data_3P5K # _model_server_result.job_id g2CwMSZtsMsDHZFi4364yg _model_server_result.datetime_utc '2024-10-20 20:41:13' _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 3p5k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":362}' # _entry.id 3P5K # _exptl.entry_id 3P5K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 485.619 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-{5-tert-butyl-3-[(1,1-dioxidothiomorpholin-4-yl)carbonyl]thiophen-2-yl}-3-naphthalen-1-ylurea _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 3P5K _cell.length_a 67.95 _cell.length_b 71.08 _cell.length_c 75.55 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3P5K _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,D _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C24 H27 N3 O4 S2' _chem_comp.formula_weight 485.619 _chem_comp.id P5K _chem_comp.mon_nstd_flag . _chem_comp.name 1-{5-tert-butyl-3-[(1,1-dioxidothiomorpholin-4-yl)carbonyl]thiophen-2-yl}-3-naphthalen-1-ylurea _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 C2 P5K sing 285 n y C1 C5 P5K doub 286 n y C2 C3 P5K doub 287 n y C2 C11 P5K sing 288 n n C3 S4 P5K sing 289 n y C3 N10 P5K sing 290 n n S4 C5 P5K sing 291 n y C5 C6 P5K sing 292 n n C6 C7 P5K sing 293 n n C6 C8 P5K sing 294 n n C6 C9 P5K sing 295 n n N10 C14 P5K sing 296 n n C11 O12 P5K doub 297 n n C11 N13 P5K sing 298 n n N13 C23 P5K sing 299 n n N13 C24 P5K sing 300 n n C14 N15 P5K sing 301 n n C14 O16 P5K doub 302 n n N15 C17 P5K sing 303 n n C17 C18 P5K doub 304 n y C17 C22 P5K sing 305 n y C18 C19 P5K sing 306 n y C19 C20 P5K doub 307 n y C20 C21 P5K sing 308 n y C21 C22 P5K doub 309 n y C21 C25 P5K sing 310 n y C22 C28 P5K sing 311 n y C23 C29 P5K sing 312 n n C24 C30 P5K sing 313 n n C25 C26 P5K doub 314 n y C26 C27 P5K sing 315 n y C27 C28 P5K doub 316 n y C29 S31 P5K sing 317 n n C30 S31 P5K sing 318 n n S31 O32 P5K doub 319 n n S31 O33 P5K doub 320 n n C1 H1 P5K sing 321 n n C7 H7 P5K sing 322 n n C7 H7A P5K sing 323 n n C7 H7B P5K sing 324 n n C8 H8 P5K sing 325 n n C8 H8A P5K sing 326 n n C8 H8B P5K sing 327 n n C9 H9 P5K sing 328 n n C9 H9A P5K sing 329 n n C9 H9B P5K sing 330 n n N10 HN10 P5K sing 331 n n N15 HN15 P5K sing 332 n n C18 H18 P5K sing 333 n n C19 H19 P5K sing 334 n n C20 H20 P5K sing 335 n n C23 H23 P5K sing 336 n n C23 H23A P5K sing 337 n n C24 H24 P5K sing 338 n n C24 H24A P5K sing 339 n n C25 H25 P5K sing 340 n n C26 H26 P5K sing 341 n n C27 H27 P5K sing 342 n n C28 H28 P5K sing 343 n n C29 H29 P5K sing 344 n n C29 H29A P5K sing 345 n n C30 H30 P5K sing 346 n n C30 H30A P5K sing 347 n n # _atom_sites.entry_id 3P5K _atom_sites.fract_transf_matrix[1][1] 0.014717 _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] 0.014069 _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] 0.013236 _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 BOG A 1 361 361 BOG BOG . C 3 P5K A 1 362 362 P5K P5K . D 4 HOH A 1 363 363 