data_5ZXB
#
_model_server_result.job_id            TAE0RaD2RuPeqhnfLZGHLw 
_model_server_result.datetime_utc      '2024-10-18 18:24:03' 
_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          5zxb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    5ZXB 
#
_exptl.entry_id    5ZXB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              659.661 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            N-{3-[7-{[6-(4-acetylpiperazin-1-yl)pyridin-3-yl]amino}-1-methyl-2-oxo-1,4-dihydropyrimido[4,5-d]pyrimidin-3(2H)-yl]-4-methylphenyl}-3-(trifluoromethyl)benzamide 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          98.34 
_cell.angle_gamma         90 
_cell.entry_id            5ZXB 
_cell.length_a            71.182 
_cell.length_b            43.12 
_cell.length_c            93.891 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5ZXB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D N N 
#
_chem_comp.formula           'C33 H32 F3 N9 O3' 
_chem_comp.formula_weight    659.661 
_chem_comp.id                9KO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              N-{3-[7-{[6-(4-acetylpiperazin-1-yl)pyridin-3-yl]amino}-1-methyl-2-oxo-1,4-dihydropyrimido[4,5-d]pyrimidin-3(2H)-yl]-4-methylphenyl}-3-(trifluoromethyl)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
C01 C02 9KO sing 1 n n 
C03 C04 9KO doub 2 n y 
C03 C02 9KO sing 3 n y 
C04 C05 9KO sing 4 n y 
C02 C20 9KO doub 5 n y 
C05 N06 9KO sing 6 n n 
C05 C19 9KO doub 7 n y 
C20 C19 9KO sing 8 n y 
C20 N21 9KO sing 9 n n 
N06 C07 9KO sing 10 n n 
N21 C47 9KO sing 11 n n 
N21 C22 9KO sing 12 n n 
C47 C46 9KO sing 13 n n 
O48 C22 9KO doub 14 n n 
C22 N23 9KO sing 15 n n 
C46 C45 9KO doub 16 n y 
C46 C25 9KO sing 17 n y 
C45 N44 9KO sing 18 n y 
C09 C10 9KO doub 19 n y 
C09 C08 9KO sing 20 n y 
C07 C08 9KO sing 21 n n 
C07 O18 9KO doub 22 n n 
C25 N23 9KO sing 23 n n 
C25 N26 9KO doub 24 n y 
N23 C24 9KO sing 25 n n 
N44 C27 9KO doub 26 n y 
C10 C11 9KO sing 27 n y 
C08 C17 9KO doub 28 n y 
N26 C27 9KO sing 29 n y 
C27 N28 9KO sing 30 n n 
C11 C12 9KO doub 31 n y 
C17 C12 9KO sing 32 n y 
N28 C29 9KO sing 33 n n 
C12 C13 9KO sing 34 n n 
C30 C29 9KO doub 35 n y 
C30 C31 9KO sing 36 n y 
C29 C34 9KO sing 37 n y 
F14 C13 9KO sing 38 n n 
C31 C32 9KO doub 39 n y 
C34 N33 9KO doub 40 n y 
C13 F16 9KO sing 41 n n 
C13 F15 9KO sing 42 n n 
C32 N33 9KO sing 43 n y 
C32 N35 9KO sing 44 n n 
O41 C39 9KO doub 45 n n 
N35 C36 9KO sing 46 n n 
N35 C43 9KO sing 47 n n 
C39 C40 9KO sing 48 n n 
C39 N38 9KO sing 49 n n 
C36 C37 9KO sing 50 n n 
C37 N38 9KO sing 51 n n 
N38 C42 9KO sing 52 n n 
C42 C43 9KO sing 53 n n 
C10 H1 9KO sing 54 n n 
C17 H2 9KO sing 55 n n 
C24 H3 9KO sing 56 n n 
C24 H4 9KO sing 57 n n 
C24 H5 9KO sing 58 n n 
C01 H6 9KO sing 59 n n 
C01 H7 9KO sing 60 n n 
C01 H8 9KO sing 61 n n 
C03 H9 9KO sing 62 n n 
C04 H10 9KO sing 63 n n 
C09 H11 9KO sing 64 n n 
C11 H12 9KO sing 65 n n 
C19 H13 9KO sing 66 n n 
C30 H14 9KO sing 67 n n 
C31 H15 9KO sing 68 n n 
C34 H16 9KO sing 69 n n 
C36 H17 9KO sing 70 n n 
C36 H18 9KO sing 71 n n 
C37 H19 9KO sing 72 n n 
C37 H20 9KO sing 73 n n 
C40 H21 9KO sing 74 n n 
C40 H22 9KO sing 75 n n 
C40 H23 9KO sing 76 n n 
C42 H24 9KO sing 77 n n 
C42 H25 9KO sing 78 n n 
C43 H26 9KO sing 79 n n 
C43 H27 9KO sing 80 n n 
C45 H28 9KO sing 81 n n 
C47 H29 9KO sing 82 n n 
C47 H30 9KO sing 83 n n 
N06 H31 9KO sing 84 n n 
N28 H32 9KO sing 85 n n 
#
_atom_sites.entry_id                     5ZXB 
_atom_sites.fract_transf_matrix[1][1]    0.014048 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00206 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.023191 
_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]    0.010765 
_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
C 2 9KO A 1 401 2 9KO LIG . 
