data_8XTD # _model_server_result.job_id QGYUZZgSdtmFXZL87-nn9A _model_server_result.datetime_utc '2025-07-20 02:00:09' _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 8xtd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8XTD # _exptl.entry_id 8XTD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 472.542 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '8-[(3R)-3-Aminopiperidin-1-yl]-7-but-2-yn-1-yl-3-methyl-1-[(4-methylquinazolin-2-yl)methyl]-3,7-dihydro-1H-purine-2,6-d ione' _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 8XTD _cell.length_a 81.217 _cell.length_b 81.217 _cell.length_c 133.485 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XTD _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C25 H28 N8 O2' _chem_comp.formula_weight 472.542 _chem_comp.id 356 _chem_comp.mon_nstd_flag . _chem_comp.name '8-[(3R)-3-Aminopiperidin-1-yl]-7-but-2-yn-1-yl-3-methyl-1-[(4-methylquinazolin-2-yl)methyl]-3,7-dihydro-1H-purine-2,6-d ione' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Linagliptin # 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 C14 N8 356 sing 1 n n C22 C17 356 sing 2 n n C22 C26 356 sing 3 n n O19 C13 356 doub 4 n n N8 C13 356 sing 5 n n N8 C3 356 sing 6 n n C17 N11 356 sing 7 n n C26 C21 356 sing 8 n n N7 C3 356 sing 9 n y N7 C5 356 doub 10 n y C13 N9 356 sing 11 n n C3 C1 356 doub 12 n y N11 C5 356 sing 13 n n N11 C16 356 sing 14 n n C5 N2 356 sing 15 n y C21 C16 356 sing 16 n n C21 N27 356 sing 17 n n C32 C29 356 sing 18 n n N9 C15 356 sing 19 n n N9 C4 356 sing 20 n n C33 C35 356 doub 21 n y C33 C30 356 sing 22 n y C1 N2 356 sing 23 n y C1 C4 356 sing 24 n n C29 C30 356 doub 25 n y C29 N25 356 sing 26 n y C35 C34 356 sing 27 n y C30 C28 356 sing 28 n y N25 C20 356 doub 29 n y C34 C31 356 doub 30 n y C28 C31 356 sing 31 n y C28 N24 356 doub 32 n y C20 N24 356 sing 33 n y C20 C15 356 sing 34 n n N2 C6 356 sing 35 n n C4 O10 356 doub 36 n n C6 C12 356 sing 37 n n C12 C18 356 trip 38 n n C18 C23 356 sing 39 n n C6 H61 356 sing 40 n n C6 H62 356 sing 41 n n C14 H141 356 sing 42 n n C14 H142 356 sing 43 n n C14 H143 356 sing 44 n n C15 H151 356 sing 45 n n C15 H152 356 sing 46 n n C16 H161 356 sing 47 n n C16 H162 356 sing 48 n n C17 H171 356 sing 49 n n C17 H172 356 sing 50 n n C21 H21 356 sing 51 n n C22 H221 356 sing 52 n n C22 H222 356 sing 53 n n C23 H231 356 sing 54 n n C23 H232 356 sing 55 n n C23 H233 356 sing 56 n n C26 H261 356 sing 57 n n C26 H262 356 sing 58 n n N27 H271 356 sing 59 n n N27 H272 356 sing 60 n n C31 H31 356 sing 61 n n C32 H321 356 sing 62 n n C32 H322 356 sing 63 n n C32 H323 356 sing 64 n n C33 H33 356 sing 65 n n C34 H34 356 sing 66 n n C35 H35 356 sing 67 n n # _atom_sites.entry_id 8XTD _atom_sites.fract_transf_matrix[1][1] 0.012313 _atom_sites.fract_transf_matrix[1][2] 0.007109 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014217 _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] 0.007491 _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 2 356 A 1 401 398 356 356 . C 3 GOL A 1 402 399 GOL GOL . D 3 GOL A 1 403 401 GOL GOL . E 3 GOL A 1 404 403 GOL GOL . F 3 GOL A 1 405 404 GOL GOL . G 3 GOL A 1 406 405 GOL GOL . H 3 GOL A 1 407 406 GOL GOL . I 4 HOH A 1 501 18 HOH HOH . I 4 HOH A 2 502 