data_4J52 # _model_server_result.job_id XuE9H_qq64LiTST5LJ9sQA _model_server_result.datetime_utc '2025-03-11 14:34:28' _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 4j52 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":400}' # _entry.id 4J52 # _exptl.entry_id 4J52 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 552.644 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-{[(7R)-9-cyclopentyl-7-ethenyl-7-fluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl]amino}-3-methoxy-N-(4-methylpiperazin-1-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 4J52 _cell.length_a 66.873 _cell.length_b 66.873 _cell.length_c 152.49 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4J52 _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 2 _struct_asym.id B _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 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc2 A SG CYS 175 A CYS 212 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc3 C ZN ZN . A ZN 401 1_555 E O HOH . A HOH 578 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.658 ? # _chem_comp.formula 'C28 H37 F N8 O3' _chem_comp.formula_weight 552.644 _chem_comp.id 1J3 _chem_comp.mon_nstd_flag . _chem_comp.name 4-{[(7R)-9-cyclopentyl-7-ethenyl-7-fluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl]amino}-3-methoxy-N-(4-methylpiperazin-1-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 1J3 sing 1 n n O2 C3 1J3 sing 2 n n O32 C31 1J3 doub 3 n n C4 C3 1J3 doub 4 n y C4 C5 1J3 sing 5 n y C3 C8 1J3 sing 6 n y C31 C5 1J3 sing 7 n n C31 N33 1J3 sing 8 n n C5 C6 1J3 doub 9 n y C8 N9 1J3 sing 10 n n C8 C7 1J3 doub 11 n y N9 C10 1J3 sing 12 n n C6 C7 1J3 sing 13 n y N33 N34 1J3 sing 14 n n N34 C35 1J3 sing 15 n n N34 C40 1J3 sing 16 n n N11 C10 1J3 doub 17 n y N11 C12 1J3 sing 18 n y C10 N28 1J3 sing 19 n y C36 C35 1J3 sing 20 n n C36 N37 1J3 sing 21 n n C39 C40 1J3 sing 22 n n C39 N37 1J3 sing 23 n n C12 C13 1J3 doub 24 n y N37 C38 1J3 sing 25 n n N28 C27 1J3 doub 26 n y C13 C27 1J3 sing 27 n y C13 N14 1J3 sing 28 n n C27 N21 1J3 sing 29 n n C15 N14 1J3 sing 30 n n N14 C16 1J3 sing 31 n n C22 N21 1J3 sing 32 n n C22 C26 1J3 sing 33 n n C22 C23 1J3 sing 34 n n N21 C20 1J3 sing 35 n n C26 C25 1J3 sing 36 n n C23 C24 1J3 sing 37 n n C16 O17 1J3 doub 38 n n C16 C18 1J3 sing 39 n n C24 C25 1J3 sing 40 n n C20 C18 1J3 sing 41 n n C29 C18 1J3 sing 42 n n C29 C30 1J3 doub 43 n n C18 F19 1J3 sing 44 n n C1 H1 1J3 sing 45 n n C1 H2 1J3 sing 46 n n C1 H3 1J3 sing 47 n n C4 H4 1J3 sing 48 n n C6 H5 1J3 sing 49 n n C7 H6 1J3 