . D 3 53V A 1 229 1 53V 53V . E 2 NDP B 1 228 207 NDP NAP . F 3 53V B 1 229 1 53V 53V . G 4 HOH A 1 230 3 HOH HOH . G 4 HOH A 2 231 5 HOH HOH . G 4 HOH A 3 232 6 HOH HOH . G 4 HOH A 4 233 7 HOH HOH . G 4 HOH A 5 234 9 HOH HOH . G 4 HOH A 6 235 14 HOH HOH . G 4 HOH A 7 236 15 HOH HOH . G 4 HOH A 8 237 19 HOH HOH . G 4 HOH A 9 238 20 HOH HOH . G 4 HOH A 10 239 21 HOH HOH . G 4 HOH A 11 240 22 HOH HOH . G 4 HOH A 12 241 25 HOH HOH . G 4 HOH A 13 242 26 HOH HOH . G 4 HOH A 14 243 29 HOH HOH . G 4 HOH A 15 244 33 HOH HOH . G 4 HOH A 16 245 36 HOH HOH . G 4 HOH A 17 246 37 HOH HOH . G 4 HOH A 18 247 39 HOH HOH . G 4 HOH A 19 248 40 HOH HOH . G 4 HOH A 20 249 41 HOH HOH . G 4 HOH A 21 250 42 HOH HOH . G 4 HOH A 22 251 45 HOH HOH . G 4 HOH A 23 252 46 HOH HOH . G 4 HOH A 24 253 48 HOH HOH . G 4 HOH A 25 254 49 HOH HOH . G 4 HOH A 26 255 53 HOH HOH . G 4 HOH A 27 256 55 HOH HOH . G 4 HOH A 28 257 56 HOH HOH . G 4 HOH A 29 258 59 HOH HOH . G 4 HOH A 30 259 61 HOH HOH . G 4 HOH A 31 260 62 HOH HOH . G 4 HOH A 32 261 63 HOH HOH . G 4 HOH A 33 262 64 HOH HOH . G 4 HOH A 34 263 65 HOH HOH . G 4 HOH A 35 264 66 HOH HOH . G 4 HOH A 36 265 70 HOH HOH . G 4 HOH A 37 266 72 HOH HOH . G 4 HOH A 38 267 73 HOH HOH . G 4 HOH A 39 268 74 HOH HOH . G 4 HOH A 40 269 76 HOH HOH . G 4 HOH A 41 270 77 HOH HOH . G 4 HOH A 42 271 78 HOH HOH . G 4 HOH A 43 272 79 HOH HOH . G 4 HOH A 44 273 84 HOH HOH . G 4 HOH A 45 274 85 HOH HOH . G 4 HOH A 46 275 87 HOH HOH . G 4 HOH A 47 276 88 HOH HOH . G 4 HOH A 48 277 89 HOH HOH . G 4 HOH A 49 278 91 HOH HOH . G 4 HOH A 50 279 93 HOH HOH . G 4 HOH A 51 280 97 HOH HOH . G 4 HOH A 52 281 100 HOH HOH . G 4 HOH A 53 282 101 HOH HOH . G 4 HOH A 54 283 102 HOH HOH . G 4 HOH A 55 284 105 HOH HOH . G 4 HOH A 56 285 106 HOH HOH . G 4 HOH A 57 286 107 HOH HOH . G 4 HOH A 58 287 108 HOH HOH . G 4 HOH A 59 288 112 HOH HOH . G 4 HOH A 60 289 113 HOH HOH . G 4 HOH A 61 290 114 HOH HOH . G 4 HOH A 62 291 115 HOH HOH . G 4 HOH A 63 292 122 HOH HOH . G 4 HOH A 64 293 123 HOH HOH . G 4 HOH A 65 294 125 HOH HOH . G 4 HOH A 66 295 126 HOH HOH . G 4 HOH A 67 296 128 HOH HOH . G 4 HOH A 68 297 129 HOH HOH . G 4 HOH A 69 298 130 HOH HOH . G 4 HOH A 70 299 132 HOH HOH . G 4 HOH A 71 300 133 HOH HOH . G 4 HOH A 72 301 134 HOH HOH . G 4 HOH A 73 302 137 HOH HOH . G 4 HOH A 74 303 138 HOH HOH . G 4 HOH A 75 304 139 HOH HOH . G 4 HOH A 76 305 140 HOH HOH . G 4 HOH A 77 306 142 HOH HOH . G 4 HOH A 78 307 145 HOH HOH . G 4 HOH A 79 308 148 HOH HOH . G 4 HOH A 80 309 149 HOH HOH . G 4 HOH A 81 310 150 HOH HOH . G 4 HOH A 82 311 154 HOH HOH . G 4 HOH A 83 312 157 HOH HOH . G 4 HOH A 84 313 158 HOH HOH . G 4 HOH A 85 314 162 HOH HOH . G 4 HOH A 86 315 163 HOH HOH . G 4 HOH A 87 316 164 HOH HOH . G 4 HOH A 88 317 170 HOH HOH . G 4 HOH A 89 318 173 HOH HOH . G 4 HOH A 90 319 174 HOH HOH . G 4 HOH A 91 320 176 HOH HOH . G 4 HOH A 92 321 181 HOH HOH . G 4 