data_4J53 # _model_server_result.job_id 569aTgBbvj4OGMCPHePnrg _model_server_result.datetime_utc '2024-11-14 07:10:29' _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 4j53 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 4J53 # _exptl.entry_id 4J53 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 561.599 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-[(9-cyclopentyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino]-2-fluoro-5-methoxy-N-(1-methylpiperidin-4-yl)benzamide _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 4J53 _cell.length_a 66.649 _cell.length_b 66.649 _cell.length_c 153.96 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4J53 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order metalc ? metalc1 A NE2 HIS 56 A HIS 93 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc2 A SG CYS 175 A CYS 212 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc3 B ZN ZN . A ZN 401 1_555 E O HOH . A HOH 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? # _chem_comp.formula 'C27 H34 F3 N7 O3' _chem_comp.formula_weight 561.599 _chem_comp.id 1J4 _chem_comp.mon_nstd_flag . _chem_comp.name 4-[(9-cyclopentyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino]-2-fluoro-5-methoxy-N-(1-methylpiperidin-4-yl)benzamide _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 O2 1J4 sing 1 n n O2 C3 1J4 sing 2 n n O7 C6 1J4 doub 3 n n C4 C3 1J4 doub 4 n y C4 C5 1J4 sing 5 n y C3 C19 1J4 sing 6 n y C6 C5 1J4 sing 7 n n C6 N8 1J4 sing 8 n n C5 C16 1J4 doub 9 n y C19 N20 1J4 sing 10 n n C19 C18 1J4 doub 11 n y N20 C21 1J4 sing 12 n n C9 N8 1J4 sing 13 n n C9 C15 1J4 sing 14 n n C9 C10 1J4 sing 15 n n C16 C18 1J4 sing 16 n y C16 F17 1J4 sing 17 n n N22 C21 1J4 doub 18 n y N22 C23 1J4 sing 19 n y C21 N40 1J4 sing 20 n y C15 C14 1J4 sing 21 n n C10 C11 1J4 sing 22 n n C14 N12 1J4 sing 23 n n C11 N12 1J4 sing 24 n n C23 C24 1J4 doub 25 n y N40 C39 1J4 doub 26 n y N12 C13 1J4 sing 27 n n C24 C39 1J4 sing 28 n y C24 N25 1J4 sing 29 n n C26 N25 1J4 sing 30 n n C39 N33 1J4 sing 31 n n N25 C27 1J4 sing 32 n n C34 N33 1J4 sing 33 n n C34 C38 1J4 sing 34 n n C34 C35 1J4 sing 35 n n N33 C32 1J4 sing 36 n n C38 C37 1J4 sing 37 n n C35 C36 1J4 sing 38 n n C27 O28 1J4 doub 39 n n C27 C29 1J4 sing 40 n n C32 C29 1J4 sing 41 n n C37 C36 1J4 sing 42 n n C29 F31 1J4 sing 43 n n C29 F30 1J4 sing 44 n n N8 H1 1J4 sing 45 n n C9 H2 1J4 sing 46 n n C10 H3 1J4 sing 47 n n C10 H4 1J4 sing 48 n n C11 H5 1J4 sing 49 n n C11 H6 1J4 sing 50 n n C13 H8 1J4 sing 51 n n C13 H9 1J4 sing 52 n n C13 H10 1J4 sing 53 n n C14 H11 1J4 sing 54 n n C14 H12 1J4 sing 55 n n C15 H13 1J4 sing 56 n n C15 H14 1J4 sing 57 n n C4 H15 1J4 sing 58 