HOH HOH . D 4 HOH A 2 364 364 HOH HOH . D 4 HOH A 3 365 365 HOH HOH . D 4 HOH A 4 366 366 HOH HOH . D 4 HOH A 5 367 367 HOH HOH . D 4 HOH A 6 368 368 HOH HOH . D 4 HOH A 7 369 369 HOH HOH . D 4 HOH A 8 370 370 HOH HOH . D 4 HOH A 9 371 371 HOH HOH . D 4 HOH A 10 372 372 HOH HOH . D 4 HOH A 11 373 373 HOH HOH . D 4 HOH A 12 374 374 HOH HOH . D 4 HOH A 13 375 375 HOH HOH . D 4 HOH A 14 376 376 HOH HOH . D 4 HOH A 15 377 377 HOH HOH . D 4 HOH A 16 378 378 HOH HOH . D 4 HOH A 17 379 379 HOH HOH . D 4 HOH A 18 380 380 HOH HOH . D 4 HOH A 19 381 381 HOH HOH . D 4 HOH A 20 382 382 HOH HOH . D 4 HOH A 21 383 383 HOH HOH . D 4 HOH A 22 384 384 HOH HOH . D 4 HOH A 23 385 385 HOH HOH . D 4 HOH A 24 386 386 HOH HOH . D 4 HOH A 25 387 387 HOH HOH . D 4 HOH A 26 388 388 HOH HOH . D 4 HOH A 27 389 389 HOH HOH . D 4 HOH A 28 390 390 HOH HOH . D 4 HOH A 29 391 391 HOH HOH . D 4 HOH A 30 392 392 HOH HOH . D 4 HOH A 31 393 393 HOH HOH . D 4 HOH A 32 394 394 HOH HOH . D 4 HOH A 33 395 395 HOH HOH . D 4 HOH A 34 396 396 HOH HOH . D 4 HOH A 35 397 397 HOH HOH . D 4 HOH A 36 398 398 HOH HOH . D 4 HOH A 37 399 399 HOH HOH . D 4 HOH A 38 400 400 HOH HOH . D 4 HOH A 39 401 401 HOH HOH . D 4 HOH A 40 402 402 HOH HOH . D 4 HOH A 41 403 403 HOH HOH . D 4 HOH A 42 404 404 HOH HOH . D 4 HOH A 43 405 405 HOH HOH . D 4 HOH A 44 406 406 HOH HOH . D 4 HOH A 45 407 407 HOH HOH . D 4 HOH A 46 408 408 HOH HOH . D 4 HOH A 47 409 409 HOH HOH . D 4 HOH A 48 410 410 HOH HOH . D 4 HOH A 49 411 411 HOH HOH . D 4 HOH A 50 412 412 HOH HOH . D 4 HOH A 51 413 413 HOH HOH . D 4 HOH A 52 414 414 HOH HOH . D 4 HOH A 53 415 415 HOH HOH . D 4 HOH A 54 416 416 HOH HOH . D 4 HOH A 55 417 417 HOH HOH . D 4 HOH A 56 418 418 HOH HOH . D 4 HOH A 57 419 419 HOH HOH . D 4 HOH A 58 420 420 HOH HOH . D 4 HOH A 59 421 421 HOH HOH . D 4 HOH A 60 422 422 HOH HOH . D 4 HOH A 61 423 423 HOH HOH . D 4 HOH A 62 424 424 HOH HOH . D 4 HOH A 63 425 425 HOH HOH . D 4 HOH A 64 426 426 HOH HOH . D 4 HOH A 65 427 427 HOH HOH . D 4 HOH A 66 428 428 HOH HOH . D 4 HOH A 67 429 429 HOH HOH . D 4 HOH A 68 430 430 HOH HOH . D 4 HOH A 69 431 431 HOH HOH . D 4 HOH A 70 432 432 HOH HOH . D 4 HOH A 71 433 433 HOH HOH . D 4 HOH A 72 434 434 HOH HOH . D 4 HOH A 73 435 435 HOH HOH . D 4 HOH A 74 436 436 HOH HOH . D 4 HOH A 75 437 437 HOH HOH . D 4 HOH A 76 438 438 HOH HOH . D 4 HOH A 77 439 439 HOH HOH . D 4 HOH A 78 440 440 HOH HOH . D 4 HOH A 79 441 441 HOH HOH . D 4 HOH A 80 442 442 HOH HOH . D 4 HOH A 81 443 443 HOH HOH . D 4 HOH A 82 444 444 HOH HOH . D 4 HOH A 83 445 445 HOH HOH . D 4 HOH A 84 446 446 HOH HOH . D 4 HOH A 85 447 447 HOH HOH . D 4 HOH A 86 448 448 HOH HOH . D 4 HOH A 87 449 449 HOH HOH . D 4 HOH A 88 450 450 HOH HOH . D 4 HOH A 89 451 451 HOH HOH . D 4 HOH A 90 452 452 HOH HOH . D 4 HOH A 91 453 453 HOH HOH . D 4 HOH A 92 454 454 HOH HOH . D 4 HOH A 93 455 455 HOH HOH . D 4 HOH A 94 456 456 HOH HOH . D 4 HOH A 95 457 457 HOH HOH . D 4 HOH A 96 