D 2 9KO B 1 401 1 9KO LIG . 
E 3 HOH A 1 501 75 HOH HOH . 
E 3 HOH A 2 502 34 HOH HOH . 
E 3 HOH A 3 503 35 HOH HOH . 
E 3 HOH A 4 504 70 HOH HOH . 
E 3 HOH A 5 505 3 HOH HOH . 
E 3 HOH A 6 506 26 HOH HOH . 
E 3 HOH A 7 507 44 HOH HOH . 
E 3 HOH A 8 508 29 HOH HOH . 
E 3 HOH A 9 509 30 HOH HOH . 
E 3 HOH A 10 510 51 HOH HOH . 
E 3 HOH A 11 511 88 HOH HOH . 
E 3 HOH A 12 512 1 HOH HOH . 
E 3 HOH A 13 513 24 HOH HOH . 
E 3 HOH A 14 514 2 HOH HOH . 
E 3 HOH A 15 515 18 HOH HOH . 
E 3 HOH A 16 516 10 HOH HOH . 
E 3 HOH A 17 517 57 HOH HOH . 
E 3 HOH A 18 518 21 HOH HOH . 
E 3 HOH A 19 519 23 HOH HOH . 
E 3 HOH A 20 520 47 HOH HOH . 
E 3 HOH A 21 521 7 HOH HOH . 
E 3 HOH A 22 522 6 HOH HOH . 
E 3 HOH A 23 523 8 HOH HOH . 
E 3 HOH A 24 524 42 HOH HOH . 
E 3 HOH A 25 525 46 HOH HOH . 
E 3 HOH A 26 526 32 HOH HOH . 
E 3 HOH A 27 527 36 HOH HOH . 
E 3 HOH A 28 528 45 HOH HOH . 
E 3 HOH A 29 529 94 HOH HOH . 
E 3 HOH A 30 530 61 HOH HOH . 
E 3 HOH A 31 531 79 HOH HOH . 
E 3 HOH A 32 532 4 HOH HOH . 
E 3 HOH A 33 533 37 HOH HOH . 
E 3 HOH A 34 534 13 HOH HOH . 
E 3 HOH A 35 535 76 HOH HOH . 
E 3 HOH A 36 536 50 HOH HOH . 
E 3 HOH A 37 537 66 HOH HOH . 
E 3 HOH A 38 538 11 HOH HOH . 
E 3 HOH A 39 539 19 HOH HOH . 
E 3 HOH A 40 540 43 HOH HOH . 
E 3 HOH A 41 541 53 HOH HOH . 
E 3 HOH A 42 542 62 HOH HOH . 
E 3 HOH A 43 543 86 HOH HOH . 
E 3 HOH A 44 544 17 HOH HOH . 
E 3 HOH A 45 545 59 HOH HOH . 
E 3 HOH A 46 546 91 HOH HOH . 
E 3 HOH A 47 547 52 HOH HOH . 
E 3 HOH A 48 548 69 HOH HOH . 
E 3 HOH A 49 549 89 HOH HOH . 
E 3 HOH A 50 550 60 HOH HOH . 
E 3 HOH A 51 551 87 HOH HOH . 
E 3 HOH A 52 552 72 HOH HOH . 
E 3 HOH A 53 553 80 HOH HOH . 
E 3 HOH A 54 554 41 HOH HOH . 
E 3 HOH A 55 555 90 HOH HOH . 
F 3 HOH B 1 501 85 HOH HOH . 
F 3 HOH B 2 502 68 HOH HOH . 
F 3 HOH B 3 503 77 HOH HOH . 
F 3 HOH B 4 504 83 HOH HOH . 
