data_7LEK
#
_model_server_result.job_id            uMEl22oTHqM7uQzHx7XOfQ 
_model_server_result.datetime_utc      '2024-11-26 22:52:28' 
_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          7lek 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":401}' 
#
_entry.id    7LEK 
#
_exptl.entry_id    7LEK 
_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          108.39 
_cell.angle_gamma         90 
_cell.entry_id            7LEK 
_cell.length_a            110.61 
_cell.length_b            99.32 
_cell.length_c            60.4 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7LEK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
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,K 1 1 
B,F,G,L 2 1 
C,H,I,M 3 1 
D,J,N 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 H N N 
? 2 J 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 385 n n 
C21 C13 VYJ sing 386 n n 
C22 N10 VYJ sing 387 n n 
C18 C19 VYJ sing 388 n n 
C18 N17 VYJ sing 389 n n 
C20 N17 VYJ sing 390 n n 
N14 C19 VYJ sing 391 n n 
N14 C13 VYJ sing 392 n n 
N14 C15 VYJ sing 393 n n 
C16 N17 VYJ sing 394 n n 
C16 C15 VYJ sing 395 n n 
C13 C12 VYJ sing 396 n n 
O23 C09 VYJ doub 397 n n 
N10 C09 VYJ sing 398 n n 
N10 C11 VYJ sing 399 n n 
C09 C08 VYJ sing 400 n n 
C12 C11 VYJ sing 401 n n 
C08 C07 VYJ doub 402 n y 
C08 C24 VYJ sing 403 n y 
C39 C40 VYJ sing 404 n n 
C39 C38 VYJ sing 405 n n 
C40 C41 VYJ sing 406 n n 
C07 C06 VYJ sing 407 n y 
C24 C04 VYJ doub 408 n y 
C41 C37 VYJ sing 409 n n 
C38 C37 VYJ sing 410 n n 
C06 C05 VYJ doub 411 n y 
C04 C05 VYJ sing 412 n y 
C04 O03 VYJ sing 413 n n 
C02 O03 VYJ sing 414 n n 
C02 C01 VYJ sing 415 n n 
C37 N34 VYJ sing 416 n n 
C05 N25 VYJ sing 417 n n 
N25 C26 VYJ sing 418 n n 
N34 C35 VYJ sing 419 n n 
N34 C33 VYJ sing 420 n n 
N36 C26 VYJ doub 421 n y 
N36 C35 VYJ sing 422 n y 
C42 C33 VYJ doub 423 n y 
C42 C43 VYJ sing 424 n y 
C26 N27 VYJ sing 425 n y 
C35 C29 VYJ doub 426 n y 
C33 C32 VYJ sing 427 n y 
C43 C44 VYJ doub 428 n y 
N27 C28 VYJ doub 429 n y 
C29 C28 VYJ sing 430 n y 
C29 N30 VYJ sing 431 n n 
C32 C31 VYJ sing 432 n n 
C32 C45 VYJ doub 433 n y 
C44 C45 VYJ sing 434 n y 
N30 C31 VYJ sing 435 n n 
N30 C47 VYJ sing 436 n n 
C31 O46 VYJ doub 437 n n 
C13 H1 VYJ sing 438 n n 
C15 H2 VYJ sing 439 n n 
C15 H3 VYJ sing 440 n n 
C20 H4 VYJ sing 441 n n 
C20 H5 VYJ sing 442 n n 
C20 H6 VYJ sing 443 n n 
C21 H7 VYJ sing 444 n n 
C21 H8 VYJ sing 445 n n 
C22 H9 VYJ sing 446 n n 
C22 H10 VYJ sing 447 n n 
C24 H11 VYJ sing 448 n n 
