data_7LBT # _model_server_result.job_id yRRMNn-6A4P-ClHYXo0yDg _model_server_result.datetime_utc '2024-11-05 06:51:26' _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 7lbt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 7LBT # _exptl.entry_id 7LBT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 638.802 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one _entity.pdbx_number_of_molecules 4 _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 7LBT _cell.length_a 100.29 _cell.length_b 165.19 _cell.length_c 108.69 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7LBT _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I 1 1 B,F,J 2 1 C,G,K 3 1 D,H,L 4 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N # _chem_comp.formula 'C36 H46 N8 O3' _chem_comp.formula_weight 638.802 _chem_comp.id VYJ _chem_comp.mon_nstd_flag . _chem_comp.name 11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-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 C21 C22 VYJ sing 376 n n C21 C13 VYJ sing 377 n n C22 N10 VYJ sing 378 n n C18 C19 VYJ sing 379 n n C18 N17 VYJ sing 380 n n C20 N17 VYJ sing 381 n n N14 C19 VYJ sing 382 n n N14 C13 VYJ sing 383 n n N14 C15 VYJ sing 384 n n C16 N17 VYJ sing 385 n n C16 C15 VYJ sing 386 n n C13 C12 VYJ sing 387 n n O23 C09 VYJ doub 388 n n N10 C09 VYJ sing 389 n n N10 C11 VYJ sing 390 n n C09 C08 VYJ sing 391 n n C12 C11 VYJ sing 392 n n C08 C07 VYJ doub 393 n y C08 C24 VYJ sing 394 n y C39 C40 VYJ sing 395 n n C39 C38 VYJ sing 396 n n C40 C41 VYJ sing 397 n n C07 C06 VYJ sing 398 n y C24 C04 VYJ doub 399 n y C41 C37 VYJ sing 400 n n C38 C37 VYJ sing 401 n n C06 C05 VYJ doub 402 n y C04 C05 VYJ sing 403 n y C04 O03 VYJ sing 404 n n C02 O03 VYJ sing 405 n n C02 C01 VYJ sing 406 n n C37 N34 VYJ sing 407 n n C05 N25 VYJ sing 408 n n N25 C26 VYJ sing 409 n n N34 C35 VYJ sing 410 n n N34 C33 VYJ sing 411 n n N36 C26 VYJ doub 412 n y N36 C35 VYJ sing 413 n y C42 C33 VYJ doub 414 n y C42 C43 VYJ sing 415 n y C26 N27 VYJ sing 416 n y C35 C29 VYJ doub 417 n y C33 C32 VYJ sing 418 n y C43 C44 VYJ doub 419 n y N27 C28 VYJ doub 420 n y C29 C28 VYJ sing 421 n y C29 N30 VYJ sing 422 n n C32 C31 VYJ sing 423 n n C32 C45 VYJ doub 424 n y C44 C45 VYJ sing 425 n y N30 C31 VYJ sing 426 n n N30 C47 VYJ sing 427 n n C31 O46 VYJ doub 428 n n C13 H1 VYJ sing 429 n n C15 H2 VYJ sing 430 n n C15 H3 VYJ sing 431 n n C20 H4 VYJ sing 432 n n C20 H5 VYJ sing 433 n n C20 H6 VYJ sing 434 n n C21 H7 VYJ sing 435 n n