data_8WDK # _model_server_result.job_id aPbWX9yQjOk_JaDDG1mVNA _model_server_result.datetime_utc '2024-12-18 18:46:13' _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 8wdk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":301}' # _entry.id 8WDK # _exptl.entry_id 8WDK _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 1043.285 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2S,4R)-1-[(2S)-3,3-dimethyl-2-[3-[4-[4-[4-[[3-oxidanylidene-1-[6-(2-oxidanylpropan-2-yl)pyridin-2-yl]-2-prop-2-enyl-pyrazolo[3,4-d]pyrimidin-6-yl]amino]phenyl]piperazin-1-yl]butoxy]propanoylamino]butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide _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 8WDK _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8WDK _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,G _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 7 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 25 _struct_conn.ptnr1_auth_asym_id R _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 45 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 63 _struct_conn.ptnr2_auth_asym_id R _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 83 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 2.037 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C55 H70 N12 O7 S' _chem_comp.formula_weight 1043.285 _chem_comp.id W6U _chem_comp.mon_nstd_flag . _chem_comp.name (2S,4R)-1-[(2S)-3,3-dimethyl-2-[3-[4-[4-[4-[[3-oxidanylidene-1-[6-(2-oxidanylpropan-2-yl)pyridin-2-yl]-2-prop-2-enyl-pyrazolo[3,4-d]pyrimidin-6-yl]amino]phenyl]piperazin-1-yl]butoxy]propanoylamino]butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide _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 N1 C4 W6U doub 374 n y N1 C2 W6U sing 375 n y C4 S1 W6U sing 376 n y C2 C1 W6U sing 377 n n C2 C3 W6U doub 378 n y S1 C3 W6U sing 379 n y C3 C5 W6U sing 380 n n C5 C55 W6U doub 381 n y C5 C6 W6U sing 382 n y C55 C54 W6U sing 383 n y C6 C7 W6U doub 384 n y C54 C8 W6U doub 385 n y C7 C8 W6U sing 386 n y C8 C9 W6U sing 387 n n C53 C50 W6U sing 388 n n C9 N2 W6U sing 389 n n O1 C10 W6U doub 390 n n C12 C13 W6U sing 391 n n C12 C11 W6U sing 392 n n N2 C10 W6U sing 393 n n C10 C11 W6U sing 394 n n C13 C14 W6U sing 395 n n C13 O2 W6U sing 396 n n C14 N3 W6U sing 397 n n C50 C52 W6U sing 398 n n C50 C51 W6U sing 399 n n C50 C16 W6U sing 400 n n C11 N3 W6U sing 401 n n N3 C15 W6U sing 402 n n C33 N8 W6U doub 403 n y C33 C34 W6U sing 404 n y N8 C32 W6U sing 405 n y C15 C16 W6U sing 406 n n C15 O3 W6U doub 407 n n C16 N4 W6U sing 408 n n C38 C37 W6U doub 409 n n O6 C35 W6U doub 410 n n C34 C35 W6U sing 411 n n C34 C39 W6U doub 412 n y C32 N7 W6U sing 413 n n C32 N11 W6U doub 414 n y N7 C31 W6U sing 415 n n C35 N9 W6U sing 416 n n C31 C30 W6U doub 417 n y C31 C48 W6U sing 418 n y C30 C29 W6U sing 419 n y C39 N11 W6U sing 420 n y C39 N10 W6U sing 421 n n C37 C36 W6U sing 422 n n N4 C17 W6U sing 423 n n N9 N10 W6U sing 424 n n N9 C36 