C28 H12 VYJ sing 449 n n 
C01 H13 VYJ sing 450 n n 
C01 H14 VYJ sing 451 n n 
C01 H15 VYJ sing 452 n n 
C02 H16 VYJ sing 453 n n 
C02 H17 VYJ sing 454 n n 
C06 H18 VYJ sing 455 n n 
C07 H19 VYJ sing 456 n n 
C11 H20 VYJ sing 457 n n 
C11 H21 VYJ sing 458 n n 
C12 H22 VYJ sing 459 n n 
C12 H23 VYJ sing 460 n n 
C16 H24 VYJ sing 461 n n 
C16 H25 VYJ sing 462 n n 
C18 H26 VYJ sing 463 n n 
C18 H27 VYJ sing 464 n n 
C19 H28 VYJ sing 465 n n 
C19 H29 VYJ sing 466 n n 
C37 H30 VYJ sing 467 n n 
C38 H31 VYJ sing 468 n n 
C38 H32 VYJ sing 469 n n 
C39 H33 VYJ sing 470 n n 
C39 H34 VYJ sing 471 n n 
C40 H35 VYJ sing 472 n n 
C40 H36 VYJ sing 473 n n 
C41 H37 VYJ sing 474 n n 
C41 H38 VYJ sing 475 n n 
C42 H39 VYJ sing 476 n n 
C43 H40 VYJ sing 477 n n 
C44 H41 VYJ sing 478 n n 
C45 H42 VYJ sing 479 n n 
C47 H43 VYJ sing 480 n n 
C47 H44 VYJ sing 481 n n 
C47 H45 VYJ sing 482 n n 
N25 H48 VYJ sing 483 n n 
#
_atom_sites.entry_id                     7LEK 
_atom_sites.fract_transf_matrix[1][1]    0.009041 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003006 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010068 
_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]    0.017447 
_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 1 401 1 VYJ ERK . 
F 2 VYJ B 1 401 3 VYJ ERK . 
G 3 CL B 1 402 1 CL CL . 
H 2 VYJ C 1 401 2 VYJ ERK . 
I 4 EDO C 1 402 1 EDO EDO . 
J 2 VYJ D 1 401 4 VYJ ERK . 
K 5 HOH A 1 501 2 HOH HOH . 
K 5 HOH A 2 502 24 HOH HOH . 
K 5 HOH A 3 503 69 HOH HOH . 
K 5 HOH A 4 504 17 HOH HOH . 
K 5 HOH A 5 505 22 HOH HOH . 
K 5 HOH A 6 506 19 HOH HOH . 
K 5 HOH A 7 507 18 HOH HOH . 
K 5 HOH A 8 508 3 HOH HOH . 
K 5 HOH A 9 509 10 HOH HOH . 
K 5 HOH A 10 510 5 HOH HOH . 
K 5 HOH A 11 511 68 HOH HOH . 
K 5 HOH A 12 512 36 HOH HOH . 
K 5 HOH A 13 513 63 HOH HOH . 
K 5 HOH A 14 514 66 HOH HOH . 
K 5 HOH A 15 515 48 HOH HOH . 
K 5 HOH A 16 516 58 HOH HOH . 
K 5 HOH A 17 517 60 HOH HOH . 
K 5 HOH A 18 518 42 HOH HOH . 
K 5 HOH A 19 519 45 HOH HOH . 
K 5 HOH A 20 520 13 HOH HOH . 
L 5 HOH B 1 501 62 HOH HOH . 
L 5 HOH B 2 502 1 HOH HOH . 
L 5 HOH B 3 503 4 HOH HOH . 
L 5 HOH B 4 504 8 HOH HOH . 
L 5 HOH B 5 505 44 HOH HOH . 
L 5 HOH B 6 506 49 HOH HOH . 
L 5 HOH B 7 507 14 HOH HOH . 
L 5 HOH B 8 508 37 HOH HOH . 
L 5 HOH B 9 509 54 HOH HOH . 
L 5 HOH B 10 510 26 HOH HOH . 
L 5 HOH B 11 511 46 HOH HOH . 
L 5 HOH B 12 512 55 HOH HOH . 
L 5 HOH B 13 513 61 HOH HOH . 
L 5 HOH B 14 514 11 HOH HOH . 
L 5 HOH B 15 515 33 HOH HOH . 
L 5 HOH B 16 516 52 HOH HOH . 
