data_6TON # _model_server_result.job_id 85efDMqukStGpHKfthAdsA _model_server_result.datetime_utc '2025-01-10 07:52:03' _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 6ton # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 6TON # _exptl.entry_id 6TON _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 503.037 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-[[5-chloranyl-2-(2,2,6,6-tetramethylmorpholin-4-yl)pyrimidin-4-yl]amino]-1-methyl-3-(3-methyl-3-oxidanyl-butyl)benzimidazol-2-one _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 120 _cell.entry_id 6TON _cell.length_a 67.503 _cell.length_b 67.503 _cell.length_c 170.053 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6TON _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,F 1 1,4 B,E,G 1 2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_555 x-y,x,z+1/6 0.5 -0.866025 0 0.866025 0.5 0 0 0 1 0 0 28.342167 3 'crystal symmetry operation' 8_545 x-y,-y-1,-z 1 0 0 0 -1 0 0 0 -1 33.7515 -58.459313 0 4 'crystal symmetry operation' 12_545 x,x-y-1,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 33.7515 -58.459313 28.342167 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C25 H35 Cl N6 O3' _chem_comp.formula_weight 503.037 _chem_comp.id NR5 _chem_comp.mon_nstd_flag . _chem_comp.name 5-[[5-chloranyl-2-(2,2,6,6-tetramethylmorpholin-4-yl)pyrimidin-4-yl]amino]-1-methyl-3-(3-methyl-3-oxidanyl-butyl)benzimidazol-2-one _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 C20 C18 NR5 sing 246 n n C21 C18 NR5 sing 247 n n C21 N5 NR5 sing 248 n n C18 C19 NR5 sing 249 n n C18 O2 NR5 sing 250 n n N4 C12 NR5 doub 251 n y N4 C11 NR5 sing 252 n y O2 C15 NR5 sing 253 n n C12 C13 NR5 sing 254 n y N5 C11 NR5 sing 255 n n N5 C14 NR5 sing 256 n n C11 N3 NR5 doub 257 n y C14 C15 NR5 sing 258 n n C15 C17 NR5 sing 259 n n C15 C16 NR5 sing 260 n n C13 CL NR5 sing 261 n n C13 C10 NR5 doub 262 n y N3 C10 NR5 sing 263 n y C10 N2 NR5 sing 264 n n N2 C9 NR5 sing 265 n n C9 C22 NR5 doub 266 n y C9 C8 NR5 sing 267 n y C22 C23 NR5 sing 268 n y C8 C7 NR5 doub 269 n y C5 C4 NR5 sing 270 n n C23 C24 NR5 doub 271 n y C6 C4 NR5 sing 272 n n C4 C3 NR5 sing 273 n n C4 O1 NR5 sing 274 n n C7 C24 NR5 sing 275 n y C7 N1 NR5 sing 276 n n C3 C2 NR5 sing 277 n n C24 N NR5 sing 278 n n N1 C2 NR5 sing 279 n n N1 C1 NR5 sing 280 n n N C NR5 sing 281 n n N C1 NR5 sing 282 n n C1 O NR5 doub 283 n n N2 H1 NR5 sing 284 n n C5 H2 NR5 sing 285 n n C5 H3 NR5 sing 286 n n C5 H4 NR5 sing 287 n n C6 H5 NR5 sing 288 n n C6 H6 NR5 sing 289 n n C6 H7 NR5 sing 290 n n C14 H8 NR5 sing 291 n n C14 H9 NR5 sing 292 n n C16 H10 NR5 sing 293 n n C16 H11 NR5 sing 294 n n C16 H12 NR5 sing 295 n n C17 H13 NR5 sing 296 n n C17 H14 NR5 sing 297 n n C17 H15 NR5 sing 298 n n C19 H16 NR5 sing 299 n n C19 H17 NR5 sing 300 n n C19 H18 NR5 sing 301 n n C20 H19 NR5 sing 302 n n C20 H20 NR5 sing 303 n n C20 H21 NR5 sing 304 n n C22 H22 NR5 sing 305 n n C23 H23 NR5 sing 306 n n C12 H24 NR5 sing 307 n n C21 H25 NR5 sing 308 n n C21 H26 NR5 sing 309 n n C8 H27 