W6U sing 425 n n O4 C17 W6U doub 426 n n C48 C49 W6U doub 427 n y C29 C28 W6U doub 428 n y N10 C40 W6U sing 429 n n C17 C18 W6U sing 430 n n C49 C28 W6U sing 431 n y C28 N6 W6U sing 432 n n C24 C25 W6U sing 433 n n C24 N5 W6U sing 434 n n C41 C40 W6U doub 435 n y C41 C42 W6U sing 436 n y C27 N5 W6U sing 437 n n C27 C26 W6U sing 438 n n C40 N12 W6U sing 439 n y C23 N5 W6U sing 440 n n C23 C22 W6U sing 441 n n N6 C25 W6U sing 442 n n N6 C26 W6U sing 443 n n C21 C22 W6U sing 444 n n C21 C20 W6U sing 445 n n C18 C19 W6U sing 446 n n C19 O5 W6U sing 447 n n C42 C43 W6U doub 448 n y N12 C44 W6U doub 449 n y C20 O5 W6U sing 450 n n C43 C44 W6U sing 451 n y C44 C45 W6U sing 452 n n C46 C45 W6U sing 453 n n C45 C47 W6U sing 454 n n C45 O7 W6U sing 455 n n C4 H1 W6U sing 456 n n C6 H2 W6U sing 457 n n C7 H3 W6U sing 458 n n C13 H4 W6U sing 459 n n C20 H5 W6U sing 460 n n C20 H6 W6U sing 461 n n C21 H7 W6U sing 462 n n C21 H8 W6U sing 463 n n C22 H9 W6U sing 464 n n C22 H10 W6U sing 465 n n C24 H11 W6U sing 466 n n C24 H12 W6U sing 467 n n C26 H13 W6U sing 468 n n C26 H14 W6U sing 469 n n C1 H15 W6U sing 470 n n C1 H16 W6U sing 471 n n C1 H17 W6U sing 472 n n C9 H18 W6U sing 473 n n C9 H19 W6U sing 474 n n N2 H20 W6U sing 475 n n C11 H21 W6U sing 476 n n C12 H22 W6U sing 477 n n C12 H23 W6U sing 478 n n O2 H24 W6U sing 479 n n C14 H25 W6U sing 480 n n C14 H26 W6U sing 481 n n C16 H27 W6U sing 482 n n N4 H28 W6U sing 483 n n C18 H29 W6U sing 484 n n C18 H30 W6U sing 485 n n C19 H31 W6U sing 486 n n C19 H32 W6U sing 487 n n C23 H33 W6U sing 488 n n C23 H34 W6U sing 489 n n C25 H36 W6U sing 490 n n C25 H37 W6U sing 491 n n C27 H38 W6U sing 492 n n C27 H39 W6U sing 493 n n C29 H40 W6U sing 494 n n C30 H41 W6U sing 495 n n N7 H42 W6U sing 496 n n C33 H43 W6U sing 497 n n C36 H44 W6U sing 498 n n C36 H45 W6U sing 499 n n C37 H46 W6U sing 500 n n C38 H47 W6U sing 501 n n C38 H48 W6U sing 502 n n C41 H49 W6U sing 503 n n C42 H50 W6U sing 504 n n C43 H51 W6U sing 505 n n C46 H52 W6U sing 506 n n C46 H53 W6U sing 507 n n C46 H54 W6U sing 508 n n C47 H55 W6U sing 509 n n C47 H56 W6U sing 510 n n C47 H57 W6U sing 511 n n O7 H58 W6U sing 512 n n C48 H59 W6U sing 513 n n C49 H60 W6U sing 514 n n C51 H61 W6U sing 515 n n C51 H62 W6U sing 516 n n C51 H63 W6U sing 517 n n C52 H64 W6U sing 518 n n C52 H65 W6U sing 519 n n C52 H66 W6U sing 520 n n C53 H67 W6U sing 521 n n C53 H68 W6U sing 522 n n C53 H69 W6U sing 523 n n C54 H70 W6U sing 524 n n C55 H71 W6U sing 525 n n # _atom_sites.entry_id 8WDK _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id G _pdbx_nonpoly_scheme.entity_id 7 _pdbx_nonpoly_scheme.mon_id W6U _pdbx_nonpoly_scheme.pdb_strand_id V _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 301 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id W6U _pdbx_nonpoly_scheme.auth_mon_id LIG _pdbx_nonpoly_scheme.pdb_ins_code . # 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 W6U . . . G 7 201.066 177.612 175.345 1 