data_5TA8 # _model_server_result.job_id EIZvILhPa2OahWpLbSp9BQ _model_server_result.datetime_utc '2025-06-24 19:56:39' _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 5ta8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 5TA8 # _exptl.entry_id 5TA8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 543.609 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-[(9-cyclopentyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino]-3-methoxy-N-(1-methylpiperidin-4-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 5TA8 _cell.length_a 67.364 _cell.length_b 67.364 _cell.length_c 151.918 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5TA8 _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 PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 3 _struct_asym.id C _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 SG CYS 225 A CYS 212 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc2 A SG CYS 268 A CYS 255 1_555 B ZN ZN . A ZN 401 6_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? # _chem_comp.formula 'C27 H35 F2 N7 O3' _chem_comp.formula_weight 543.609 _chem_comp.id 79C _chem_comp.mon_nstd_flag . _chem_comp.name 4-[(9-cyclopentyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino]-3-methoxy-N-(1-methylpiperidin-4-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 F19 C18 79C sing 1 n n C18 F20 79C sing 2 n n C18 C21 79C sing 3 n n C18 C16 79C sing 4 n n O17 C16 79C doub 5 n n C21 N22 79C sing 6 n n C26 C25 79C sing 7 n n C26 C27 79C sing 8 n n C25 C24 79C sing 9 n n C16 N14 79C sing 10 n n C24 C23 79C sing 11 n n C27 C23 79C sing 12 n n N22 C23 79C sing 13 n n N22 C28 79C sing 14 n n N14 C15 79C sing 15 n n N14 C13 79C sing 16 n n C28 C13 79C doub 17 n y C28 N29 79C sing 18 n y C13 C12 79C sing 19 n y C37 N36 79C sing 20 n n N36 C35 79C sing 21 n n N36 C38 79C sing 22 n n N29 C10 79C doub 23 n y C35 C34 79C sing 24 n n C12 N11 79C doub 25 n y C34 C33 79C sing 26 n n C38 C39 79C sing 27 n n C39 C33 79C sing 28 n n C10 N11 79C sing 29 n y C10 N9 79C sing 30 n n C7 C6 79C doub 31 n y C7 C8 79C sing 32 n y N32 C33 79C sing 33 n n N32 C30 79C sing 34 n n C6 C5 79C sing 35 n y N9 C8 79C sing 36 n n C8 C3 79C doub 37 n y C5 C30 79C sing 38 n n C5 C4 79C doub 39 n y C30 O31 79C doub 40 n n C3 C4 79C sing 41 n y C3 O2 79C sing 42 n n O2 C1 79C sing 43 n n C4 H1 79C sing 44 n n C6 H2 79C sing 45 n n C7 H3 79C sing 46 n n C15 H4 79C sing 47 n n C15 H5 79C sing 48 n n C15 H6 79C sing 49 n n C21 H7 79C sing 50 n n C21 H8 79C sing 51 n n C24 H9 79C sing 52 n n C24 H10 79C sing 53 n n C26 H11 79C sing 54 n n C26 H12 79C sing 55 n n C1 H13 79C sing 56 n n C1 H14 