data_6TOM # _model_server_result.job_id Kfrpv7CVvCrdq6w-PxMVnQ _model_server_result.datetime_utc '2025-01-25 07:28:38' _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 6tom # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 6TOM # _exptl.entry_id 6TOM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 508.992 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-[[2-[(3~{S},5~{R})-4,4-bis(fluoranyl)-3,5-dimethyl-piperidin-1-yl]-5-chloranyl-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 6TOM _cell.length_a 67.279 _cell.length_b 67.279 _cell.length_c 166.379 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6TOM _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 12_565 x,x-y+1,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -33.6395 58.265323 27.729833 # _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 # _chem_comp.formula 'C24 H31 Cl F2 N6 O2' _chem_comp.formula_weight 508.992 _chem_comp.id NQZ _chem_comp.mon_nstd_flag . _chem_comp.name 5-[[2-[(3~{S},5~{R})-4,4-bis(fluoranyl)-3,5-dimethyl-piperidin-1-yl]-5-chloranyl-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 C5 C4 NQZ sing 246 n n C3 C4 NQZ sing 247 n n C3 N NQZ sing 248 n n C4 C6 NQZ sing 249 n n N5 C23 NQZ doub 250 n y N5 C7 NQZ sing 251 n y F C6 NQZ sing 252 n n C23 C22 NQZ sing 253 n y C6 F1 NQZ sing 254 n n C6 C1 NQZ sing 255 n n N C7 NQZ sing 256 n n N C2 NQZ sing 257 n n C7 N1 NQZ doub 258 n y C2 C1 NQZ sing 259 n n C22 CL NQZ sing 260 n n C22 C8 NQZ doub 261 n y C1 C NQZ sing 262 n n N1 C8 NQZ sing 263 n y C8 N2 NQZ sing 264 n n N2 C9 NQZ sing 265 n n C9 C14 NQZ doub 266 n y C9 C10 NQZ sing 267 n y C14 C13 NQZ sing 268 n y C21 C19 NQZ sing 269 n n C10 C11 NQZ doub 270 n y C20 C19 NQZ sing 271 n n C13 C12 NQZ doub 272 n y C19 C18 NQZ sing 273 n n C19 O1 NQZ sing 274 n n C18 C17 NQZ sing 275 n n C11 C12 NQZ sing 276 n y C11 N4 NQZ sing 277 n n C12 N3 NQZ sing 278 n n N4 C17 NQZ sing 279 n n N4 C16 NQZ sing 280 n n N3 C16 NQZ sing 281 n n N3 C15 NQZ sing 282 n n C16 O NQZ doub 283 n n C23 H1 NQZ sing 284 n n C2 H2 NQZ sing 285 n n C2 H3 NQZ sing 286 n n C3 H4 NQZ sing 287 n n C3 H5 NQZ sing 288 n n C4 H6 NQZ sing 289 n n C5 H7 NQZ sing 290 n n C5 H8 NQZ sing 291 n n C5 H9 NQZ sing 292 n n C1 H10 NQZ sing 293 n n C H11 NQZ sing 294 n n C H12 NQZ sing 295 n n C H13 NQZ sing 296 n n N2 H14 NQZ sing 297 n n C14 H15 NQZ sing 298 n n C13 H16 NQZ sing 299 n n C15 H17 NQZ sing 300 n n C15 H18 NQZ sing 301 n n C15 H19 NQZ sing 302 n n C10 H20 NQZ sing 303 n n C17 H21 NQZ sing 304 n n C17 H22 NQZ sing 305 n n C18 H23 NQZ sing 306 n n C18 H24 NQZ sing 307 n n O1 H25 NQZ sing 308 n n C21 H26 NQZ sing 309 n n C21 H27 NQZ sing 310 n n C21 H28 NQZ sing 311 n n C20 H29 NQZ sing 312 n n C20 H30 NQZ sing 313 n n C20 H31 NQZ sing 314 n n # _atom_sites.entry_id 6TOM _atom_sites.fract_transf_matrix[1][1] 0.014863 _atom_sites.fract_transf_matrix[1][2] 0.008581 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017163 _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] 0.00601 _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 NQZ A 1 201 200 NQZ 260 . C 3 EDO A 1 202 1 EDO EDO . D 3 EDO A 1 203 2 EDO EDO . E 3 EDO A 1 204 4 EDO EDO . F 4 HOH A 1 301 98 HOH HOH . F 4 HOH A 2 302 32 HOH HOH . F 4 HOH A 3 303 57 HOH HOH . F 4 HOH A 4 304 45 HOH HOH . F 4 HOH A 5 305 48 HOH HOH . F 4 HOH A 6 306 74 HOH HOH . F 4 HOH A 7 307 41 HOH HOH . F 4 HOH A 8 308 19 HOH HOH . F 4 HOH A 9 309 35 HOH HOH . F 4 HOH A 10 310 72 HOH HOH . F 4 HOH A 11 311 28 HOH HOH . F 4 HOH A 12 312 6 HOH HOH . F 4 HOH A 13 313 67 HOH HOH . F 4 HOH A 14 314 60 HOH HOH . F 4 HOH A 15 315 71 HOH HOH . F 4 HOH A 16 316 23 HOH HOH . F 4 HOH A 17 317 88 HOH HOH . F 4 HOH A 18 318 54 HOH HOH . F 4 HOH A 19 319 58 HOH HOH . F 4 HOH A 20 320 108 HOH HOH . F 4 HOH A 21 321 95 HOH HOH . F 4 HOH A 22 322 39 HOH HOH . F 4 HOH A 23 323 33 HOH HOH . F 4 HOH A 24 324 8 HOH HOH . F 4 HOH A 25 325 14 HOH HOH . F 4 HOH A 26 326 62 HOH HOH . F 4 HOH A 27 327 103 HOH HOH . F 4 HOH A 28 328 24 HOH HOH . F 4 HOH A 29 329 15 HOH HOH . F 4 HOH A 30 330 89 HOH HOH . F 4 HOH A 31 331 56 HOH HOH . F 4 HOH A 32 332 11 HOH HOH . F 4 HOH A 33 333 97 HOH HOH . F 4 HOH A 34 334 77 HOH HOH . F 4 HOH A 35 335 78 HOH HOH . F 4 HOH A 36 336 70 HOH HOH . F 4 HOH A 37 337 2 HOH HOH . F 4 HOH A 38 338 18 HOH HOH . F 4 HOH A 39 339 1 HOH HOH . F 4 HOH A 40 340 5 HOH HOH . F 4 HOH A 41 341 59 HOH HOH . F 4 HOH A 42 342 87 HOH HOH . F 4 HOH A 43 343 49 HOH HOH . F 4 HOH A 44 344 4 HOH HOH . F 4 HOH A 45 345 61 HOH HOH . F 4 HOH A 46 346 50 HOH HOH . F 4 HOH A 47 347 99 HOH HOH . F 4 HOH A 48 348 52 HOH HOH . F 4 HOH A 49 349 20 HOH HOH . F 4 HOH A 50 350 43 HOH HOH . F 4 HOH A 51 351 10 HOH HOH . F 4 HOH A 52 352 66 HOH HOH . F 4 HOH A 53 353 42 HOH HOH . F 4 HOH A 54 354 7 HOH HOH . F 4 HOH A 55 355 3 HOH HOH . F 4 HOH A 56 356 91 HOH HOH . F 4 HOH A 57 357 94 HOH HOH . F 4 HOH A 58 358 79 HOH HOH . F 4 HOH A 59 359 80 HOH HOH . F 4 HOH A 60 360 21 HOH HOH . F 4 HOH A 61 361 68 HOH HOH . F 4 HOH A 62 362 25 HOH HOH . F 4 HOH A 63 363 22 HOH HOH . F 4 HOH A 64 364 17 HOH HOH . F 4 HOH A 65 365 55 HOH HOH . F 4 HOH A 66 366 27 HOH HOH . F 4 HOH A 67 367 44 HOH HOH . F 4 HOH A 68 368 46 HOH HOH . F 4 HOH A 69 369 51 HOH HOH . F 4 HOH A 70 370 85 HOH HOH . F 4 HOH A 71 371 69 HOH HOH . F 4 HOH A 72 372 64 HOH HOH . F 4 HOH A 73 373 26 HOH HOH . F 4 HOH A 74 374 90 HOH HOH . F 4 HOH A 75 375 81 HOH HOH . F 4 HOH A 76 376 96 HOH HOH . F 4 HOH A 77 377 16 HOH HOH . F 4 HOH A 78 378 47 HOH HOH . F 4 HOH A 79 379 65 HOH HOH . F 4 HOH A 80 380 106 HOH HOH . F 4 HOH A 81 381 107 HOH HOH . F 4 HOH A 82 382 13 HOH HOH . F 4 HOH A 83 383 102 HOH HOH . F 4 HOH A 84 384 9 HOH HOH . F 4 HOH A 85 385 93 HOH HOH . F 4 HOH A 86 386 86 HOH HOH . F 4 HOH A 87 387 109 HOH HOH . F 4 HOH A 88 388 83 HOH HOH . F 4 HOH A 89 389 100 HOH HOH . F 4 HOH A 90 390 84 HOH HOH . F 4 HOH A 91 391 104 HOH HOH . F 4 HOH A 92 392 73 HOH HOH . F 4 HOH A 93 393 101 HOH HOH . F 4 HOH A 94 394 34 HOH HOH . F 4 HOH A 95 395 29 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 CL CL NQZ . . . B 2 -28.837 11.177 13.782 0.75 64.11 ? CL NQZ 201 A 1 HETATM 2 C C22 NQZ . . . B 2 -27.403 10.431 13.172 0.75 62.69 ? C22 NQZ 201 A 1 HETATM 3 C C23 NQZ . . . B 2 -27.289 10.071 11.84 0.75 62.7 ? C23 NQZ 201 A 1 HETATM 4 N N5 NQZ . . . B 2 -26.279 9.319 11.379 0.75 65.31 ? N5 NQZ 201 A 1 HETATM 5 C C7 NQZ . . . B 2 -25.376 8.923 12.296 0.75 66.49 ? C7 NQZ 201 A 1 HETATM 6 N N NQZ . . . B 2 -24.531 7.942 11.937 0.75 72.31 ? N NQZ 201 A 1 HETATM 7 C C2 NQZ . . . B 2 -23.616 7.266 12.856 0.75 74.43 ? C2 NQZ 201 A 1 HETATM 8 C C3 NQZ . . . B 2 -24.539 7.286 10.63 0.75 74.32 ? C3 NQZ 201 A 1 HETATM 9 C C4 NQZ . . . B 2 -25.045 5.856 10.742 0.75 75.63 ? C4 NQZ 201 A 1 HETATM 10 C C5 NQZ . . . B 2 -24.9 5.139 9.401 0.75 75.91 ? C5 NQZ 201 A 1 HETATM 11 C C6 NQZ . . . B 2 -24.257 5.1 11.882 0.75 77.58 ? C6 NQZ 201 A 1 HETATM 12 F F NQZ . . . B 2 -23.016 4.778 11.421 0.75 78.68 ? F NQZ 201 A 1 HETATM 13 F F1 NQZ . . . B 2 -24.861 3.904 12.136 0.75 79.62 ? F1 NQZ 201 A 1 HETATM 14 C C1 NQZ . . . B 2 -24.151 5.893 13.219 0.75 76.18 ? C1 NQZ 201 A 1 HETATM 15 C C NQZ . . . B 2 -23.225 5.213 14.224 0.75 76.88 ? C NQZ 201 A 1 HETATM 16 C C8 NQZ . . . B 2 -26.397 9.993 14.042 0.75 62.52 ? C8 NQZ 201 A 1 HETATM 17 N N1 NQZ . . . B 2 -25.373 9.258 13.597 0.75 64.16 ? N1 NQZ 201 A 1 HETATM 18 N N2 NQZ . . . B 2 -26.485 10.277 15.366 0.75 61.69 ? N2 NQZ 201 A 1 HETATM 19 C C9 NQZ . . . B 2 -25.6 9.895 16.382 0.75 58.93 ? C9 NQZ 201 A 1 HETATM 20 C C14 NQZ . . . B 2 -25.354 8.547 16.631 0.75 58.63 ? C14 NQZ 201 A 1 HETATM 21 C C13 NQZ . . . B 2 -24.391 8.158 17.546 0.75 60.07 ? C13 NQZ 201 A 1 HETATM 22 C C12 NQZ . . . B 2 -23.697 9.144 18.231 0.75 61.76 ? C12 NQZ 201 A 1 HETATM 23 N N3 NQZ . . . B 2 -22.69 9.077 19.186 0.75 62.44 ? N3 NQZ 201 A 1 HETATM 24 C C15 NQZ . . . B 2 -22.068 7.862 19.697 0.75 62.37 ? C15 NQZ 201 A 1 HETATM 25 C C16 NQZ . . . B 2 -22.343 10.345 19.59 0.75 62.72 ? C16 NQZ 201 A 1 HETATM 26 O O NQZ . . . B 2 -21.5 10.645 20.411 0.75 63.29 ? O NQZ 201 A 1 HETATM 27 N N4 NQZ . . . B 2 -23.143 11.209 18.871 0.75 61.66 ? N4 NQZ 201 A 1 HETATM 28 C C11 NQZ . . . B 2 -23.986 10.485 18.03 0.75 60.74 ? C11 NQZ 201 A 1 HETATM 29 C C10 NQZ . . . B 2 -24.946 10.879 17.116 0.75 58.93 ? C10 NQZ 201 A 1 HETATM 30 C C17 NQZ . . . B 2 -23.063 12.668 18.974 0.75 61.74 ? C17 NQZ 201 A 1 HETATM 31 C C18 NQZ . . . B 2 -22.14 13.28 17.927 0.75 61.07 ? C18 NQZ 201 A 1 HETATM 32 C C19 NQZ . . . B 2 -22.197 14.807 17.922 0.75 60.21 ? C19 NQZ 201 A 1 HETATM 33 O O1 NQZ . . . B 2 -21.927 15.28 19.25 0.75 63.66 ? O1 NQZ 201 A 1 HETATM 34 C C21 NQZ . . . B 2 -21.134 15.387 17.008 0.75 61.6 ? C21 NQZ 201 A 1 HETATM 35 C C20 NQZ . . . B 2 -23.574 15.311 17.535 0.75 52.3 ? C20 NQZ 201 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 35 #