HOH A 93 322 183 HOH HOH . G 4 HOH A 94 323 184 HOH HOH . G 4 HOH A 95 324 186 HOH HOH . G 4 HOH A 96 325 187 HOH HOH . G 4 HOH A 97 326 189 HOH HOH . G 4 HOH A 98 327 193 HOH HOH . G 4 HOH A 99 328 194 HOH HOH . G 4 HOH A 100 329 195 HOH HOH . G 4 HOH A 101 330 196 HOH HOH . G 4 HOH A 102 331 200 HOH HOH . G 4 HOH A 103 332 201 HOH HOH . G 4 HOH A 104 333 203 HOH HOH . G 4 HOH A 105 334 204 HOH HOH . G 4 HOH A 106 335 205 HOH HOH . H 4 HOH B 1 230 1 HOH HOH . H 4 HOH B 2 231 2 HOH HOH . H 4 HOH B 3 232 4 HOH HOH . H 4 HOH B 4 233 8 HOH HOH . H 4 HOH B 5 234 10 HOH HOH . H 4 HOH B 6 235 11 HOH HOH . H 4 HOH B 7 236 12 HOH HOH . H 4 HOH B 8 237 13 HOH HOH . H 4 HOH B 9 238 16 HOH HOH . H 4 HOH B 10 239 17 HOH HOH . H 4 HOH B 11 240 18 HOH HOH . H 4 HOH B 12 241 23 HOH HOH . H 4 HOH B 13 242 24 HOH HOH . H 4 HOH B 14 243 27 HOH HOH . H 4 HOH B 15 244 28 HOH HOH . H 4 HOH B 16 245 30 HOH HOH . H 4 HOH B 17 246 31 HOH HOH . H 4 HOH B 18 247 32 HOH HOH . H 4 HOH B 19 248 34 HOH HOH . H 4 HOH B 20 249 35 HOH HOH . H 4 HOH B 21 250 38 HOH HOH . H 4 HOH B 22 251 43 HOH HOH . H 4 HOH B 23 252 44 HOH HOH . H 4 HOH B 24 253 47 HOH HOH . H 4 HOH B 25 254 50 HOH HOH . H 4 HOH B 26 255 51 HOH HOH . H 4 HOH B 27 256 52 HOH HOH . H 4 HOH B 28 257 54 HOH HOH . H 4 HOH B 29 258 57 HOH HOH . H 4 HOH B 30 259 58 HOH HOH . H 4 HOH B 31 260 60 HOH HOH . H 4 HOH B 32 261 67 HOH HOH . H 4 HOH B 33 262 68 HOH HOH . H 4 HOH B 34 263 69 HOH HOH . H 4 HOH B 35 264 71 HOH HOH . H 4 HOH B 36 265 75 HOH HOH . H 4 HOH B 37 266 80 HOH HOH . H 4 HOH B 38 267 81 HOH HOH . H 4 HOH B 39 268 82 HOH HOH . H 4 HOH B 40 269 83 HOH HOH . H 4 HOH B 41 270 86 HOH HOH . H 4 HOH B 42 271 90 HOH HOH . H 4 HOH B 43 272 92 HOH HOH . H 4 HOH B 44 273 94 HOH HOH . H 4 HOH B 45 274 95 HOH HOH . H 4 HOH B 46 275 96 HOH HOH . H 4 HOH B 47 276 98 HOH HOH . H 4 HOH B 48 277 99 HOH HOH . H 4 HOH B 49 278 103 HOH HOH . H 4 HOH B 50 279 104 HOH HOH . H 4 HOH B 51 280 109 HOH HOH . H 4 HOH B 52 281 110 HOH HOH . H 4 HOH B 53 282 111 HOH HOH . H 4 HOH B 54 283 116 HOH HOH . H 4 HOH B 55 284 117 HOH HOH . H 4 HOH B 56 285 118 HOH HOH . H 4 HOH B 57 286 119 HOH HOH . H 4 HOH B 58 287 120 HOH HOH . H 4 HOH B 59 288 121 HOH HOH . H 4 HOH B 60 289 124 HOH HOH . H 4 HOH B 61 290 127 HOH HOH . H 4 HOH B 62 291 131 HOH HOH . H 4 HOH B 63 292 135 HOH HOH . H 4 HOH B 64 293 136 HOH HOH . H 4 HOH B 65 294 141 HOH HOH . H 4 HOH B 66 295 143 HOH HOH . H 4 HOH B 67 296 144 HOH HOH . H 4 HOH B 68 297 146 HOH HOH . H 4 HOH B 69 298 147 HOH HOH . H 4 HOH B 70 299 151 HOH HOH . H 4 HOH B 71 300 152 HOH HOH . H 4 HOH B 72 301 153 HOH HOH . H 4 HOH B 73 302 155 HOH HOH . H 4 HOH B 74 303 156 HOH HOH . H 4 HOH B 75 304 159 HOH HOH . H 4 HOH B 76 305 160 HOH HOH . H 4 HOH B 77 306 161 HOH HOH . H 4 HOH B 78 307 165 HOH HOH . H 4 HOH B 79 308 166 HOH HOH . H 4 HOH B 80 309 167 HOH HOH . H 4 HOH B 81 310 168 