M 5 HOH C 1 501 15 HOH HOH . 
M 5 HOH C 2 502 59 HOH HOH . 
M 5 HOH C 3 503 53 HOH HOH . 
M 5 HOH C 4 504 7 HOH HOH . 
M 5 HOH C 5 505 34 HOH HOH . 
M 5 HOH C 6 506 28 HOH HOH . 
M 5 HOH C 7 507 35 HOH HOH . 
M 5 HOH C 8 508 23 HOH HOH . 
M 5 HOH C 9 509 51 HOH HOH . 
M 5 HOH C 10 510 39 HOH HOH . 
M 5 HOH C 11 511 20 HOH HOH . 
N 5 HOH D 1 501 56 HOH HOH . 
N 5 HOH D 2 502 21 HOH HOH . 
N 5 HOH D 3 503 25 HOH HOH . 
N 5 HOH D 4 504 64 HOH HOH . 
N 5 HOH D 5 505 38 HOH HOH . 
N 5 HOH D 6 506 43 HOH HOH . 
N 5 HOH D 7 507 30 HOH HOH . 
N 5 HOH D 8 508 32 HOH HOH . 
N 5 HOH D 9 509 67 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 . . . J 2 17.996 -27.341 5.119 1 52.34 ? C13 VYJ 401 D 1 
HETATM 2 C C15 VYJ . . . J 2 17.516 -28.734 3.456 1 64.78 ? C15 VYJ 401 D 1 
HETATM 3 C C20 VYJ . . . J 2 18.924 -27.222 0.583 1 70.33 ? C20 VYJ 401 D 1 
HETATM 4 C C21 VYJ . . . J 2 18.234 -28.226 6.339 1 35.22 ? C21 VYJ 401 D 1 
HETATM 5 C C22 VYJ . . . J 2 17.052 -28.428 7.362 1 26.04 ? C22 VYJ 401 D 1 
HETATM 6 C C24 VYJ . . . J 2 14.376 -30.176 7.919 1 40.27 ? C24 VYJ 401 D 1 
HETATM 7 C C26 VYJ . . . J 2 13.506 -33.144 11.916 1 33.17 ? C26 VYJ 401 D 1 
HETATM 8 C C28 VYJ . . . J 2 13.285 -34.767 13.613 1 41.49 ? C28 VYJ 401 D 1 
HETATM 9 C C01 VYJ . . . J 2 15.312 -34.485 6.678 1 34.93 ? C01 VYJ 401 D 1 
HETATM 10 C C02 VYJ . . . J 2 15.437 -33.005 7.238 1 30.72 ? C02 VYJ 401 D 1 
HETATM 11 C C04 VYJ . . . J 2 14.114 -31.391 8.519 1 38.03 ? C04 VYJ 401 D 1 
HETATM 12 C C05 VYJ . . . J 2 13.78 -31.442 9.93 1 32.67 ? C05 VYJ 401 D 1 
HETATM 13 C C06 VYJ . . . J 2 13.72 -30.269 10.666 1 37.42 ? C06 VYJ 401 D 1 
HETATM 14 C C07 VYJ . . . J 2 14.001 -28.98 10.036 1 34.21 ? C07 VYJ 401 D 1 
HETATM 15 C C08 VYJ . . . J 2 14.328 -28.951 8.689 1 30.96 ? C08 VYJ 401 D 1 
HETATM 16 C C09 VYJ . . . J 2 14.627 -27.624 7.946 1 37.85 ? C09 VYJ 401 D 1 
HETATM 17 C C11 VYJ . . . J 2 16.325 -26.209 6.564 1 32.78 ? C11 VYJ 401 D 1 
HETATM 18 C C12 VYJ . . . J 2 16.662 -26.63 5.187 1 46.15 ? C12 VYJ 401 D 1 
HETATM 19 C C16 VYJ . . . J 2 17.608 -27.996 2.092 1 70.18 ? C16 VYJ 401 D 1 
HETATM 20 C C18 VYJ . . . J 2 19.703 -27.291 2.532 1 60.14 ? C18 VYJ 401 D 1 