79C sing 57 n n C1 H15 79C sing 58 n n N9 H16 79C sing 59 n n C12 H17 79C sing 60 n n C23 H18 79C sing 61 n n C25 H19 79C sing 62 n n C25 H20 79C sing 63 n n C27 H21 79C sing 64 n n C27 H22 79C sing 65 n n N32 H23 79C sing 66 n n C33 H24 79C sing 67 n n C34 H25 79C sing 68 n n C34 H26 79C sing 69 n n C35 H27 79C sing 70 n n C35 H28 79C sing 71 n n C37 H30 79C sing 72 n n C37 H31 79C sing 73 n n C37 H32 79C sing 74 n n C38 H33 79C sing 75 n n C38 H34 79C sing 76 n n C39 H35 79C sing 77 n n C39 H36 79C sing 78 n n # _atom_sites.entry_id 5TA8 _atom_sites.fract_transf_matrix[1][1] 0.014845 _atom_sites.fract_transf_matrix[1][2] 0.008571 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017141 _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] 0.006582 _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 ZN A 1 401 999 ZN ZN . C 3 79C A 1 402 1000 79C LIG . D 4 HOH A 1 501 1023 HOH HOH . D 4 HOH A 2 502 1014 HOH HOH . D 4 HOH A 3 503 1018 HOH HOH . D 4 HOH A 4 504 1024 HOH HOH . D 4 HOH A 5 505 1019 HOH HOH . D 4 HOH A 6 506 1036 HOH HOH . D 4 HOH A 7 507 1001 HOH HOH . D 4 HOH A 8 508 1044 HOH HOH . D 4 HOH A 9 509 1025 HOH HOH . D 4 HOH A 10 510 1005 HOH HOH . D 4 HOH A 11 511 1004 HOH HOH . D 4 HOH A 12 512 1037 HOH HOH . D 4 HOH A 13 513 1013 HOH HOH . D 4 HOH A 14 514 1040 HOH HOH . D 4 HOH A 15 515 1012 HOH HOH . D 4 HOH A 16 516 1008 HOH HOH . D 4 HOH A 17 517 1010 HOH HOH . D 4 HOH A 18 518 1038 HOH HOH . D 4 HOH A 19 519 1003 HOH HOH . D 4 HOH A 20 520 1042 HOH HOH . D 4 HOH A 21 521 1017 HOH HOH . D 4 HOH A 22 522 1009 HOH HOH . D 4 HOH A 23 523 1030 HOH HOH . D 4 HOH A 24 524 1021 HOH HOH . D 4 HOH A 25 525 1002 HOH HOH . D 4 HOH A 26 526 1039 HOH HOH . D 4 HOH A 27 527 1033 HOH HOH . D 4 HOH A 28 528 1020 HOH HOH . D 4 HOH A 29 529 1015 HOH HOH . D 4 HOH A 30 530 1035 HOH HOH . D 4 HOH A 31 531 1032 HOH HOH . D 4 HOH A 32 532 1031 HOH HOH . D 4 HOH A 33 533 1006 HOH HOH . D 4 HOH A 34 534 1028 HOH HOH . D 4 HOH A 35 535 1043 HOH HOH . D 4 HOH A 36 536 1029 HOH HOH . D 4 HOH A 37 537 1022 HOH HOH . D 4 HOH A 38 538 1007 HOH HOH . D 4 HOH A 39 539 1041 HOH HOH . D 4 HOH A 40 540 1034 HOH HOH . D 4 HOH A 41 541 1027 HOH HOH . D 4 HOH A 42 542 1011 HOH HOH . D 4 HOH A 43 543 1016 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 C4 79C . . . C 3 0.084 21.079 70.063 1 73.52 ? C4 79C 402 A 1 HETATM 2 C C5 79C . . . C 3 -1.046 20.8 69.288 1 76.98 ? C5 79C 402 A 1 HETATM 3 C C6 79C . . . C 3 -1.504 21.777 68.382 1 79.29 ? C6 79C 402 A 1 HETATM 4 C C7 79C . . . C 3 -0.855 22.998 68.254 1 75.75 ? C7 79C 402 A 1 HETATM 5 C C8 79C . . . C 3 0.279 23.272 69.03 1 76.3 ? C8 79C 402 A 1 