F 3 HOH B 5 505 48 HOH HOH . 
F 3 HOH B 6 506 22 HOH HOH . 
F 3 HOH B 7 507 56 HOH HOH . 
F 3 HOH B 8 508 33 HOH HOH . 
F 3 HOH B 9 509 49 HOH HOH . 
F 3 HOH B 10 510 64 HOH HOH . 
F 3 HOH B 11 511 63 HOH HOH . 
F 3 HOH B 12 512 54 HOH HOH . 
F 3 HOH B 13 513 5 HOH HOH . 
F 3 HOH B 14 514 71 HOH HOH . 
F 3 HOH B 15 515 12 HOH HOH . 
F 3 HOH B 16 516 9 HOH HOH . 
F 3 HOH B 17 517 20 HOH HOH . 
F 3 HOH B 18 518 15 HOH HOH . 
F 3 HOH B 19 519 14 HOH HOH . 
F 3 HOH B 20 520 39 HOH HOH . 
F 3 HOH B 21 521 38 HOH HOH . 
F 3 HOH B 22 522 78 HOH HOH . 
F 3 HOH B 23 523 93 HOH HOH . 
F 3 HOH B 24 524 81 HOH HOH . 
F 3 HOH B 25 525 28 HOH HOH . 
F 3 HOH B 26 526 31 HOH HOH . 
F 3 HOH B 27 527 40 HOH HOH . 
F 3 HOH B 28 528 55 HOH HOH . 
F 3 HOH B 29 529 25 HOH HOH . 
F 3 HOH B 30 530 65 HOH HOH . 
F 3 HOH B 31 531 16 HOH HOH . 
F 3 HOH B 32 532 82 HOH HOH . 
F 3 HOH B 33 533 84 HOH HOH . 
F 3 HOH B 34 534 92 HOH HOH . 
F 3 HOH B 35 535 74 HOH HOH . 
F 3 HOH B 36 536 67 HOH HOH . 
F 3 HOH B 37 537 58 HOH HOH . 
F 3 HOH B 38 538 73 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 C10 9KO . . . C 2 -14.86 -8.225 -20.443 1 49.34 ? C10 9KO 401 A 1 
HETATM 2 C C13 9KO . . . C 2 -16.229 -6.162 -23.357 1 54.12 ? C13 9KO 401 A 1 
HETATM 3 C C17 9KO . . . C 2 -17.157 -8.018 -21.955 1 48.33 ? C17 9KO 401 A 1 
HETATM 4 C C20 9KO . . . C 2 -21.594 -12.255 -19.123 1 47.46 ? C20 9KO 401 A 1 
HETATM 5 C C22 9KO . . . C 2 -22.694 -14.075 -20.4 1 47.02 ? C22 9KO 401 A 1 
HETATM 6 C C24 9KO . . . C 2 -23.761 -15.954 -21.669 1 48.35 ? C24 9KO 401 A 1 
HETATM 7 C C01 9KO . . . C 2 -22.824 -13.32 -17.153 1 45.92 ? C01 9KO 401 A 1 
HETATM 8 C C02 9KO . . . C 2 -21.641 -12.542 -17.759 1 53.99 ? C02 9KO 401 A 1 
HETATM 9 C C03 9KO . . . C 2 -20.608 -12.128 -16.935 1 47.1 ? C03 9KO 401 A 1 
HETATM 10 C C04 9KO . . . C 2 -19.549 -11.437 -17.485 1 49.29 ? C04 9KO 401 A 1 
HETATM 11 C C05 9KO . . . C 2 -19.5 -11.166 -18.841 1 49.04 ? C05 9KO 401 A 1 
HETATM 12 C C07 9KO . . . C 2 -18.285 -9.831 -20.694 1 50.49 ? C07 9KO 401 A 1 
HETATM 13 C C08 9KO . . . C 2 -17.065 -8.972 -20.962 1 49.04 ? C08 9KO 401 A 1 
HETATM 14 C C09 9KO . . . C 2 -15.93 -9.066 -20.169 1 48.65 ? C09 9KO 401 A 1 
HETATM 15 C C11 9KO . . . C 2 -14.945 -7.283 -21.469 1 50.59 ? C11 9KO 401 A 1 
HETATM 16 C C12 9KO . . . C 2 -16.091 -7.191 -22.233 1 45.79 ? C12 9KO 401 A 1 
HETATM 17 C C19 9KO . . . C 2 -20.537 -11.564 -19.669 1 46.59 ? C19 9KO 401 A 1 
HETATM 18 C C25 9KO . . . C 2 -24.952 -13.676 -21.478 1 45.08 ? C25 9KO 401 A 1 