C21 H8 VYJ sing 436 n n C22 H9 VYJ sing 437 n n C22 H10 VYJ sing 438 n n C24 H11 VYJ sing 439 n n C28 H12 VYJ sing 440 n n C01 H13 VYJ sing 441 n n C01 H14 VYJ sing 442 n n C01 H15 VYJ sing 443 n n C02 H16 VYJ sing 444 n n C02 H17 VYJ sing 445 n n C06 H18 VYJ sing 446 n n C07 H19 VYJ sing 447 n n C11 H20 VYJ sing 448 n n C11 H21 VYJ sing 449 n n C12 H22 VYJ sing 450 n n C12 H23 VYJ sing 451 n n C16 H24 VYJ sing 452 n n C16 H25 VYJ sing 453 n n C18 H26 VYJ sing 454 n n C18 H27 VYJ sing 455 n n C19 H28 VYJ sing 456 n n C19 H29 VYJ sing 457 n n C37 H30 VYJ sing 458 n n C38 H31 VYJ sing 459 n n C38 H32 VYJ sing 460 n n C39 H33 VYJ sing 461 n n C39 H34 VYJ sing 462 n n C40 H35 VYJ sing 463 n n C40 H36 VYJ sing 464 n n C41 H37 VYJ sing 465 n n C41 H38 VYJ sing 466 n n C42 H39 VYJ sing 467 n n C43 H40 VYJ sing 468 n n C44 H41 VYJ sing 469 n n C45 H42 VYJ sing 470 n n C47 H43 VYJ sing 471 n n C47 H44 VYJ sing 472 n n C47 H45 VYJ sing 473 n n N25 H48 VYJ sing 474 n n # _atom_sites.entry_id 7LBT _atom_sites.fract_transf_matrix[1][1] 0.009971 _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] 0.006054 _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] 0.0092 _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 E 2 VYJ A 1 501 3 VYJ ERK . F 2 VYJ B 1 501 1 VYJ ERK . G 2 VYJ C 1 501 2 VYJ ERK . H 2 VYJ D 1 501 4 VYJ ERK . I 3 HOH A 1 601 54 HOH HOH . I 3 HOH A 2 602 30 HOH HOH . I 3 HOH A 3 603 50 HOH HOH . I 3 HOH A 4 604 44 HOH HOH . I 3 HOH A 5 605 31 HOH HOH . I 3 HOH A 6 606 38 HOH HOH . I 3 HOH A 7 607 39 HOH HOH . I 3 HOH A 8 608 14 HOH HOH . I 3 HOH A 9 609 10 HOH HOH . I 3 HOH A 10 610 45 HOH HOH . I 3 HOH A 11 611 56 HOH HOH . I 3 HOH A 12 612 21 HOH HOH . I 3 HOH A 13 613 26 HOH HOH . I 3 HOH A 14 614 67 HOH HOH . I 3 HOH A 15 615 46 HOH HOH . I 3 HOH A 16 616 57 HOH HOH . I 3 HOH A 17 617 24 HOH HOH . I 3 HOH A 18 618 40 HOH HOH . I 3 HOH A 19 619 20 HOH HOH . I 3 HOH A 20 620 55 HOH HOH . I 3 HOH A 21 621 11 HOH HOH . J 3 HOH B 1 601 36 HOH HOH . J 3 HOH B 2 602 41 HOH HOH . J 3 HOH B 3 603 8 HOH HOH . J 3 HOH B 4 604 3 HOH HOH . J 3 HOH B 5 605 33 HOH HOH . J 3 HOH B 6 606 68 HOH HOH . J 3 HOH B 7 607 6 HOH HOH . J 3 HOH B 8 608 62 HOH HOH . J 3 HOH B 9 609 25 HOH HOH . J 3 HOH B 10 610 64 HOH HOH . J 3 HOH B 11 611 2 HOH HOH . J 3 HOH B 12 612 4 HOH HOH . J 3 HOH B 13 613 35 HOH HOH . J 3 HOH B 14 614 23 HOH HOH . J 3 HOH B 15 615 9 HOH HOH . J 3 HOH B 16 616 49 HOH HOH . J 3 HOH B 17 617 48 HOH HOH . J 3 HOH B 18 618 