n n C1 H16 1J4 sing 59 n n C1 H17 1J4 sing 60 n n C1 H18 1J4 sing 61 n n C18 H19 1J4 sing 62 n n N20 H20 1J4 sing 63 n n C23 H21 1J4 sing 64 n n C26 H22 1J4 sing 65 n n C26 H23 1J4 sing 66 n n C26 H24 1J4 sing 67 n n C32 H25 1J4 sing 68 n n C32 H26 1J4 sing 69 n n C34 H27 1J4 sing 70 n n C35 H28 1J4 sing 71 n n C35 H29 1J4 sing 72 n n C36 H30 1J4 sing 73 n n C36 H31 1J4 sing 74 n n C37 H32 1J4 sing 75 n n C37 H33 1J4 sing 76 n n C38 H34 1J4 sing 77 n n C38 H35 1J4 sing 78 n n # _atom_sites.entry_id 4J53 _atom_sites.fract_transf_matrix[1][1] 0.015004 _atom_sites.fract_transf_matrix[1][2] 0.008663 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017325 _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] 0.006495 _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 ZN A 1 401 401 ZN ZN . C 3 ACT A 1 402 402 ACT ACT . D 4 1J4 A 1 403 403 1J4 LIG . E 5 HOH A 1 501 404 HOH HOH . E 5 HOH A 2 502 405 HOH HOH . E 5 HOH A 3 503 406 HOH HOH . E 5 HOH A 4 504 407 HOH HOH . E 5 HOH A 5 505 408 HOH HOH . E 5 HOH A 6 506 409 HOH HOH . E 5 HOH A 7 507 410 HOH HOH . E 5 HOH A 8 508 411 HOH HOH . E 5 HOH A 9 509 412 HOH HOH . E 5 HOH A 10 510 413 HOH HOH . E 5 HOH A 11 511 414 HOH HOH . E 5 HOH A 12 512 415 HOH HOH . E 5 HOH A 13 513 416 HOH HOH . E 5 HOH A 14 514 417 HOH HOH . E 5 HOH A 15 515 418 HOH HOH . E 5 HOH A 16 516 419 HOH HOH . E 5 HOH A 17 517 420 HOH HOH . E 5 HOH A 18 518 421 HOH HOH . E 5 HOH A 19 519 422 HOH HOH . E 5 HOH A 20 520 423 HOH HOH . E 5 HOH A 21 521 424 HOH HOH . E 5 HOH A 22 522 425 HOH HOH . E 5 HOH A 23 523 426 HOH HOH . E 5 HOH A 24 524 427 HOH HOH . E 5 HOH A 25 525 428 HOH HOH . E 5 HOH A 26 526 429 HOH HOH . E 5 HOH A 27 527 430 HOH HOH . E 5 HOH A 28 528 431 HOH HOH . E 5 HOH A 29 529 432 HOH HOH . E 5 HOH A 30 530 433 HOH HOH . E 5 HOH A 31 531 434 HOH HOH . E 5 HOH A 32 532 435 HOH HOH . E 5 HOH A 33 533 436 HOH HOH . E 5 HOH A 34 534 437 HOH HOH . E 5 HOH A 35 535 438 HOH HOH . E 5 HOH A 36 536 439 HOH HOH . E 5 HOH A 37 537 440 HOH HOH . E 5 HOH A 38 538 441 HOH HOH . E 5 HOH A 39 539 442 HOH HOH . E 5 HOH A 40 540 443 HOH HOH . E 5 HOH A 41 541 444 HOH HOH . E 5 HOH A 42 542 445 HOH HOH . E 5 HOH A 43 543 446 HOH HOH . E 5 HOH A 44 544 447 HOH HOH . E 5 HOH A 45 545 448 HOH HOH . E 5 HOH A 46 546 449 HOH HOH . E 5 HOH A 47 547 450 HOH HOH . E 5 HOH A 48 548 451 HOH HOH . E 5 HOH A 49 549 452 HOH HOH . E 5 HOH A 50 550 453 HOH HOH . E 5 HOH A 51 551 454 HOH HOH . E 5 HOH A 52 552 455 HOH HOH . E 5 HOH A 53 553 456 HOH HOH . E 5 HOH A 54 554 457 HOH HOH . E 5 HOH A 55 555 458 HOH HOH . E 5 HOH A 56 556 459 HOH HOH . E 5 HOH A 57 557 460 HOH HOH . E 5 HOH A 58 558 461 HOH HOH . E 5 HOH A 59 559 462 HOH HOH . E 5 HOH A 60 560 463 HOH HOH . E 5 HOH A 61 561 464 HOH HOH . E 5 HOH A 62 562 465 HOH HOH . E 5 HOH A 63 563 466 HOH HOH . E 5 HOH A 64 564 468 HOH HOH . E 5 HOH A 65 565 469 HOH HOH . E 5 HOH A 66 566 470 HOH HOH . E 5 HOH A 67 567 471 HOH HOH . E 5 HOH A 68 568 472 HOH HOH . E 5 HOH A 69 569 473 HOH HOH . E 5 HOH A 70 570 474 HOH HOH . E 5 HOH A 71 571 475 HOH HOH . E 5 HOH A 72 572 476 HOH HOH . E 5 HOH A 73 573 477 HOH HOH . E 5 HOH A 74 574 478 HOH HOH . E 5 HOH A 75 575 479 HOH HOH . E 5 HOH A 76 576 480 HOH HOH . E 5 HOH A 77 577 481 HOH HOH . E 5 HOH A 78 578 482 HOH HOH . E 5 HOH A 79 579 483 HOH HOH . E 5 HOH A 80 580 484 HOH HOH . E 5 HOH A 81 581 485 HOH HOH . E 5 HOH A 82 582 486 HOH HOH . E 5 HOH A 83 583 487 HOH HOH . E 5 HOH A 84 584 488 HOH HOH . E 5 HOH A 85 585 489 HOH HOH . E 5 HOH A 86 586 490 HOH HOH . E 5 HOH A 87 587 491 HOH HOH . E 5 HOH A 88 588 492 HOH HOH . E 5 HOH A 89 589 493 HOH HOH . E 5 HOH A 90 590 494 HOH HOH . E 5 HOH A 91 591 495 HOH HOH . E 5 HOH A 92 592 496 HOH HOH . E 5 HOH A 93 593 497 HOH HOH . E 5 HOH A 94 594 498 HOH HOH . E 5 HOH A 95 595 499 HOH HOH . E 5 HOH A 96 596 500 HOH HOH . E 5 HOH A 97 597 501 HOH HOH . E 5 HOH A 98 598 502 HOH HOH . E 5 HOH A 99 599 503 HOH HOH . E 5 HOH A 100 600 504 HOH HOH . E 5 HOH A 101 601 505 HOH HOH . E 5 HOH A 102 602 506 HOH HOH . E 5 HOH A 103 603 507 HOH HOH . E 5 HOH A 104 604 508 HOH HOH . E 5 HOH A 105 605 509 HOH HOH . E 5 HOH A 106 606 510 HOH HOH . E 5 HOH A 107 607 511 HOH HOH . E 5 HOH A 108 608 512 HOH HOH . E 5 HOH A 109 609 513 HOH HOH . E 5 HOH A 110 610 514 HOH HOH . E 5 HOH A 111 611 515 HOH HOH . E 5 HOH A 112 612 516 HOH HOH . E 5 HOH A 113 613 517 HOH HOH . E 5 HOH A 114 614 518 HOH HOH . E 5 HOH A 115 615 519 HOH HOH . E 5 HOH A 116 616 520 HOH HOH . E 5 HOH A 117 617 521 HOH HOH . E 5 HOH A 118 618 522 HOH HOH . E 5 HOH A 119 619 523 HOH HOH . E 5 HOH A 120 620 524 HOH HOH . E 5 HOH A 121 621 525 HOH HOH . E 5 HOH A 122 622 526 HOH HOH . E 5 HOH A 123 623 527 HOH HOH . E 5 HOH A 124 624 528 HOH HOH . E 5 HOH A 125 625 529 HOH HOH . E 5 HOH A 126 626 530 HOH HOH . E 5 HOH A 127 627 531 HOH HOH . E 5 HOH A 128 628 532 HOH HOH . E 5 HOH A 129 629 533 HOH HOH . E 5 HOH A 130 630 534 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 O O7 1J4 . . . D 4 51.058 11.352 31.074 1 76.18 ? O7 1J4 403 A 1 HETATM 2 C C6 1J4 . . . D 4 50.581 11.208 32.179 1 73.75 ? C6 1J4 403 A 1 HETATM 3 N N8 1J4 . . . D 4 51.345 10.945 33.246 1 75.64 ? N8 1J4 403 A 1 HETATM 4 C C9 1J4 . . . D 4 52.808 10.834 33.234 1 80.2 ? C9 1J4 403 A 1 HETATM 5 C C10 1J4 . . . D 4 53.357 12.01 34.04 1 79.35 ? C10 1J4 403 A 1 HETATM 6 C C11 1J4 . . . D 4 54.858 11.887 