data_7LBT
#
_model_server_result.job_id            lZ5UsN8br--oxaAgzk_TUw 
_model_server_result.datetime_utc      '2025-08-05 06:28:00' 
_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":"H","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 . . . H 2 -16.341 -23.348 14.117 1 88.36 ? C13 VYJ 501 D 1 
HETATM 2 C C15 VYJ . . . H 2 -16.27 -25.246 12.304 1 88.51 ? C15 VYJ 501 D 1 
HETATM 3 C C20 VYJ . . . H 2 -16.589 -29.08 12.779 1 84.01 ? C20 VYJ 501 D 1 
HETATM 4 C C21 VYJ . . . H 2 -16.572 -23.143 15.643 1 84.01 ? C21 VYJ 501 D 1 
HETATM 5 C C22 VYJ . . . H 2 -16.728 -21.649 16.081 1 83.05 ? C22 VYJ 501 D 1 
HETATM 6 C C24 VYJ . . . H 2 -14.993 -17.842 15.934 1 70.95 ? C24 VYJ 501 D 1 
HETATM 7 C C26 VYJ . . . H 2 -12.554 -15.196 12.552 1 46.55 ? C26 VYJ 501 D 1 
HETATM 8 C C28 VYJ . . . H 2 -10.937 -14.13 11.193 1 46.76 ? C28 VYJ 501 D 1 
HETATM 9 C C01 VYJ . . . H 2 -12.54 -15.109 18.367 1 34.66 ? C01 VYJ 501 D 1 
HETATM 10 C C02 VYJ . . . H 2 -13.604 -15.56 17.341 1 41.92 ? C02 VYJ 501 D 1 
HETATM 11 C C04 VYJ . . . H 2 -14.004 -16.94 15.481 1 60.75 ? C04 VYJ 501 D 1 
HETATM 12 C C05 VYJ . . . H 2 -14.014 -16.498 14.132 1 56.69 ? C05 VYJ 501 D 1 
HETATM 13 C C06 VYJ . . . H 2 -15.031 -16.979 13.285 1 59.22 ? C06 VYJ 501 D 1 
HETATM 14 C C07 VYJ . . . H 2 -16 -17.87 13.745 1 66.47 ? C07 VYJ 501 D 1 
HETATM 15 C C08 VYJ . . . H 2 -16.02 -18.331 15.083 1 73.11 ? C08 VYJ 501 D 1 
HETATM 16 C C09 VYJ . . . H 2 -17.057 -19.258 15.469 1 76.21 ? C09 VYJ 501 D 1 
HETATM 17 C C11 VYJ . . . H 2 -17.341 -21.027 13.714 1 89.98 ? C11 VYJ 501 D 1 
HETATM 18 C C12 VYJ . . . H 2 -17.433 -22.542 13.358 1 89.06 ? C12 VYJ 501 D 1 
HETATM 19 C C16 VYJ . . . H 2 -16.917 -26.65 12.133 1 86.73 ? C16 VYJ 501 D 1 
HETATM 20 C C18 VYJ . . . H 2 -16.344 -27.25 14.487 1 92.23 ? C18 VYJ 501 D 1 
HETATM 21 C C19 VYJ . . . H 2 -15.694 -25.851 14.7 1 95.27 ? C19 VYJ 501 D 1 
HETATM 22 C C29 VYJ . . . H 2 -11.681 -14.335 10.003 1 42.71 ? C29 VYJ 501 D 1 
HETATM 23 C C31 VYJ . . . H 2 -11.329 -14.564 7.598 1 40.07 ? C31 VYJ 501 D 1 
HETATM 24 C C32 VYJ . . . H 2 -11.994 -15.826 7.453 1 45.3 ? C32 VYJ 501 D 1 
HETATM 25 C C33 VYJ . . . H 2 -13.172 -16.178 8.198 1 45.93 ? C33 VYJ 501 D 1 
HETATM 26 C C35 VYJ . . . H 2 -12.929 -15.014 10.17 1 45.36 ? C35 VYJ 501 D 1 
HETATM 27 C C37 VYJ . . . H 2 -15.231 -15.324 9.268 1 26.35 ? C37 VYJ 501 D 1 
HETATM 28 C C38 VYJ . . . H 2 -16.018 -15.26 7.922 1 18.33 ? C38 VYJ 501 D 1 
HETATM 29 C C39 VYJ . . . H 2 -17.436 -14.738 8.226 1 19.1 ? C39 VYJ 501 D 1 
HETATM 30 C C40 VYJ . . . H 2 -17.258 -13.839 9.468 1 19.73 ? C40 VYJ 501 D 1 
HETATM 31 C C41 VYJ . . . H 2 -15.91 -14.219 10.134 1 19.52 ? C41 VYJ 501 D 1 
HETATM 32 C C42 VYJ . . . H 2 -13.734 -17.471 7.987 1 46.19 ? C42 VYJ 501 D 1 
HETATM 33 C C43 VYJ . . . H 2 -13.186 -18.38 7.076 1 44.89 ? C43 VYJ 501 D 1 
HETATM 34 C C44 VYJ . . . H 2 -12.039 -18.039 6.351 1 41.3 ? C44 VYJ 501 D 1 
HETATM 35 C C45 VYJ . . . H 2 -11.455 -16.78 6.546 1 41.21 ? C45 VYJ 501 D 1 
HETATM 36 C C47 VYJ . . . H 2 -10.906 -12.443 8.645 1 21.68 ? C47 VYJ 501 D 1 
HETATM 37 N N10 VYJ . . . H 2 -17.192 -20.633 15.118 1 86.25 ? N10 VYJ 501 D 1 
HETATM 38 N N14 VYJ . . . H 2 -16.209 -24.81 13.743 1 92.55 ? N14 VYJ 501 D 1 
HETATM 39 N N17 VYJ . . . H 2 -16.26 -27.648 13.044 1 90.51 ? N17 VYJ 501 D 1 
HETATM 40 N N25 VYJ . . . H 2 -13.027 -15.631 13.752 1 50.25 ? N25 VYJ 501 D 1 
HETATM 41 N N27 VYJ . . . H 2 -11.376 -14.55 12.404 1 46.95 ? N27 VYJ 501 D 1 
HETATM 42 N N30 VYJ . . . H 2 -11.192 -13.867 8.784 1 33.57 ? N30 VYJ 501 D 1 
HETATM 43 N N34 VYJ . . . H 2 -13.766 -15.321 9.122 1 39.17 ? N34 VYJ 501 D 1 
HETATM 44 N N36 VYJ . . . H 2 -13.298 -15.413 11.43 1 47.98 ? N36 VYJ 501 D 1 
HETATM 45 O O03 VYJ . . . H 2 -13.057 -16.513 16.385 1 52.54 ? O03 VYJ 501 D 1 
HETATM 46 O O23 VYJ . . . H 2 -17.938 -18.716 16.195 1 65.18 ? O23 VYJ 501 D 1 
HETATM 47 O O46 VYJ . . . H 2 -10.816 -14.054 6.569 1 42.85 ? O46 VYJ 501 D 1 
#
_model_server_stats.io_time_ms              177 
_model_server_stats.parse_time_ms           55 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           47 
#