sing 50 n n N9 H7 1J3 sing 51 n n C12 H8 1J3 sing 52 n n C15 H9 1J3 sing 53 n n C15 H10 1J3 sing 54 n n C15 H11 1J3 sing 55 n n C20 H12 1J3 sing 56 n n C20 H13 1J3 sing 57 n n C22 H14 1J3 sing 58 n n C23 H15 1J3 sing 59 n n C23 H16 1J3 sing 60 n n C24 H17 1J3 sing 61 n n C24 H18 1J3 sing 62 n n C25 H19 1J3 sing 63 n n C25 H20 1J3 sing 64 n n C26 H21 1J3 sing 65 n n C26 H22 1J3 sing 66 n n C29 H23 1J3 sing 67 n n C30 H24 1J3 sing 68 n n C30 H25 1J3 sing 69 n n N33 H26 1J3 sing 70 n n C35 H27 1J3 sing 71 n n C35 H28 1J3 sing 72 n n C36 H29 1J3 sing 73 n n C36 H30 1J3 sing 74 n n C38 H32 1J3 sing 75 n n C38 H33 1J3 sing 76 n n C38 H34 1J3 sing 77 n n C39 H35 1J3 sing 78 n n C39 H36 1J3 sing 79 n n C40 H37 1J3 sing 80 n n C40 H38 1J3 sing 81 n n # _atom_sites.entry_id 4J52 _atom_sites.fract_transf_matrix[1][1] 0.014954 _atom_sites.fract_transf_matrix[1][2] 0.008634 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017267 _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] 0.006558 _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 1J3 A 1 400 400 1J3 LIG . C 3 ZN A 1 401 401 ZN ZN . D 4 ACT A 1 402 402 ACT ACT . E 5 HOH A 1 501 403 HOH HOH . E 5 HOH A 2 502 404 HOH HOH . E 5 HOH A 3 503 405 HOH HOH . E 5 HOH A 4 504 406 HOH HOH . E 5 HOH A 5 505 407 HOH HOH . E 5 HOH A 6 506 408 HOH HOH . E 5 HOH A 7 507 409 HOH HOH . E 5 HOH A 8 508 410 HOH HOH . E 5 HOH A 9 509 411 HOH HOH . E 5 HOH A 10 510 412 HOH HOH . E 5 HOH A 11 511 413 HOH HOH . E 5 HOH A 12 512 414 HOH HOH . E 5 HOH A 13 513 415 HOH HOH . E 5 HOH A 14 514 416 HOH HOH . E 5 HOH A 15 515 417 HOH HOH . E 5 HOH A 16 516 418 HOH HOH . E 5 HOH A 17 517 419 HOH HOH . E 5 HOH A 18 518 420 HOH HOH . E 5 HOH A 19 519 421 HOH HOH . E 5 HOH A 20 520 422 HOH HOH . E 5 HOH A 21 521 423 HOH HOH . E 5 HOH A 22 522 424 HOH HOH . E 5 HOH A 23 523 425 HOH HOH . E 5 HOH A 24 524 426 HOH HOH . E 5 HOH A 25 525 427 HOH HOH . E 5 HOH A 26 526 428 HOH HOH . E 5 HOH A 27 527 429 HOH HOH . E 5 HOH A 28 528 430 HOH HOH . E 5 HOH A 29 529 431 HOH HOH . E 5 HOH A 30 530 432 HOH HOH . E 5 HOH A 31 531 433 HOH HOH . E 5 HOH A 32 532 434 HOH HOH . E 5 HOH A 33 533 435 HOH HOH . E 5 HOH A 34 534 436 HOH HOH . E 5 HOH A 35 535 437 HOH HOH . E 5 HOH A 36 536 438 HOH HOH . E 5 HOH A 37 537 439 HOH HOH . E 5 HOH A 38 538 440 HOH HOH . E 5 HOH A 39 539 441 HOH HOH . E 5 HOH A 40 540 442 HOH HOH . E 5 HOH A 41 541 443 HOH HOH . E 5 HOH A 42 542 444 HOH HOH . E 5 HOH A 43 543 445 HOH HOH . E 5 HOH A 44 544 446 HOH HOH . E 5 HOH A 45 545 447 HOH HOH . E 5 HOH A 46 546 448 