458 458 HOH HOH . D 4 HOH A 97 459 459 HOH HOH . D 4 HOH A 98 460 460 HOH HOH . D 4 HOH A 99 461 461 HOH HOH . D 4 HOH A 100 462 462 HOH HOH . D 4 HOH A 101 463 463 HOH HOH . D 4 HOH A 102 464 464 HOH HOH . D 4 HOH A 103 465 465 HOH HOH . D 4 HOH A 104 466 466 HOH HOH . D 4 HOH A 105 467 467 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 P5K . . . C 3 49.388 27.334 -16.943 1 18.98 ? C1 P5K 362 A 1 HETATM 2 C C2 P5K . . . C 3 50.599 28.037 -16.765 1 20.93 ? C2 P5K 362 A 1 HETATM 3 C C3 P5K . . . C 3 51.09 28.611 -17.958 1 22.74 ? C3 P5K 362 A 1 HETATM 4 S S4 P5K . . . C 3 49.889 28.289 -19.201 1 19.39 ? S4 P5K 362 A 1 HETATM 5 C C5 P5K . . . C 3 48.869 27.324 -18.226 1 17.63 ? C5 P5K 362 A 1 HETATM 6 C C6 P5K . . . C 3 47.613 26.732 -18.838 1 23.4 ? C6 P5K 362 A 1 HETATM 7 C C7 P5K . . . C 3 46.792 27.653 -19.715 1 19.78 ? C7 P5K 362 A 1 HETATM 8 C C8 P5K . . . C 3 46.681 26.43 -17.689 1 17.19 ? C8 P5K 362 A 1 HETATM 9 C C9 P5K . . . C 3 47.983 25.589 -19.759 1 23.51 ? C9 P5K 362 A 1 HETATM 10 N N10 P5K . . . C 3 52.215 29.351 -18.084 1 18.93 ? N10 P5K 362 A 1 HETATM 11 C C11 P5K . . . C 3 51.361 28.121 -15.44 1 28.12 ? C11 P5K 362 A 1 HETATM 12 O O12 P5K . . . C 3 51.733 27.125 -14.956 1 33.49 ? O12 P5K 362 A 1 HETATM 13 N N13 P5K . . . C 3 51.684 29.181 -14.668 1 34.41 ? N13 P5K 362 A 1 HETATM 14 C C14 P5K . . . C 3 52.404 30.28 -19.043 1 21.98 ? C14 P5K 362 A 1 HETATM 15 N N15 P5K . . . C 3 53.533 30.934 -19.179 1 23.56 ? N15 P5K 362 A 1 HETATM 16 O O16 P5K . . . C 3 51.407 30.502 -19.867 1 21.08 ? O16 P5K 362 A 1 HETATM 17 C C17 P5K . . . C 3 53.813 32.004 -20.003 1 22.12 ? C17 P5K 362 A 1 HETATM 18 C C18 P5K . . . C 3 53.007 33.139 -19.912 1 24.79 ? C18 P5K 362 A 1 HETATM 19 C C19 P5K . . . C 3 53.262 34.245 -20.769 1 25.1 ? C19 P5K 362 A 1 HETATM 20 C C20 P5K . . . C 3 54.347 34.203 -21.648 1 24.08 ? C20 P5K 362 A 1 HETATM 21 C C21 P5K . . . C 3 55.164 33.031 -21.777 1 20.38 ? C21 P5K 362 A 1 HETATM 22 C C22 P5K . . . C 3 54.914 31.964 -20.939 1 22.36 ? C22 P5K 362 A 1 HETATM 23 C C23 P5K . . . C 3 51.557 30.584 -15.101 1 32.92 ? C23 P5K 362 A 1 HETATM 24 C C24 P5K . . . C 3 52.243 28.924 -13.277 1 31.08 ? C24 P5K 362 A 1 HETATM 25 C C25 P5K . . . C 3 56.219 33.024 -22.703 1 26.97 ? C25 P5K 362 A 1 HETATM 26 C C26 P5K . . . C 3 57.084 31.93 -22.849 1 22.83 ? C26 P5K 362 A 1 HETATM 27 C C27 P5K . . . C 3 56.812 30.84 -22.012 1 23.82 ? C27 P5K 362 A 1 HETATM 28 C C28 P5K . . . C 3 55.762 30.846 -21.078 1 24.03 ? C28 P5K 362 A 1 HETATM 29 C C29 P5K . . . C 3 50.745 31.328 -14.014 1 37.68 ? C29 P5K 362 A 1 HETATM 30 C C30 P5K . . . C 3 51.515 29.66 -12.126 1 28.77 ? C30 P5K 362 A 1 HETATM 31 S S31 P5K . . . C 3 51.654 31.301 -12.532 1 34.44 ? S31 P5K 362 A 1 HETATM 32 O O32 P5K . . . C 3 50.648 32.409 -11.698 1 43.96 ? O32 P5K 362 A 1 HETATM 33 O O33 P5K . . . C 3 53.038 31.931 -13.286 1 35.69 ? O33 P5K 362 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 33 #