HETATM 6 C C10 79C . . . C 3 0.922 25.505 68.014 1 69.77 ? C10 79C 402 A 1 HETATM 7 C C13 79C . . . C 3 0.84 27.568 66.259 1 66.54 ? C13 79C 402 A 1 HETATM 8 C C15 79C . . . C 3 0.708 30.019 66.004 1 67.9 ? C15 79C 402 A 1 HETATM 9 C C21 79C . . . C 3 -0.35 26.3 63.698 1 68.65 ? C21 79C 402 A 1 HETATM 10 C C24 79C . . . C 3 -3.156 25.623 64.251 1 58.18 ? C24 79C 402 A 1 HETATM 11 C C26 79C . . . C 3 -2.513 23.289 63.82 1 60.31 ? C26 79C 402 A 1 HETATM 12 C C28 79C . . . C 3 -0.023 26.454 66.107 1 65.15 ? C28 79C 402 A 1 HETATM 13 C C1 79C . . . C 3 2.802 21.553 70.974 1 86.91 ? C1 79C 402 A 1 HETATM 14 O O2 79C . . . C 3 1.839 22.581 70.703 1 79.63 ? O2 79C 402 A 1 HETATM 15 C C3 79C . . . C 3 0.739 22.3 69.939 1 77.82 ? C3 79C 402 A 1 HETATM 16 N N9 79C . . . C 3 1.008 24.477 68.956 1 71.87 ? N9 79C 402 A 1 HETATM 17 N N11 79C . . . C 3 1.736 26.545 68.174 1 72.52 ? N11 79C 402 A 1 HETATM 18 C C12 79C . . . C 3 1.72 27.579 67.334 1 68.05 ? C12 79C 402 A 1 HETATM 19 N N14 79C . . . C 3 0.766 28.685 65.391 1 74.42 ? N14 79C 402 A 1 HETATM 20 C C16 79C . . . C 3 0.672 28.611 64.037 1 79.74 ? C16 79C 402 A 1 HETATM 21 O O17 79C . . . C 3 0.591 29.637 63.382 1 80 ? O17 79C 402 A 1 HETATM 22 C C18 79C . . . C 3 0.719 27.303 63.302 1 80.34 ? C18 79C 402 A 1 HETATM 23 F F19 79C . . . C 3 0.526 27.569 61.943 1 98.43 ? F19 79C 402 A 1 HETATM 24 F F20 79C . . . C 3 1.979 26.721 63.494 1 96.62 ? F20 79C 402 A 1 HETATM 25 N N22 79C . . . C 3 -0.932 26.398 65.042 1 65.88 ? N22 79C 402 A 1 HETATM 26 C C23 79C . . . C 3 -1.928 25.314 65.149 1 60.36 ? C23 79C 402 A 1 HETATM 27 C C25 79C . . . C 3 -3.739 24.227 63.915 1 61.56 ? C25 79C 402 A 1 HETATM 28 C C27 79C . . . C 3 -1.374 23.975 64.594 1 60.09 ? C27 79C 402 A 1 HETATM 29 N N29 79C . . . C 3 0.059 25.462 67.002 1 69.45 ? N29 79C 402 A 1 HETATM 30 C C30 79C . . . C 3 -1.725 19.487 69.424 1 86.07 ? C30 79C 402 A 1 HETATM 31 O O31 79C . . . C 3 -1.739 18.906 70.492 1 92.38 ? O31 79C 402 A 1 HETATM 32 N N32 79C . . . C 3 -2.306 18.924 68.338 1 95.09 ? N32 79C 402 A 1 HETATM 33 C C33 79C . . . C 3 -3.003 17.632 68.345 1 98.61 ? C33 79C 402 A 1 HETATM 34 C C34 79C . . . C 3 -4.234 17.763 67.431 1 99.37 ? C34 79C 402 A 1 HETATM 35 C C35 79C . . . C 3 -4.944 16.419 67.234 1 102.15 ? C35 79C 402 A 1 HETATM 36 N N36 79C . . . C 3 -3.984 15.434 66.708 1 112.14 ? N36 79C 402 A 1 HETATM 37 C C37 79C . . . C 3 -4.659 14.165 66.396 1 110.22 ? C37 79C 402 A 1 HETATM 38 C C38 79C . . . C 3 -2.838 15.224 67.618 1 108.19 ? C38 79C 402 A 1 HETATM 39 C C39 79C . . . C 3 -2.059 16.532 67.834 1 102.02 ? C39 79C 402 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 39 #