8 HOH HOH . I 4 HOH A 3 503 11 HOH HOH . I 4 HOH A 4 504 7 HOH HOH . I 4 HOH A 5 505 12 HOH HOH . I 4 HOH A 6 506 6 HOH HOH . I 4 HOH A 7 507 4 HOH HOH . I 4 HOH A 8 508 14 HOH HOH . I 4 HOH A 9 509 19 HOH HOH . I 4 HOH A 10 510 17 HOH HOH . I 4 HOH A 11 511 13 HOH HOH . I 4 HOH A 12 512 10 HOH HOH . I 4 HOH A 13 513 2 HOH HOH . I 4 HOH A 14 514 5 HOH HOH . I 4 HOH A 15 515 9 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 C1 356 . . . B 2 -27.339 7.047 -51.123 1 135.61 0 C1 356 401 A 1 HETATM 2 N N2 356 . . . B 2 -26.674 7.516 -52.268 1 124.58 0 N2 356 401 A 1 HETATM 3 C C3 356 . . . B 2 -28.484 6.42 -51.557 1 130.19 0 C3 356 401 A 1 HETATM 4 C C4 356 . . . B 2 -27.015 7.134 -49.738 1 137.57 0 C4 356 401 A 1 HETATM 5 C C5 356 . . . B 2 -27.492 7.138 -53.355 1 123.47 0 C5 356 401 A 1 HETATM 6 C C6 356 . . . B 2 -25.396 8.244 -52.264 1 105.58 0 C6 356 401 A 1 HETATM 7 N N7 356 . . . B 2 -28.589 6.447 -52.913 1 126.77 0 N7 356 401 A 1 HETATM 8 N N8 356 . . . B 2 -29.373 5.853 -50.669 1 113.8 0 N8 356 401 A 1 HETATM 9 N N9 356 . . . B 2 -27.958 6.525 -48.88 1 107.87 0 N9 356 401 A 1 HETATM 10 O O10 356 . . . B 2 -26.007 7.658 -49.279 1 172.3 0 O10 356 401 A 1 HETATM 11 N N11 356 . . . B 2 -27.231 7.397 -54.733 1 106.84 0 N11 356 401 A 1 HETATM 12 C C12 356 . . . B 2 -25.488 9.714 -52.222 1 89.89 0 C12 356 401 A 1 HETATM 13 C C13 356 . . . B 2 -29.125 5.918 -49.315 1 91.08 0 C13 356 401 A 1 HETATM 14 C C14 356 . . . B 2 -30.587 5.184 -51.147 1 119.15 0 C14 356 401 A 1 HETATM 15 C C15 356 . . . B 2 -27.712 6.533 -47.419 1 120.5 0 C15 356 401 A 1 HETATM 16 C C16 356 . . . B 2 -26.348 8.426 -55.3 1 93.16 0 C16 356 401 A 1 HETATM 17 C C17 356 . . . B 2 -27.988 6.669 -55.762 1 102.04 0 C17 356 401 A 1 HETATM 18 C C18 356 . . . B 2 -25.663 10.992 -52.232 1 78 0 C18 356 401 A 1 HETATM 19 O O19 356 . . . B 2 -29.893 5.427 -48.511 1 92.36 0 O19 356 401 A 1 HETATM 20 C C20 356 . . . B 2 -27.033 5.3 -46.849 1 135.82 0 C20 356 401 A 1 HETATM 21 C C21 356 . . . B 2 -27.173 9.521 -56.036 1 84.87 0 C21 356 401 A 1 HETATM 22 C C22 356 . . . B 2 -28.124 7.445 -57.063 1 87.74 0 C22 356 401 A 1 HETATM 23 C C23 356 . . . B 2 -25.986 12.429 -52.33 1 63.08 0 C23 356 401 A 1 HETATM 24 N N24 356 . . . B 2 -25.967 5.484 -46.054 1 135.25 0 N24 356 401 A 1 HETATM 25 N N25 356 . . . B 2 -27.555 4.093 -47.126 1 140.77 0 N25 356 401 A 1 HETATM 26 C C26 356 . . . B 2 -28.348 8.931 -56.813 1 77.06 0 C26 356 401 A 1 HETATM 27 N N27 356 . . . B 2 -27.648 10.583 -55.136 1 80.3 0 N27 356 401 A 1 HETATM 28 C C28 356 . . . B 2 -25.35 4.383 -45.51 1 148.11 0 C28 356 401 A 1 HETATM 29 C C29 356 . . . B 2 -26.993 2.985 -46.609 1 144.29 0 C29 356 401 A 1 HETATM 30 C C30 356 . . . B 2 -25.842 3.079 -45.77 1 154.6 0 C30 356 401 A 1 HETATM 31 C C31 356 . . . B 2 -24.213 4.533 -44.687 1 144.76 0 C31 356 401 A 1 HETATM 32 C C32 356 . . . B 2 -27.63 1.679 -46.972 1 131.62 0 C32 356 401 A 1 HETATM 33 C C33 356 . . . B 2 -25.184 1.957 -45.199 1 157.6 0 C33 356 401 A 1 HETATM 34 C C34 356 . . . B 2 -23.605 3.432 -44.153 1 153.37 0 C34 356 401 A 1 HETATM 35 C C35 356 . . . B 2 -24.09 2.137 -44.407 1 154.14 0 C35 356 401 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 235 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 35 #