HOH HOH . E 5 HOH A 47 547 449 HOH HOH . E 5 HOH A 48 548 450 HOH HOH . E 5 HOH A 49 549 451 HOH HOH . E 5 HOH A 50 550 452 HOH HOH . E 5 HOH A 51 551 453 HOH HOH . E 5 HOH A 52 552 454 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 64 564 467 HOH HOH . E 5 HOH A 65 565 468 HOH HOH . E 5 HOH A 66 566 469 HOH HOH . E 5 HOH A 67 567 470 HOH HOH . E 5 HOH A 68 568 471 HOH HOH . E 5 HOH A 69 569 472 HOH HOH . E 5 HOH A 70 570 473 HOH HOH . E 5 HOH A 71 571 474 HOH HOH . E 5 HOH A 72 572 475 HOH HOH . E 5 HOH A 73 573 476 HOH HOH . E 5 HOH A 74 574 477 HOH HOH . E 5 HOH A 75 575 478 HOH HOH . E 5 HOH A 76 576 479 HOH HOH . E 5 HOH A 77 577 480 HOH HOH . E 5 HOH A 78 578 481 HOH HOH . E 5 HOH A 79 579 482 HOH HOH . E 5 HOH A 80 580 483 HOH HOH . E 5 HOH A 81 581 484 HOH HOH . E 5 HOH A 82 582 485 HOH HOH . E 5 HOH A 83 583 486 HOH HOH . E 5 HOH A 84 584 487 HOH HOH . E 5 HOH A 85 585 488 HOH HOH . E 5 HOH A 86 586 489 HOH HOH . E 5 HOH A 87 587 490 HOH HOH . E 5 HOH A 88 588 491 HOH HOH . E 5 HOH A 89 589 492 HOH HOH . E 5 HOH A 90 590 493 HOH HOH . E 5 HOH A 91 591 494 HOH HOH . E 5 HOH A 92 592 495 HOH HOH . E 5 HOH A 93 593 496 HOH HOH . E 5 HOH A 94 594 497 HOH HOH . E 5 HOH A 95 595 498 HOH HOH . E 5 HOH A 96 596 499 HOH HOH . E 5 HOH A 97 597 500 HOH HOH . E 5 HOH A 98 598 501 HOH HOH . E 5 HOH A 99 599 502 HOH HOH . E 5 HOH A 100 600 503 HOH HOH . E 5 HOH A 101 601 504 HOH HOH . E 5 HOH A 102 602 505 HOH HOH . E 5 HOH A 103 603 506 HOH HOH . E 5 HOH A 104 604 507 HOH HOH . E 5 HOH A 105 605 508 HOH HOH . E 5 HOH A 106 606 509 HOH HOH . E 5 HOH A 107 607 510 HOH HOH . E 5 HOH A 108 608 511 HOH HOH . E 5 HOH A 109 609 512 HOH HOH . E 5 HOH A 110 610 513 HOH HOH . E 5 HOH A 111 611 514 HOH HOH . E 5 HOH A 112 612 515 HOH HOH . E 5 HOH A 113 613 516 HOH HOH . E 5 HOH A 114 614 517 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 . # 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 1J3 . . . B 2 30.893 -36.254 -20.997 1 52.67 ? C1 1J3 400 A 1 HETATM 2 O O2 1J3 . . . B 2 31.64 -35.238 -20.301 1 51.78 ? O2 1J3 400 A 1 HETATM 3 C C3 1J3 . . . B 2 32.711 -35.595 -19.529 1 49.57 ? C3 1J3 400 A 1 HETATM 4 C C4 1J3 . . . B 2 33.341 -36.831 -19.673 1 51.03 ? C4 1J3 400 A 1 HETATM 5 C C5 1J3 . . . B 2 34.436 -37.155 -18.852 1 51.86 ? C5 1J3 400 A 1 HETATM 6 C C6 1J3 . . . B 2 34.866 -36.223 -17.888 1 50.05 ? C6 1J3 400 A 1 HETATM 7 C C7 1J3 . . . B 2 34.24 -34.991 -17.746 1 47.6 ? C7 1J3 400 A 1 HETATM 8 C C8 1J3 . . . B 2 33.149 -34.676 -18.568 1 47.89 ? C8 1J3 400 A 1 HETATM 9 N N9 1J3 . . . B 