data_2YHD # _model_server_result.job_id mnM2U9X4rRAcboybpAy-0w _model_server_result.datetime_utc '2024-10-12 17:21:46' _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 2yhd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1921}' # _entry.id 2YHD # _exptl.entry_id 2YHD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 278.305 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-(2,3-dihydro-1H-perimidin-2-yl)benzene-1,2-diol _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 2YHD _cell.length_a 57.53 _cell.length_b 66.75 _cell.length_c 73.68 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YHD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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,E _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C17 H14 N2 O2' _chem_comp.formula_weight 278.305 _chem_comp.id AV6 _chem_comp.mon_nstd_flag . _chem_comp.name 4-(2,3-dihydro-1H-perimidin-2-yl)benzene-1,2-diol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '4-{2,4-DIAZATRICYCLO[7.3.1.0]TRIDECA- 1(12),5,7,9(13),10-PENTAEN-3-YL}BENZENE-1,2-DIOL' # 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 C6 C1 AV6 doub 70 n y C1 C2 AV6 sing 71 n y C1 C10 AV6 sing 72 n y C3 C2 AV6 doub 73 n y C2 N13 AV6 sing 74 n n C4 C3 AV6 sing 75 n y C3 H3 AV6 sing 76 n n C5 C4 AV6 doub 77 n y C4 H4 AV6 sing 78 n n C5 C6 AV6 sing 79 n y C5 H5 AV6 sing 80 n n C7 C6 AV6 sing 81 n y C7 C8 AV6 doub 82 n y C7 H7 AV6 sing 83 n n C8 C9 AV6 sing 84 n y C8 H8 AV6 sing 85 n n C9 C10 AV6 doub 86 n y C9 H9 AV6 sing 87 n n C10 N11 AV6 sing 88 n n N11 C12 AV6 sing 89 n n N13 C12 AV6 sing 90 n n C12 C15 AV6 sing 91 n n C15 C16 AV6 doub 92 n y C15 C20 AV6 sing 93 n y C16 C17 AV6 sing 94 n y C16 H16 AV6 sing 95 n n C17 O22 AV6 sing 96 n n C17 C18 AV6 doub 97 n y C19 C18 AV6 sing 98 n y C18 O21 AV6 sing 99 n n C20 C19 AV6 doub 100 n y C19 H19 AV6 sing 101 n n C20 H20 AV6 sing 102 n n O21 HO21 AV6 sing 103 n n O22 HO22 AV6 sing 104 n n N11 HN11 AV6 sing 105 n n N13 HN13 AV6 sing 106 n n C12 H12 AV6 sing 107 n n # _atom_sites.entry_id 2YHD _atom_sites.fract_transf_matrix[1][1] 0.017382 _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] 0.014981 _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] 0.013572 _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 SO4 A 1 1000 1000 SO4 SO4 . C 3 TES A 1 1920 1920 TES TES . D 4 AV6 A 1 1921 1921 AV6 AV6 . E 5 HOH A 1 2001 2001 HOH HOH . E 5 HOH A 2 2002 2002 HOH HOH . E 5 HOH A 3 2003 2003 HOH HOH . E 5 HOH A 4 2004 2004 HOH HOH . E 5 HOH A 5 2005 2005 HOH HOH . E 5 HOH A 6 2006 2006 HOH HOH . E 5 HOH A 7 2007 2007 HOH HOH . E 5 HOH A 8 2008 2008 HOH HOH . E 5 HOH A 9 2009 2009 HOH HOH . E 5 HOH A 10 2010 2010 HOH HOH . E 5 HOH A 11 2011 2011 HOH HOH . E 5 HOH A 12 2012 2012 HOH HOH . E 5 HOH A 13 2013 2013 HOH HOH . E 5 HOH A 14 2014 2014 HOH HOH . E 5 HOH A 15 2015 2015 HOH HOH . E 5 HOH A 16 2016 2016 HOH HOH . E 5 HOH A 17 2017 2017 HOH HOH . E 5 HOH A 18 2018 2018 HOH HOH . E 5 HOH A 19 2019 2019 HOH HOH . E 5 HOH A 20 2020 2020 HOH HOH . E 5 HOH A 21 2021 2021 HOH HOH . E 5 HOH A 22 2022 2022 HOH HOH . E 5 HOH A 23 2023 2023 HOH HOH . E 5 HOH A 24 2024 2024 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 AV6 . . . D 4 36.218 7.879 18.374 0.5 55.58 ? C1 AV6 1921 A 1 HETATM 2 C C2 AV6 . . . D 4 36.799 9.09 18.948 0.5 55.88 ? C2 AV6 1921 A 1 HETATM 3 C C3 AV6 . . . D 4 37.827 9.742 18.318 0.5 56.07 ? C3 AV6 1921 A 1 HETATM 4 C C4 AV6 . . . D 4 38.309 9.237 17.126 0.5 56.33 ? C4 AV6 1921 A 1 HETATM 5 C C5 AV6 . . . D 4 37.802 8.089 16.536 0.5 56.3 ? C5 AV6 1921 A 1 HETATM 6 C C6 AV6 . . . D 4 36.757 7.382 17.095 0.5 55.74 ? C6 AV6 1921 A 1 HETATM 7 C C7 AV6 . . . D 4 36.216 6.253 16.513 0.5 54.23 ? C7 AV6 1921 A 1 HETATM 8 C C8 AV6 . . . D 4 35.181 5.634 17.194 0.5 53.41 ? C8 AV6 1921 A 1 HETATM 9 C C9 AV6 . . . D 4 34.639 6.066 18.407 0.5 53.24 ? C9 AV6 1921 A 1 HETATM 10 C C10 AV6 . . . D 4 35.124 7.175 19.049 0.5 54.41 ? C10 AV6 1921 A 1 HETATM 11 N N11 AV6 . . . D 4 34.658 7.64 20.206 0.5 55.08 ? N11 AV6 1921 A 1 HETATM 12 C C12 AV6 . . . D 4 35.229 8.868 20.76 0.5 56.15 ? C12 AV6 1921 A 1 HETATM 13 N N13 AV6 . . . D 4 36.321 9.546 20.08 0.5 56.97 ? N13 AV6 1921 A 1 HETATM 14 C C15 AV6 . . . D 4 35.125 9.272 22.157 0.5 56.49 ? C15 AV6 1921 A 1 HETATM 15 C C16 AV6 . . . D 4 36.087 10.151 22.686 0.5 57.1 ? C16 AV6 1921 A 1 HETATM 16 C C17 AV6 . . . D 4 36.015 10.561 24.011 0.5 56.88 ? C17 AV6 1921 A 1 HETATM 17 C C18 AV6 . . . D 4 34.895 10.045 24.804 0.5 56.59 ? C18 AV6 1921 A 1 HETATM 18 C C19 AV6 . . . D 4 33.974 9.2 24.224 0.5 56.45 ? C19 AV6 1921 A 1 HETATM 19 C C20 AV6 . . . D 4 34.08 8.834 22.906 0.5 56.02 ? C20 AV6 1921 A 1 HETATM 20 O O21 AV6 . . . D 4 34.729 10.393 26.094 0.5 57.85 ? O21 AV6 1921 A 1 HETATM 21 O O22 AV6 . . . D 4 36.939 11.391 24.556 0.5 56.63 ? O22 AV6 1921 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 21 #