data_6KDZ # _model_server_result.job_id bHaQSuTzMZUkP3djym0yhA _model_server_result.datetime_utc '2025-07-31 18:19:31' _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 6kdz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":803}' # _entry.id 6KDZ # _exptl.entry_id 6KDZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 360.373 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-[2-(5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)ethyl]-3,7,8,10-tetrazatricyclo[7.4.0.0^{2,7}]trideca-1,3,5,8,10,12-hexaen-6-ol _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 90 _cell.entry_id 6KDZ _cell.length_a 50.218 _cell.length_b 81.044 _cell.length_c 162.136 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KDZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E 1 1 B,F,G 2 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 4 _struct_asym.id E _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 NE2 HIS 85 A HIS 529 1_555 C ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc2 A NE2 HIS 119 A HIS 563 1_555 C ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc3 A OD2 ASP 120 A ASP 564 1_555 C ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc4 A OD1 ASP 120 A ASP 564 1_555 D MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc5 A OD1 ASP 230 A ASP 674 1_555 C ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc6 B NE2 HIS 85 B HIS 529 1_555 F ZN ZN . B ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc7 B NE2 HIS 119 B HIS 563 1_555 F ZN ZN . B ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc8 B OD2 ASP 120 B ASP 564 1_555 F ZN ZN . B ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc9 B OD1 ASP 120 B ASP 564 1_555 G MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc10 B OD1 ASP 230 B ASP 674 1_555 F ZN ZN . B ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? # _chem_comp.formula 'C18 H16 N8 O' _chem_comp.formula_weight 360.373 _chem_comp.id D79 _chem_comp.mon_nstd_flag . _chem_comp.name 4-[2-(5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)ethyl]-3,7,8,10-tetrazatricyclo[7.4.0.0^{2,7}]trideca-1,3,5,8,10,12-hexaen-6-ol _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 O21 C16 D79 sing 83 n n N20 C23 D79 doub 84 n y N20 N19 D79 sing 85 n y N24 C23 D79 sing 86 n y N24 C25 D79 doub 87 n y C23 C22 D79 sing 88 n y C16 N19 D79 sing 89 n y C16 C15 D79 doub 90 n y N19 C18 D79 sing 91 n y C25 C26 D79 sing 92 n y C15 C4 D79 sing 93 n y C22 C18 D79 doub 94 n y C22 C27 D79 sing 95 n y C18 N17 D79 sing 96 n y C26 C27 D79 doub 97 n y C4 N17 D79 doub 98 n y C4 C6 D79 sing 99 n n C5 C6 D79 sing 100 n n C5 C3 D79 sing 101 n n N2 C3 D79 doub 102 n y N2 N7 D79 sing 103 n y C3 N1 D79 sing 104 n y C14 C12 D79 sing 105 n n N7 C12 D79 sing 106 n y N7 C8 D79 sing 107 n y N1 C8 D79 doub 108 n y C12 C11 D79 doub 109 n y C8 N9 D79 sing 110 n y C11 C10 D79 sing 111 n y N9 C10 D79 doub 112 n y C10 C13 D79 sing 