HETATM 21 C C19 VYJ . . . J 2 19.696 -28.069 3.864 1 50.03 ? C19 VYJ 401 D 1 
HETATM 22 C C29 VYJ . . . J 2 13.492 -33.738 14.533 1 34.76 ? C29 VYJ 401 D 1 
HETATM 23 C C31 VYJ . . . J 2 14.253 -33.46 16.995 1 31.42 ? C31 VYJ 401 D 1 
HETATM 24 C C32 VYJ . . . J 2 15.277 -32.371 16.771 1 28.34 ? C32 VYJ 401 D 1 
HETATM 25 C C33 VYJ . . . J 2 15.127 -31.291 15.906 1 35.72 ? C33 VYJ 401 D 1 
HETATM 26 C C35 VYJ . . . J 2 13.673 -32.393 14.047 1 34.01 ? C35 VYJ 401 D 1 
HETATM 27 C C37 VYJ . . . J 2 12.935 -30.141 15.4 1 33.11 ? C37 VYJ 401 D 1 
HETATM 28 C C38 VYJ . . . J 2 13.128 -28.542 15.682 1 32.65 ? C38 VYJ 401 D 1 
HETATM 29 C C39 VYJ . . . J 2 11.981 -27.973 15.252 1 30.02 ? C39 VYJ 401 D 1 
HETATM 30 C C40 VYJ . . . J 2 11.159 -29.117 14.327 1 25.25 ? C40 VYJ 401 D 1 
HETATM 31 C C41 VYJ . . . J 2 12.073 -30.121 14.074 1 34.13 ? C41 VYJ 401 D 1 
HETATM 32 C C42 VYJ . . . J 2 16.176 -30.317 15.76 1 36.44 ? C42 VYJ 401 D 1 
HETATM 33 C C43 VYJ . . . J 2 17.394 -30.46 16.591 1 34.65 ? C43 VYJ 401 D 1 
HETATM 34 C C44 VYJ . . . J 2 17.531 -31.552 17.5 1 35.25 ? C44 VYJ 401 D 1 
HETATM 35 C C45 VYJ . . . J 2 16.512 -32.511 17.617 1 33.14 ? C45 VYJ 401 D 1 
HETATM 36 C C47 VYJ . . . J 2 12.527 -35.099 16.399 1 27.04 ? C47 VYJ 401 D 1 
HETATM 37 N N10 VYJ . . . J 2 15.96 -27.419 7.305 1 36.43 ? N10 VYJ 401 D 1 
HETATM 38 N N14 VYJ . . . J 2 18.411 -28.317 4.358 1 61.73 ? N14 VYJ 401 D 1 
HETATM 39 N N17 VYJ . . . J 2 18.913 -27.877 1.629 1 71.75 ? N17 VYJ 401 D 1 
HETATM 40 N N25 VYJ . . . J 2 13.511 -32.806 10.456 1 33.6 ? N25 VYJ 401 D 1 
HETATM 41 N N27 VYJ . . . J 2 13.29 -34.469 12.338 1 39.91 ? N27 VYJ 401 D 1 
HETATM 42 N N30 VYJ . . . J 2 13.493 -34.019 15.971 1 31.85 ? N30 VYJ 401 D 1 
HETATM 43 N N34 VYJ . . . J 2 13.961 -31.187 15.077 1 30.54 ? N34 VYJ 401 D 1 
HETATM 44 N N36 VYJ . . . J 2 13.708 -32.186 12.745 1 39.37 ? N36 VYJ 401 D 1 
HETATM 45 O O03 VYJ . . . J 2 14.15 -32.63 7.781 1 28.21 ? O03 VYJ 401 D 1 
HETATM 46 O O23 VYJ . . . J 2 13.762 -26.776 7.866 1 33.93 ? O23 VYJ 401 D 1 
HETATM 47 O O46 VYJ . . . J 2 14.089 -33.844 18.061 1 34.71 ? O46 VYJ 401 D 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           47 
#