7 HOH HOH . J 3 HOH B 19 619 43 HOH HOH . J 3 HOH B 20 620 65 HOH HOH . J 3 HOH B 21 621 75 HOH HOH . J 3 HOH B 22 622 32 HOH HOH . J 3 HOH B 23 623 12 HOH HOH . J 3 HOH B 24 624 19 HOH HOH . J 3 HOH B 25 625 74 HOH HOH . J 3 HOH B 26 626 47 HOH HOH . J 3 HOH B 27 627 59 HOH HOH . J 3 HOH B 28 628 42 HOH HOH . J 3 HOH B 29 629 77 HOH HOH . K 3 HOH C 1 601 76 HOH HOH . K 3 HOH C 2 602 15 HOH HOH . K 3 HOH C 3 603 16 HOH HOH . K 3 HOH C 4 604 1 HOH HOH . K 3 HOH C 5 605 22 HOH HOH . K 3 HOH C 6 606 66 HOH HOH . K 3 HOH C 7 607 78 HOH HOH . K 3 HOH C 8 608 17 HOH HOH . K 3 HOH C 9 609 5 HOH HOH . K 3 HOH C 10 610 53 HOH HOH . K 3 HOH C 11 611 60 HOH HOH . K 3 HOH C 12 612 73 HOH HOH . K 3 HOH C 13 613 71 HOH HOH . K 3 HOH C 14 614 13 HOH HOH . K 3 HOH C 15 615 28 HOH HOH . K 3 HOH C 16 616 27 HOH HOH . K 3 HOH C 17 617 37 HOH HOH . K 3 HOH C 18 618 29 HOH HOH . K 3 HOH C 19 619 63 HOH HOH . K 3 HOH C 20 620 69 HOH HOH . L 3 HOH D 1 601 34 HOH HOH . L 3 HOH D 2 602 18 HOH HOH . L 3 HOH D 3 603 72 HOH HOH . L 3 HOH D 4 604 51 HOH HOH . L 3 HOH D 5 605 58 HOH HOH . L 3 HOH D 6 606 61 HOH HOH . L 3 HOH D 7 607 70 HOH HOH . L 3 HOH D 8 608 52 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 C13 VYJ . . . E 2 -39.649 -30.664 1.625 1 88.09 ? C13 VYJ 501 A 1 HETATM 2 C C15 VYJ . . . E 2 -40.541 -29.841 -0.694 1 86.58 ? C15 VYJ 501 A 1 HETATM 3 C C20 VYJ . . . E 2 -38.104 -27.91 -3.037 1 77.02 ? C20 VYJ 501 A 1 HETATM 4 C C21 VYJ . . . E 2 -40.917 -31.142 2.382 1 85.33 ? C21 VYJ 501 A 1 HETATM 5 C C22 VYJ . . . E 2 -40.626 -32.499 3.096 1 84.94 ? C22 VYJ 501 A 1 HETATM 6 C C24 VYJ . . . E 2 -36.415 -34.984 2.966 1 48.85 ? C24 VYJ 501 A 1 HETATM 7 C C26 VYJ . . . E 2 -33.51 -35.5 -1.042 1 30.46 ? C26 VYJ 501 A 1 HETATM 8 C C28 VYJ . . . E 2 -31.773 -35.862 -2.612 1 28.7 ? C28 VYJ 501 A 1 HETATM 9 C C01 VYJ . . . E 2 -32.529 -35.879 4.705 1 32.12 ? C01 VYJ 501 A 1 HETATM 10 C C02 VYJ . . . E 2 -33.911 -35.371 4.248 1 42.62 ? C02 VYJ 501 A 1 HETATM 11 C C04 VYJ . . . E 2 -35.24 -35.306 2.23 1 46.27 ? C04 VYJ 501 A 1 HETATM 12 C C05 VYJ . . . E 2 -35.212 -35.189 0.819 1 39.55 ? C05 VYJ 501 A 1 HETATM 13 C C06 VYJ . . . E 2 -36.38 -34.734 0.166 1 36.72 ? C06 VYJ 501 A 1 HETATM 14 C C07 VYJ . . . E 2 -37.531 -34.41 0.89 1 47.37 ? C07 VYJ 501 A 1 HETATM 15 C C08 VYJ . . . E 2 -37.594 -34.534 2.304 1 56.87 ? C08 VYJ 501 A 1 HETATM 16 C C09 VYJ . . . E 2 -38.848 -34.16 2.909 1 64.59 ? C09 VYJ 501 A 1 HETATM 17 C C11 VYJ . . . E 2 -38.227 -31.807 