34.281 1 83.17 ? C11 1J4 403 A 1 HETATM 7 N N12 1J4 . . . D 4 55.196 10.61 34.933 1 86.57 ? N12 1J4 403 A 1 HETATM 8 C C13 1J4 . . . D 4 56.662 10.509 35.101 1 88.09 ? C13 1J4 403 A 1 HETATM 9 C C14 1J4 . . . D 4 54.701 9.471 34.133 1 87.15 ? C14 1J4 403 A 1 HETATM 10 C C15 1J4 . . . D 4 53.186 9.545 33.956 1 83.45 ? C15 1J4 403 A 1 HETATM 11 C C5 1J4 . . . D 4 49.081 11.298 32.336 1 75.12 ? C5 1J4 403 A 1 HETATM 12 C C4 1J4 . . . D 4 48.271 10.516 31.507 1 76.51 ? C4 1J4 403 A 1 HETATM 13 C C3 1J4 . . . D 4 46.874 10.557 31.628 1 75.81 ? C3 1J4 403 A 1 HETATM 14 O O2 1J4 . . . D 4 46.067 9.788 30.816 1 78.01 ? O2 1J4 403 A 1 HETATM 15 C C1 1J4 . . . D 4 46.323 8.408 30.541 1 78.62 ? C1 1J4 403 A 1 HETATM 16 C C16 1J4 . . . D 4 48.47 12.133 33.281 1 72.34 ? C16 1J4 403 A 1 HETATM 17 F F17 1J4 . . . D 4 49.181 12.922 34.112 1 72.17 ? F17 1J4 403 A 1 HETATM 18 C C18 1J4 . . . D 4 47.083 12.171 33.391 1 70.15 ? C18 1J4 403 A 1 HETATM 19 C C19 1J4 . . . D 4 46.27 11.388 32.568 1 71.18 ? C19 1J4 403 A 1 HETATM 20 N N20 1J4 . . . D 4 44.91 11.333 32.653 1 69.76 ? N20 1J4 403 A 1 HETATM 21 C C21 1J4 . . . D 4 44.114 11.897 33.606 1 64.65 ? C21 1J4 403 A 1 HETATM 22 N N22 1J4 . . . D 4 42.782 11.728 33.467 1 61.21 ? N22 1J4 403 A 1 HETATM 23 C C23 1J4 . . . D 4 41.917 12.254 34.324 1 59.92 ? C23 1J4 403 A 1 HETATM 24 C C24 1J4 . . . D 4 42.369 12.984 35.418 1 63.11 ? C24 1J4 403 A 1 HETATM 25 N N25 1J4 . . . D 4 41.405 13.586 36.265 1 67.83 ? N25 1J4 403 A 1 HETATM 26 C C26 1J4 . . . D 4 40.236 14.119 35.547 1 67.06 ? C26 1J4 403 A 1 HETATM 27 C C27 1J4 . . . D 4 41.498 13.786 37.592 1 70.07 ? C27 1J4 403 A 1 HETATM 28 O O28 1J4 . . . D 4 40.576 14.363 38.164 1 68.17 ? O28 1J4 403 A 1 HETATM 29 N N40 1J4 . . . D 4 44.583 12.608 34.652 1 62.92 ? N40 1J4 403 A 1 HETATM 30 C C39 1J4 . . . D 4 43.749 13.18 35.553 1 64.88 ? C39 1J4 403 A 1 HETATM 31 N N33 1J4 . . . D 4 44.267 13.924 36.649 1 67.56 ? N33 1J4 403 A 1 HETATM 32 C C32 1J4 . . . D 4 44.021 13.151 37.875 1 71.48 ? C32 1J4 403 A 1 HETATM 33 C C29 1J4 . . . D 4 42.629 13.316 38.484 1 71.47 ? C29 1J4 403 A 1 HETATM 34 F F30 1J4 . . . D 4 42.716 14.189 39.474 1 77.19 ? F30 1J4 403 A 1 HETATM 35 F F31 1J4 . . . D 4 42.306 12.135 38.979 1 71.02 ? F31 1J4 403 A 1 HETATM 36 C C34 1J4 . . . D 4 45.707 14.313 36.521 1 68.44 ? C34 1J4 403 A 1 HETATM 37 C C35 1J4 . . . D 4 46.01 15.546 37.376 1 67.63 ? C35 1J4 403 A 1 HETATM 38 C C36 1J4 . . . D 4 47.304 15.308 38.136 1 69.26 ? C36 1J4 403 A 1 HETATM 39 C C37 1J4 . . . D 4 47.623 13.828 38.024 1 70.31 ? C37 1J4 403 A 1 HETATM 40 C C38 1J4 . . . D 4 46.738 13.249 36.928 1 69.81 ? C38 1J4 403 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 40 #