59.86 ? N1 W6U 301 V 1 HETATM 2 N N3 W6U . . . G 7 208.726 179.803 183.741 1 59.86 ? N3 W6U 301 V 1 HETATM 3 C C4 W6U . . . G 7 201.261 178.892 175.383 1 59.86 ? C4 W6U 301 V 1 HETATM 4 C C5 W6U . . . G 7 202.806 177.616 178.671 1 59.86 ? C5 W6U 301 V 1 HETATM 5 C C6 W6U . . . G 7 203.042 178.644 179.579 1 59.86 ? C6 W6U 301 V 1 HETATM 6 C C7 W6U . . . G 7 203.735 178.412 180.753 1 59.86 ? C7 W6U 301 V 1 HETATM 7 C C8 W6U . . . G 7 204.234 177.156 181.049 1 59.86 ? C8 W6U 301 V 1 HETATM 8 C C10 W6U . . . G 7 206.861 178.348 182.92 1 59.86 ? C10 W6U 301 V 1 HETATM 9 N N12 W6U . . . G 7 217.296 163.526 188.623 1 59.86 ? N12 W6U 301 V 1 HETATM 10 C C13 W6U . . . G 7 207.945 181.9 183.09 1 59.86 ? C13 W6U 301 V 1 HETATM 11 C C15 W6U . . . G 7 209.462 178.881 184.376 1 59.86 ? C15 W6U 301 V 1 HETATM 12 C C17 W6U . . . G 7 211.961 179.741 186.642 1 59.86 ? C17 W6U 301 V 1 HETATM 13 C C20 W6U . . . G 7 216.118 178.698 188.948 1 59.86 ? C20 W6U 301 V 1 HETATM 14 C C21 W6U . . . G 7 216.581 177.838 187.793 1 59.86 ? C21 W6U 301 V 1 HETATM 15 C C22 W6U . . . G 7 216.408 176.333 187.987 1 59.86 ? C22 W6U 301 V 1 HETATM 16 C C24 W6U . . . G 7 213.412 174.076 187.398 1 59.86 ? C24 W6U 301 V 1 HETATM 17 C C26 W6U . . . G 7 215.424 172.159 188.035 1 59.86 ? C26 W6U 301 V 1 HETATM 18 C C28 W6U . . . G 7 213.857 170.527 186.973 1 59.86 ? C28 W6U 301 V 1 HETATM 19 C C1 W6U . . . G 7 201.208 175.563 176.697 1 59.86 ? C1 W6U 301 V 1 HETATM 20 C C2 W6U . . . G 7 201.466 177.029 176.525 1 59.86 ? C2 W6U 301 V 1 HETATM 21 C C3 W6U . . . G 7 202.069 177.886 177.416 1 59.86 ? C3 W6U 301 V 1 HETATM 22 S S1 W6U . . . G 7 201.902 179.501 176.841 1 59.86 ? S1 W6U 301 V 1 HETATM 23 C C9 W6U . . . G 7 204.993 176.911 182.327 1 59.86 ? C9 W6U 301 V 1 HETATM 24 N N2 W6U . . . G 7 205.548 178.131 182.886 1 59.86 ? N2 W6U 301 V 1 HETATM 25 O O1 W6U . . . G 7 207.693 177.578 182.442 1 59.86 ? O1 W6U 301 V 1 HETATM 26 C C11 W6U . . . G 7 207.278 179.655 183.586 1 59.86 ? C11 W6U 301 V 1 HETATM 27 C C12 W6U . . . G 7 206.908 180.86 182.708 1 59.86 ? C12 W6U 301 V 1 HETATM 28 O O2 W6U . . . G 7 207.64 182.393 184.385 1 59.86 ? O2 W6U 301 V 1 HETATM 29 C C14 W6U . . . G 7 209.213 181.063 183.155 1 59.86 ? C14 W6U 301 V 1 HETATM 30 O O3 W6U . . . G 7 208.951 177.875 184.856 1 59.86 ? O3 W6U 301 V 1 HETATM 31 C C16 W6U . . . G 7 210.965 179.132 184.495 1 59.86 ? C16 W6U 301 V 1 HETATM 32 N N4 W6U . . . G 7 211.373 178.838 185.857 1 59.86 ? N4 W6U 301 V 1 HETATM 33 O O4 W6U . . . G 7 212.047 180.926 186.327 1 59.86 ? O4 W6U 301 V 1 HETATM 34 C C18 W6U . . . G 7 212.545 179.22 187.937 1 59.86 ? C18 W6U 301 V 1 HETATM 35 C C19 W6U . . . G 7 214.032 179.247 187.966 1 59.86 ? C19 W6U 301 V 1 HETATM 36 O O5 W6U . . . G 7 214.702 178.638 189.061 1 59.86 ? O5 W6U 301 V 1 HETATM 37 C C23 W6U . . . G 7 215.027 175.867 187.557 1 59.86 ? C23 W6U 301 V 1 HETATM 38 N N5 W6U . . . G 7 214.698 174.495 187.969 1 59.86 ? N5 W6U 301 V 1 HETATM 39 C C25 W6U . . . G 7 