2 32.424 -33.475 -18.499 1 46.16 ? N9 1J3 400 A 1 HETATM 10 C C10 1J3 . . . B 2 32.513 -32.454 -17.568 1 44.12 ? C10 1J3 400 A 1 HETATM 11 N N11 1J3 . . . B 2 31.698 -31.422 -17.716 1 45.55 ? N11 1J3 400 A 1 HETATM 12 C C12 1J3 . . . B 2 31.751 -30.383 -16.877 1 42.81 ? C12 1J3 400 A 1 HETATM 13 C C13 1J3 . . . B 2 32.658 -30.394 -15.835 1 42 ? C13 1J3 400 A 1 HETATM 14 N N14 1J3 . . . B 2 32.72 -29.258 -14.997 1 41.27 ? N14 1J3 400 A 1 HETATM 15 C C15 1J3 . . . B 2 32.687 -27.933 -15.635 1 41.78 ? C15 1J3 400 A 1 HETATM 16 C C16 1J3 . . . B 2 32.872 -29.301 -13.647 1 42.41 ? C16 1J3 400 A 1 HETATM 17 O O17 1J3 . . . B 2 32.935 -28.243 -13.011 1 39.59 ? O17 1J3 400 A 1 HETATM 18 C C18 1J3 . . . B 2 32.924 -30.614 -12.919 1 42.15 ? C18 1J3 400 A 1 HETATM 19 F F19 1J3 . . . B 2 33.121 -30.323 -11.582 1 48.75 ? F19 1J3 400 A 1 HETATM 20 C C20 1J3 . . . B 2 34.11 -31.486 -13.284 1 43.72 ? C20 1J3 400 A 1 HETATM 21 N N21 1J3 . . . B 2 34.476 -31.651 -14.692 1 44.11 ? N21 1J3 400 A 1 HETATM 22 C C22 1J3 . . . B 2 35.371 -32.826 -14.819 1 45.63 ? C22 1J3 400 A 1 HETATM 23 C C23 1J3 . . . B 2 36.738 -32.567 -14.11 1 44.54 ? C23 1J3 400 A 1 HETATM 24 C C24 1J3 . . . B 2 37.113 -33.935 -13.49 1 47.33 ? C24 1J3 400 A 1 HETATM 25 C C25 1J3 . . . B 2 35.767 -34.537 -13.076 1 45.58 ? C25 1J3 400 A 1 HETATM 26 C C26 1J3 . . . B 2 34.779 -34.092 -14.161 1 45.23 ? C26 1J3 400 A 1 HETATM 27 C C27 1J3 . . . B 2 33.513 -31.524 -15.696 1 42.02 ? C27 1J3 400 A 1 HETATM 28 N N28 1J3 . . . B 2 33.393 -32.5 -16.579 1 43.35 ? N28 1J3 400 A 1 HETATM 29 C C29 1J3 . . . B 2 31.628 -31.388 -13.037 1 44.84 ? C29 1J3 400 A 1 HETATM 30 C C30 1J3 . . . B 2 30.983 -31.827 -11.98 1 43.38 ? C30 1J3 400 A 1 HETATM 31 C C31 1J3 . . . B 2 35.09 -38.488 -18.992 1 53.03 ? C31 1J3 400 A 1 HETATM 32 O O32 1J3 . . . B 2 35.299 -38.973 -20.077 1 51.97 ? O32 1J3 400 A 1 HETATM 33 N N33 1J3 . . . B 2 35.409 -39.182 -17.883 1 54.86 ? N33 1J3 400 A 1 HETATM 34 N N34 1J3 . . . B 2 35.98 -40.426 -17.878 1 59.22 ? N34 1J3 400 A 1 HETATM 35 C C35 1J3 . . . B 2 37.332 -40.375 -17.286 1 58.46 ? C35 1J3 400 A 1 HETATM 36 C C36 1J3 . . . B 2 37.97 -41.76 -17.391 1 60.02 ? C36 1J3 400 A 1 HETATM 37 N N37 1J3 . . . B 2 37.118 -42.709 -16.657 1 62.69 ? N37 1J3 400 A 1 HETATM 38 C C38 1J3 . . . B 2 37.754 -44.026 -16.543 1 64.83 ? C38 1J3 400 A 1 HETATM 39 C C39 1J3 . . . B 2 35.756 -42.775 -17.225 1 62.54 ? C39 1J3 400 A 1 HETATM 40 C C40 1J3 . . . B 2 35.116 -41.382 -17.154 1 58.89 ? C40 1J3 400 A 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 40 #