HOH HOH . H 4 HOH B 82 311 169 HOH HOH . H 4 HOH B 83 312 171 HOH HOH . H 4 HOH B 84 313 172 HOH HOH . H 4 HOH B 85 314 175 HOH HOH . H 4 HOH B 86 315 177 HOH HOH . H 4 HOH B 87 316 178 HOH HOH . H 4 HOH B 88 317 179 HOH HOH . H 4 HOH B 89 318 180 HOH HOH . H 4 HOH B 90 319 182 HOH HOH . H 4 HOH B 91 320 185 HOH HOH . H 4 HOH B 92 321 188 HOH HOH . H 4 HOH B 93 322 190 HOH HOH . H 4 HOH B 94 323 191 HOH HOH . H 4 HOH B 95 324 192 HOH HOH . H 4 HOH B 96 325 197 HOH HOH . H 4 HOH B 97 326 198 HOH HOH . H 4 HOH B 98 327 199 HOH HOH . H 4 HOH B 99 328 202 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 C1 53V . . . F 3 30.462 5.685 33.46 1 17.87 ? C1 53V 229 B 1 HETATM 2 C C2 53V . . . F 3 22.493 6.903 36.559 1 27.94 ? C2 53V 229 B 1 HETATM 3 C C3 53V . . . F 3 32.224 4.835 34.734 1 17.36 ? C3 53V 229 B 1 HETATM 4 C C6 53V . . . F 3 29.957 6.305 34.633 1 19.48 ? C6 53V 229 B 1 HETATM 5 C C12 53V . . . F 3 26.528 8.498 34.37 1 24.98 ? C12 53V 229 B 1 HETATM 6 C C13 53V . . . F 3 26.434 9.365 33.122 1 25.69 ? C13 53V 229 B 1 HETATM 7 C C14 53V . . . F 3 25.95 9.111 35.623 1 29.93 ? C14 53V 229 B 1 HETATM 8 C C15 53V . . . F 3 24.691 8.547 35.823 1 33.4 ? C15 53V 229 B 1 HETATM 9 C C16 53V . . . F 3 23.89 8.922 36.896 1 35.16 ? C16 53V 229 B 1 HETATM 10 C C17 53V . . . F 3 24.417 9.898 37.764 1 35.07 ? C17 53V 229 B 1 HETATM 11 C C18 53V . . . F 3 25.704 10.479 37.591 1 34.62 ? C18 53V 229 B 1 HETATM 12 C C26 53V . . . F 3 24.902 9.93 40.299 1 39.4 ? C26 53V 229 B 1 HETATM 13 C C20 53V . . . F 3 25.682 11.192 39.906 1 36.31 ? C20 53V 229 B 1 HETATM 14 C C21 53V . . . F 3 25.962 12.11 40.937 1 37.48 ? C21 53V 229 B 1 HETATM 15 C C22 53V . . . F 3 26.632 13.308 40.68 1 36.7 ? C22 53V 229 B 1 HETATM 16 C C23 53V . . . F 3 27.016 13.563 39.349 1 38.33 ? C23 53V 229 B 1 HETATM 17 C C24 53V . . . F 3 26.738 12.663 38.3 1 38.86 ? C24 53V 229 B 1 HETATM 18 C C27 53V . . . F 3 27.242 13.087 36.924 1 39.47 ? C27 53V 229 B 1 HETATM 19 C C25 53V . . . F 3 26.066 11.433 38.563 1 34.88 ? C25 53V 229 B 1 HETATM 20 C C19 53V . . . F 3 26.502 10.078 36.485 1 32.71 ? C19 53V 229 B 1 HETATM 21 O O17 53V . . . F 3 22.624 8.325 37.056 1 34.76 ? O17 53V 229 B 1 HETATM 22 C C11 53V . . . F 3 27.79 7.77 34.551 1 22.56 ? C11 53V 229 B 1 HETATM 23 C C10 53V . . . F 3 28.789 7.098 34.593 1 19.68 ? C10 53V 229 B 1 HETATM 24 C C5 53V . . . F 3 30.645 6.169 35.86 1 20.05 ? C5 53V 229 B 1 HETATM 25 C C8 53V . . . F 3 30.179 6.835 37.204 1 18.36 ? C8 53V 229 B 1 HETATM 26 N N4 53V . . . F 3 31.758 5.425 35.857 1 18.56 ? N4 53V 229 B 1 HETATM 27 N N7 53V . . . F 3 33.345 4.123 34.83 1 17.38 ? N7 53V 229 B 1 HETATM 28 N N2 53V . . . F 3 31.613 4.975 33.563 1 13.55 ? N2 53V 229 B 1 HETATM 29 N N9 53V . . . F 3 29.823 5.798 32.276 1 13.6 ? N9 53V 229 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 354 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 29 #