213.037 172.698 187.892 1 59.86 ? C25 W6U 301 V 1 HETATM 40 N N6 W6U . . . G 7 214.094 171.727 187.589 1 59.86 ? N6 W6U 301 V 1 HETATM 41 C C27 W6U . . . G 7 215.732 173.549 187.53 1 59.86 ? C27 W6U 301 V 1 HETATM 42 C C29 W6U . . . G 7 212.619 170.267 186.364 1 59.86 ? C29 W6U 301 V 1 HETATM 43 C C30 W6U . . . G 7 212.381 169.065 185.755 1 59.86 ? C30 W6U 301 V 1 HETATM 44 C C31 W6U . . . G 7 213.35 168.066 185.752 1 59.86 ? C31 W6U 301 V 1 HETATM 45 N N7 W6U . . . G 7 213.029 166.85 185.104 1 59.86 ? N7 W6U 301 V 1 HETATM 46 C C32 W6U . . . G 7 213.616 165.627 185.097 1 59.86 ? C32 W6U 301 V 1 HETATM 47 N N8 W6U . . . G 7 213.062 164.75 184.24 1 59.86 ? N8 W6U 301 V 1 HETATM 48 C C33 W6U . . . G 7 213.567 163.523 184.168 1 59.86 ? C33 W6U 301 V 1 HETATM 49 C C34 W6U . . . G 7 214.648 163.155 184.978 1 59.86 ? C34 W6U 301 V 1 HETATM 50 C C35 W6U . . . G 7 215.425 161.968 185.168 1 59.86 ? C35 W6U 301 V 1 HETATM 51 O O6 W6U . . . G 7 215.333 160.875 184.615 1 59.86 ? O6 W6U 301 V 1 HETATM 52 N N9 W6U . . . G 7 216.36 162.279 186.147 1 59.86 ? N9 W6U 301 V 1 HETATM 53 C C36 W6U . . . G 7 217.376 161.357 186.644 1 59.86 ? C36 W6U 301 V 1 HETATM 54 C C37 W6U . . . G 7 218.628 161.405 185.843 1 59.86 ? C37 W6U 301 V 1 HETATM 55 C C38 W6U . . . G 7 218.737 161.171 184.591 1 59.86 ? C38 W6U 301 V 1 HETATM 56 N N10 W6U . . . G 7 216.199 163.615 186.551 1 59.86 ? N10 W6U 301 V 1 HETATM 57 C C39 W6U . . . G 7 215.143 164.135 185.837 1 59.86 ? C39 W6U 301 V 1 HETATM 58 N N11 W6U . . . G 7 214.647 165.38 185.926 1 59.86 ? N11 W6U 301 V 1 HETATM 59 C C40 W6U . . . G 7 216.995 164.251 187.545 1 59.86 ? C40 W6U 301 V 1 HETATM 60 C C41 W6U . . . G 7 217.364 165.582 187.413 1 59.86 ? C41 W6U 301 V 1 HETATM 61 C C42 W6U . . . G 7 218.119 166.143 188.419 1 59.86 ? C42 W6U 301 V 1 HETATM 62 C C43 W6U . . . G 7 218.459 165.39 189.524 1 59.86 ? C43 W6U 301 V 1 HETATM 63 C C44 W6U . . . G 7 218.035 164.076 189.597 1 59.86 ? C44 W6U 301 V 1 HETATM 64 C C45 W6U . . . G 7 218.376 163.193 190.795 1 59.86 ? C45 W6U 301 V 1 HETATM 65 C C46 W6U . . . G 7 218.508 161.729 190.387 1 59.86 ? C46 W6U 301 V 1 HETATM 66 C C47 W6U . . . G 7 219.655 163.658 191.482 1 59.86 ? C47 W6U 301 V 1 HETATM 67 O O7 W6U . . . G 7 217.332 163.262 191.763 1 59.86 ? O7 W6U 301 V 1 HETATM 68 C C48 W6U . . . G 7 214.58 168.311 186.356 1 59.86 ? C48 W6U 301 V 1 HETATM 69 C C49 W6U . . . G 7 214.83 169.514 186.962 1 59.86 ? C49 W6U 301 V 1 HETATM 70 C C50 W6U . . . G 7 211.81 178.308 183.512 1 59.86 ? C50 W6U 301 V 1 HETATM 71 C C51 W6U . . . G 7 211.786 176.827 183.902 1 59.86 ? C51 W6U 301 V 1 HETATM 72 C C52 W6U . . . G 7 213.261 178.794 183.534 1 59.86 ? C52 W6U 301 V 1 HETATM 73 C C53 W6U . . . G 7 211.273 178.441 182.085 1 59.86 ? C53 W6U 301 V 1 HETATM 74 C C54 W6U . . . G 7 204.016 176.131 180.144 1 59.86 ? C54 W6U 301 V 1 HETATM 75 C C55 W6U . . . G 7 203.322 176.356 178.969 1 59.86 ? C55 W6U 301 V 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 75 #