NR5 sing 310 n n C H28 NR5 sing 311 n n C H29 NR5 sing 312 n n C H30 NR5 sing 313 n n C2 H31 NR5 sing 314 n n C2 H32 NR5 sing 315 n n C3 H33 NR5 sing 316 n n C3 H34 NR5 sing 317 n n O1 H35 NR5 sing 318 n n # _atom_sites.entry_id 6TON _atom_sites.fract_transf_matrix[1][1] 0.014814 _atom_sites.fract_transf_matrix[1][2] 0.008553 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017106 _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] 0.005881 _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 NR5 A 1 201 200 NR5 400 . D 4 EDO A 1 202 2 EDO EDO . E 4 EDO B 1 101 1 EDO EDO . F 5 HOH A 1 301 111 HOH HOH . F 5 HOH A 2 302 90 HOH HOH . F 5 HOH A 3 303 39 HOH HOH . F 5 HOH A 4 304 102 HOH HOH . F 5 HOH A 5 305 95 HOH HOH . F 5 HOH A 6 306 71 HOH HOH . F 5 HOH A 7 307 2 HOH HOH . F 5 HOH A 8 308 5 HOH HOH . F 5 HOH A 9 309 114 HOH HOH . F 5 HOH A 10 310 21 HOH HOH . F 5 HOH A 11 311 100 HOH HOH . F 5 HOH A 12 312 1 HOH HOH . F 5 HOH A 13 313 81 HOH HOH . F 5 HOH A 14 314 107 HOH HOH . F 5 HOH A 15 315 10 HOH HOH . F 5 HOH A 16 316 3 HOH HOH . F 5 HOH A 17 317 34 HOH HOH . F 5 HOH A 18 318 105 HOH HOH . F 5 HOH A 19 319 109 HOH HOH . F 5 HOH A 20 320 15 HOH HOH . F 5 HOH A 21 321 22 HOH HOH . F 5 HOH A 22 322 6 HOH HOH . F 5 HOH A 23 323 48 HOH HOH . F 5 HOH A 24 324 8 HOH HOH . F 5 HOH A 25 325 51 HOH HOH . F 5 HOH A 26 326 25 HOH HOH . F 5 HOH A 27 327 32 HOH HOH . F 5 HOH A 28 328 12 HOH HOH . F 5 HOH A 29 329 4 HOH HOH . F 5 HOH A 30 330 53 HOH HOH . F 5 HOH A 31 331 11 HOH HOH . F 5 HOH A 32 332 52 HOH HOH . F 5 HOH A 33 333 36 HOH HOH . F 5 HOH A 34 334 7 HOH HOH . F 5 HOH A 35 335 19 HOH HOH . F 5 HOH A 36 336 113 HOH HOH . F 5 HOH A 37 337 28 HOH HOH . F 5 HOH A 38 338 64 HOH HOH . F 5 HOH A 39 339 96 HOH HOH . F 5 HOH A 40 340 89 HOH HOH . F 5 HOH A 41 341 44 HOH HOH . F 5 HOH A 42 342 27 HOH HOH . F 5 HOH A 43 343 9 HOH HOH . F 5 HOH A 44 344 33 HOH HOH . F 5 HOH A 45 345 24 HOH HOH . F 5 HOH A 46 346 20 HOH HOH . F 5 HOH A 47 347 38 HOH HOH . F 5 HOH A 48 348 23 HOH HOH . F 5 HOH A 49 349 108 HOH HOH . F 5 HOH A 50 350 13 HOH HOH . F 5 HOH A 51 351 83 HOH HOH . F 5 HOH A 52 352 50 HOH HOH . F 5 HOH A 53 353 79 HOH HOH . F 5 HOH A 54 354 56 HOH HOH . F 5 HOH A 55 355 37 HOH HOH . F 5 HOH A 56 356 26 HOH HOH . F 5 HOH A 57 357 88 HOH HOH . F 5 HOH A 58 358 17 HOH HOH . F 5 HOH A 59 359 14 HOH HOH . F 5 HOH A 60 360 18 HOH HOH . F 5 HOH A 61 361 94 HOH HOH . F 5 HOH A 62 362 55 HOH HOH . F 5 HOH A 63 363 112 HOH HOH . F 5 HOH A 64 364 86 HOH HOH . F 5 HOH A 65 365 91 HOH HOH . F 5 HOH A 66 366 85 HOH HOH . F 5 HOH A 67 367 29 HOH HOH . F 5 HOH A 68 368 45 HOH HOH . F 5 HOH A 69 369 110 HOH HOH . F 5 HOH A 70 370 30 HOH HOH . F 5 HOH A 71 371 31 HOH HOH . F 5 HOH A 72 372 80 HOH HOH . F 5 HOH A 73 373 106 HOH HOH . F 5 HOH A 74 374 99 HOH HOH . F 5 HOH A 75 375 103 HOH HOH . F 5 HOH A 76 376 63 HOH HOH . F 5 HOH A 77 377 69 HOH HOH . F 5 HOH A 78 378 62 HOH HOH . F 5 HOH A 79 379 77 HOH HOH . F 5 HOH A 80 380 35 HOH HOH . F 5 HOH A 81 381 74 HOH HOH . F 5 HOH A 