113 n n C26 H1 D79 sing 114 n n C27 H2 D79 sing 115 n n C25 H3 D79 sing 116 n n C11 H4 D79 sing 117 n n C15 H5 D79 sing 118 n n C14 H7 D79 sing 119 n n C14 H8 D79 sing 120 n n C14 H9 D79 sing 121 n n C13 H10 D79 sing 122 n n C13 H11 D79 sing 123 n n C13 H12 D79 sing 124 n n C5 H13 D79 sing 125 n n C5 H14 D79 sing 126 n n C6 H15 D79 sing 127 n n C6 H16 D79 sing 128 n n O21 H6 D79 sing 129 n n # _atom_sites.entry_id 6KDZ _atom_sites.fract_transf_matrix[1][1] 0.019913 _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] 0.012339 _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] 0.006168 _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 ZN A 1 801 801 ZN ZN . D 3 MG A 1 802 802 MG MG . E 4 D79 A 1 803 1 D79 UNL . F 2 ZN B 1 801 801 ZN ZN . G 3 MG B 1 802 802 MG MG . # 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 C26 D79 . . . E 4 26.77 4.566 57.264 1 61.1 ? C26 D79 803 A 1 HETATM 2 C C27 D79 . . . E 4 25.495 4.61 57.791 1 59.66 ? C27 D79 803 A 1 HETATM 3 C C25 D79 . . . E 4 27.016 4.917 55.945 1 62.93 ? C25 D79 803 A 1 HETATM 4 C C22 D79 . . . E 4 24.648 5.039 56.793 1 60.16 ? C22 D79 803 A 1 HETATM 5 C C23 D79 . . . E 4 24.911 5.39 55.464 1 61.36 ? C23 D79 803 A 1 HETATM 6 C C18 D79 . . . E 4 23.301 5.2 56.96 1 60.56 ? C18 D79 803 A 1 HETATM 7 C C3 D79 . . . E 4 18.986 3.298 59.948 1 55.13 ? C3 D79 803 A 1 HETATM 8 C C8 D79 . . . E 4 18.445 2.998 61.937 1 53.54 ? C8 D79 803 A 1 HETATM 9 C C11 D79 . . . E 4 16.086 1.948 62.899 1 52.19 ? C11 D79 803 A 1 HETATM 10 C C15 D79 . . . E 4 20.626 5.734 56.599 1 59.46 ? C15 D79 803 A 1 HETATM 11 C C12 D79 . . . E 4 16.255 2.069 61.585 1 51.69 ? C12 D79 803 A 1 HETATM 12 C C16 D79 . . . E 4 21.474 5.896 55.58 1 59.86 ? C16 D79 803 A 1 HETATM 13 C C10 D79 . . . E 4 17.233 2.419 63.703 1 52.76 ? C10 D79 803 A 1 HETATM 14 C C4 D79 . . . E 4 21.272 5.263 57.843 1 58.05 ? C4 D79 803 A 1 HETATM 15 C C14 D79 . . . E 4 15.195 1.65 60.634 1 47.82 ? C14 D79 803 A 1 HETATM 16 C C13 D79 . . . E 4 17.045 2.299 65.166 1 55.51 ? C13 D79 803 A 1 HETATM 17 C C5 D79 . . . E 4 19.797 3.681 58.791 1 57.47 ? C5 D79 803 A 1 HETATM 18 C C6 D79 . . . E 4 20.409 5.043 59.015 1 59.9 ? C6 D79 803 A 1 HETATM 19 N N24 D79 . . . E 4 26.165 5.331 54.989 1 62.17 ? N24 D79 803 A 1 HETATM 20 N N20 D79 . . . E 4 23.783 5.748 54.842 1 60.25 ? N20 D79 803 A 1 HETATM 21 N N1 D79 . . . E 4 19.445 3.449 61.227 1 54.43 ? N1 D79 803 A 1 HETATM 22 N N2 D79 . . . E 4 17.766 2.79 59.816 1 50.96 ? N2 D79 803 A 1 HETATM 23 N N17 D79 . . . E 4 22.518 5.004 58.033 1 60.33 ? N17 D79 803 A 1 HETATM 24 N N9 D79 . . . E 4 18.349 2.916 63.282 1 51.99 ? N9 D79 803 A 1 HETATM 25 N N19 D79 . . . E 4 22.805 5.635 55.759 1 58.57 ? N19 D79 803 A 1 HETATM 26 N N7 D79 . . . E 4 17.428 2.596 61.104 1 53.65 ? N7 D79 803 A 1 HETATM 27 O O21 D79 . . . E 4 21.024 6.32 54.341 1 58.28 ? O21 D79 803 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 27 #