HETATM 19 C C27 9KO . . . C 2 -27.022 -13.335 -22.446 1 44.09 ? C27 9KO 401 A 1 
HETATM 20 C C29 9KO . . . C 2 -28.46 -15.217 -23.489 1 44.01 ? C29 9KO 401 A 1 
HETATM 21 C C30 9KO . . . C 2 -29.797 -15.582 -23.634 1 48.9 ? C30 9KO 401 A 1 
HETATM 22 C C31 9KO . . . C 2 -30.086 -16.909 -23.94 1 45.6 ? C31 9KO 401 A 1 
HETATM 23 C C32 9KO . . . C 2 -29.049 -17.804 -24.1 1 47.65 ? C32 9KO 401 A 1 
HETATM 24 C C34 9KO . . . C 2 -27.472 -16.163 -23.684 1 48.13 ? C34 9KO 401 A 1 
HETATM 25 C C36 9KO . . . C 2 -30.498 -19.688 -25.179 1 64.43 ? C36 9KO 401 A 1 
HETATM 26 C C37 9KO . . . C 2 -30.909 -21.119 -24.834 1 62.91 ? C37 9KO 401 A 1 
HETATM 27 C C39 9KO . . . C 2 -29.693 -23.171 -25.702 1 80.91 ? C39 9KO 401 A 1 
HETATM 28 C C40 9KO . . . C 2 -28.443 -24.06 -25.632 1 77.78 ? C40 9KO 401 A 1 
HETATM 29 C C42 9KO . . . C 2 -28.8 -21.607 -23.93 1 63.73 ? C42 9KO 401 A 1 
HETATM 30 C C43 9KO . . . C 2 -28.242 -20.248 -24.328 1 57.13 ? C43 9KO 401 A 1 
HETATM 31 C C45 9KO . . . C 2 -26.078 -11.556 -21.313 1 49.45 ? C45 9KO 401 A 1 
HETATM 32 C C46 9KO . . . C 2 -24.96 -12.377 -21.019 1 43.71 ? C46 9KO 401 A 1 
HETATM 33 C C47 9KO . . . C 2 -23.794 -11.838 -20.207 1 43.76 ? C47 9KO 401 A 1 
HETATM 34 F F14 9KO . . . C 2 -16.79 -5.062 -22.78 1 58.77 ? F14 9KO 401 A 1 
HETATM 35 F F15 9KO . . . C 2 -17.028 -6.588 -24.389 1 47.93 ? F15 9KO 401 A 1 
HETATM 36 F F16 9KO . . . C 2 -15.017 -5.857 -23.885 1 49.21 ? F16 9KO 401 A 1 
HETATM 37 N N06 9KO . . . C 2 -18.386 -10.398 -19.345 1 52 ? N06 9KO 401 A 1 
HETATM 38 N N21 9KO . . . C 2 -22.708 -12.716 -19.921 1 46.85 ? N21 9KO 401 A 1 
HETATM 39 N N23 9KO . . . C 2 -23.8 -14.579 -21.197 1 49.4 ? N23 9KO 401 A 1 
HETATM 40 N N26 9KO . . . C 2 -26.004 -14.135 -22.195 1 43.12 ? N26 9KO 401 A 1 
HETATM 41 N N28 9KO . . . C 2 -28.144 -13.819 -23.216 1 45.37 ? N28 9KO 401 A 1 
HETATM 42 N N33 9KO . . . C 2 -27.797 -17.411 -23.974 1 52.67 ? N33 9KO 401 A 1 
HETATM 43 N N35 9KO . . . C 2 -29.309 -19.204 -24.405 1 54.31 ? N35 9KO 401 A 1 
HETATM 44 N N38 9KO . . . C 2 -29.803 -21.996 -24.836 1 71.69 ? N38 9KO 401 A 1 
HETATM 45 N N44 9KO . . . C 2 -27.082 -12.067 -22.029 1 48.13 ? N44 9KO 401 A 1 
HETATM 46 O O18 9KO . . . C 2 -19.112 -9.972 -21.535 1 47.06 ? O18 9KO 401 A 1 
HETATM 47 O O41 9KO . . . C 2 -30.568 -23.446 -26.458 1 82.86 ? O41 9KO 401 A 1 
HETATM 48 O O48 9KO . . . C 2 -21.779 -14.779 -20.16 1 39.97 ? O48 9KO 401 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           48 
#