82 382 70 HOH HOH . F 5 HOH A 83 383 67 HOH HOH . G 5 HOH B 1 201 101 HOH HOH . G 5 HOH B 2 202 72 HOH HOH . G 5 HOH B 3 203 84 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 NR5 . . . C 3 21.536 -11.196 20.677 0.95 39.23 ? C1 NR5 201 A 1 HETATM 2 N N2 NR5 . . . C 3 25.046 -11.117 15.977 0.95 39.85 ? N2 NR5 201 A 1 HETATM 3 N N3 NR5 . . . C 3 24.129 -9.914 14.364 0.95 36.11 ? N3 NR5 201 A 1 HETATM 4 C C4 NR5 . . . C 3 21.223 -15.36 18.827 0.95 28.37 ? C4 NR5 201 A 1 HETATM 5 C C5 NR5 . . . C 3 19.956 -15.546 18.027 0.95 25.63 ? C5 NR5 201 A 1 HETATM 6 C C6 NR5 . . . C 3 22.36 -16.151 18.225 0.95 26.1 ? C6 NR5 201 A 1 HETATM 7 C C7 NR5 . . . C 3 22.938 -11.284 18.916 0.95 37.78 ? C7 NR5 201 A 1 HETATM 8 C C10 NR5 . . . C 3 25.205 -10.574 14.773 0.95 37.37 ? C10 NR5 201 A 1 HETATM 9 C C11 NR5 . . . C 3 24.092 -9.477 13.12 0.95 37.52 ? C11 NR5 201 A 1 HETATM 10 C C13 NR5 . . . C 3 26.253 -10.813 13.892 0.95 36.16 ? C13 NR5 201 A 1 HETATM 11 C C14 NR5 . . . C 3 21.887 -8.677 13.701 0.95 38.81 ? C14 NR5 201 A 1 HETATM 12 C C15 NR5 . . . C 3 21.777 -7.161 13.887 0.95 38.74 ? C15 NR5 201 A 1 HETATM 13 C C16 NR5 . . . C 3 20.524 -6.83 14.656 0.95 39.63 ? C16 NR5 201 A 1 HETATM 14 C C17 NR5 . . . C 3 22.992 -6.576 14.569 0.95 33.95 ? C17 NR5 201 A 1 HETATM 15 C C19 NR5 . . . C 3 23.774 -6.127 11.479 0.95 37.75 ? C19 NR5 201 A 1 HETATM 16 C C20 NR5 . . . C 3 21.669 -6.494 10.201 0.95 37 ? C20 NR5 201 A 1 HETATM 17 C C22 NR5 . . . C 3 23.777 -9.371 17.133 0.95 37.9 ? C22 NR5 201 A 1 HETATM 18 C C23 NR5 . . . C 3 22.927 -9.002 18.16 0.95 37.7 ? C23 NR5 201 A 1 HETATM 19 C C24 NR5 . . . C 3 22.497 -9.98 19.042 0.95 39.76 ? C24 NR5 201 A 1 HETATM 20 CL CL NR5 . . . C 3 27.663 -11.706 14.333 0.95 36.07 ? CL NR5 201 A 1 HETATM 21 C C12 NR5 . . . C 3 26.13 -10.293 12.615 0.95 35.05 ? C12 NR5 201 A 1 HETATM 22 N N4 NR5 . . . C 3 25.048 -9.626 12.209 0.95 36.43 ? N4 NR5 201 A 1 HETATM 23 N N5 NR5 . . . C 3 22.962 -8.876 12.743 0.95 37.86 ? N5 NR5 201 A 1 HETATM 24 C C21 NR5 . . . C 3 22.702 -8.399 11.392 0.95 39.23 ? C21 NR5 201 A 1 HETATM 25 C C18 NR5 . . . C 3 22.47 -6.889 11.418 0.95 39.85 ? C18 NR5 201 A 1 HETATM 26 O O2 NR5 . . . C 3 21.679 -6.517 12.584 0.95 40.41 ? O2 NR5 201 A 1 HETATM 27 C C9 NR5 . . . C 3 24.197 -10.692 16.997 0.95 40.31 ? C9 NR5 201 A 1 HETATM 28 C C8 NR5 . . . C 3 23.819 -11.646 17.921 0.95 39.38 ? C8 NR5 201 A 1 HETATM 29 N N NR5 . . . C 3 21.636 -9.937 20.13 0.95 39.89 ? N NR5 201 A 1 HETATM 30 C C NR5 . . . C 3 20.928 -8.749 20.587 0.95 36.46 ? C NR5 201 A 1 HETATM 31 N N1 NR5 . . . C 3 22.343 -12.014 19.918 0.95 34.86 ? N1 NR5 201 A 1 HETATM 32 O O NR5 . . . C 3 20.877 -11.52 21.638 0.95 39.83 ? O NR5 201 A 1 HETATM 33 C C2 NR5 . . . C 3 22.468 -13.452 20.11 0.95 27.62 ? C2 NR5 201 A 1 HETATM 34 C C3 NR5 . . . C 3 21.573 -13.885 18.954 0.95 25.43 ? C3 NR5 201 A 1 HETATM 35 O O1 NR5 . . . C 3 20.985 -15.878 20.141 0.95 29.67 ? O1 NR5 201 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 33 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 35 #