3.414 1 76.98 ? C11 VYJ 501 A 1 HETATM 18 C C12 VYJ . . . E 2 -38.56 -30.446 2.723 1 81.38 ? C12 VYJ 501 A 1 HETATM 19 C C16 VYJ . . . E 2 -39.581 -29.618 -1.897 1 86.59 ? C16 VYJ 501 A 1 HETATM 20 C C18 VYJ . . . E 2 -38.242 -28.021 -0.525 1 93.97 ? C18 VYJ 501 A 1 HETATM 21 C C19 VYJ . . . E 2 -39.174 -28.242 0.708 1 91.13 ? C19 VYJ 501 A 1 HETATM 22 C C29 VYJ . . . E 2 -32.568 -35.443 -3.702 1 30.87 ? C29 VYJ 501 A 1 HETATM 23 C C31 VYJ . . . E 2 -32.74 -35.833 -6.108 1 28.22 ? C31 VYJ 501 A 1 HETATM 24 C C32 VYJ . . . E 2 -34.125 -36.195 -6.123 1 25.91 ? C32 VYJ 501 A 1 HETATM 25 C C33 VYJ . . . E 2 -35.109 -35.598 -5.253 1 27.2 ? C33 VYJ 501 A 1 HETATM 26 C C35 VYJ . . . E 2 -33.894 -35.038 -3.379 1 26.08 ? C35 VYJ 501 A 1 HETATM 27 C C37 VYJ . . . E 2 -35.742 -33.543 -4.02 1 19.6 ? C37 VYJ 501 A 1 HETATM 28 C C38 VYJ . . . E 2 -36.394 -32.856 -5.245 1 17.49 ? C38 VYJ 501 A 1 HETATM 29 C C39 VYJ . . . E 2 -36.906 -31.475 -4.795 1 20.31 ? C39 VYJ 501 A 1 HETATM 30 C C40 VYJ . . . E 2 -36.237 -31.196 -3.439 1 25.51 ? C40 VYJ 501 A 1 HETATM 31 C C41 VYJ . . . E 2 -35.183 -32.303 -3.274 1 24.75 ? C41 VYJ 501 A 1 HETATM 32 C C42 VYJ . . . E 2 -36.46 -36.044 -5.344 1 21.88 ? C42 VYJ 501 A 1 HETATM 33 C C43 VYJ . . . E 2 -36.833 -37.026 -6.272 1 19.59 ? C43 VYJ 501 A 1 HETATM 34 C C44 VYJ . . . E 2 -35.878 -37.606 -7.119 1 19.1 ? C44 VYJ 501 A 1 HETATM 35 C C45 VYJ . . . E 2 -34.539 -37.196 -7.042 1 18.66 ? C45 VYJ 501 A 1 HETATM 36 C C47 VYJ . . . E 2 -30.649 -35.025 -5.152 1 19.46 ? C47 VYJ 501 A 1 HETATM 37 N N10 VYJ . . . E 2 -39.229 -32.879 3.374 1 77.7 ? N10 VYJ 501 A 1 HETATM 38 N N14 VYJ . . . E 2 -39.941 -29.533 0.656 1 90.24 ? N14 VYJ 501 A 1 HETATM 39 N N17 VYJ . . . E 2 -38.93 -28.266 -1.841 1 89.28 ? N17 VYJ 501 A 1 HETATM 40 N N25 VYJ . . . E 2 -34.018 -35.525 0.229 1 34.34 ? N25 VYJ 501 A 1 HETATM 41 N N27 VYJ . . . E 2 -32.248 -35.875 -1.345 1 29.54 ? N27 VYJ 501 A 1 HETATM 42 N N30 VYJ . . . E 2 -32.036 -35.432 -4.983 1 25.59 ? N30 VYJ 501 A 1 HETATM 43 N N34 VYJ . . . E 2 -34.796 -34.621 -4.319 1 20.51 ? N34 VYJ 501 A 1 HETATM 44 N N36 VYJ . . . E 2 -34.297 -35.092 -2.073 1 27.08 ? N36 VYJ 501 A 1 HETATM 45 O O03 VYJ . . . E 2 -34.098 -35.755 2.859 1 47.18 ? O03 VYJ 501 A 1 HETATM 46 O O23 VYJ . . . E 2 -39.689 -35.11 2.949 1 57.81 ? O23 VYJ 501 A 1 HETATM 47 O O46 VYJ . . . E 2 -32.12 -35.887 -7.205 1 31.92 ? O46 VYJ 501 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 21 _model_server_stats.element_count 47 #