data_2YIR # _model_server_result.job_id dLyR6JLNnHCCUQ86Ls9wnQ _model_server_result.datetime_utc '2025-03-11 07:00:28' _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 2yir # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":600}' # _entry.id 2YIR # _exptl.entry_id 2YIR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 405.41 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (E)-N-(5-(2-CARBAMIMIDOYLHYDRAZONO)-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)-7-NITRO-1H-INDOLE-2-CARBOXAMIDE _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 2YIR _cell.length_a 91.243 _cell.length_b 91.243 _cell.length_c 93.466 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YIR _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 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_555 x-y,-y,-z+1/3 1 0 0 0 -1 0 0 0 -1 0 0 31.155333 # _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 'C20 H19 N7 O3' _chem_comp.formula_weight 405.41 _chem_comp.id YIR _chem_comp.mon_nstd_flag . _chem_comp.name (E)-N-(5-(2-CARBAMIMIDOYLHYDRAZONO)-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)-7-NITRO-1H-INDOLE-2-CARBOXAMIDE _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 OBC NAA YIR sing 379 n n NAA OBB YIR doub 380 n n NAA CAM YIR sing 381 n n CAH CAM YIR doub 382 n y CAH CAI YIR sing 383 n y CAM CAL YIR sing 384 n y CAI CAJ YIR doub 385 n y CAL NAB YIR sing 386 n y CAL CAK YIR doub 387 n y CAJ CAK YIR sing 388 n y NAB CAO YIR sing 389 n y CAK CAN YIR sing 390 n y CAO CAN YIR doub 391 n y CAO CAP YIR sing 392 n n OBD CAP YIR doub 393 n n CAP NAC YIR sing 394 n n NAC CAQ YIR sing 395 n n CAQ CAR YIR sing 396 n y CAQ CAV YIR doub 397 n y CAR CAS YIR doub 398 n y CAV CAU YIR sing 399 n y CAS CAW YIR sing 400 n n CAS CAT YIR sing 401 n y CAW CAX YIR sing 402 n n CAU CAT YIR doub 403 n y CAX CAY YIR sing 404 n n CAT CAZ YIR sing 405 n n CAZ CAY YIR sing 406 n n CAZ NAD YIR doub 407 n n NAD NAE YIR sing 408 n n NAE CBA YIR sing 409 n n NAG CBA YIR doub 410 n n CBA NAF YIR sing 411 n n NAB HNAB YIR sing 412 n n NAC HNAC YIR sing 413 n n NAF H1AF YIR sing 414 n n NAF H2AF YIR sing 415 n n NAG HAG YIR sing 416 n n CAH HAH YIR sing 417 n n CAI HAI YIR sing 418 n n CAJ HAJ YIR sing 419 n n CAN HAN YIR sing 420 n n CAR HAR YIR sing 421 n n CAU HAU YIR sing 422 n n CAV HAV YIR sing 423 n n CAW H1AW YIR sing 424 n n CAW H2AW YIR sing 425 n n CAX H1AX YIR sing 426 n n CAX H2AX YIR sing 427 e n CAY H1AY YIR sing 428 n n CAY H2AY YIR sing 429 n n NAE HAE YIR sing 430 n n # _atom_sites.entry_id 2YIR _atom_sites.fract_transf_matrix[1][1] 0.01096 _atom_sites.fract_transf_matrix[1][2] 0.006328 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012655 _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] 0.010699 _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 YIR A 1 600 600 YIR YIR . C 3 NO3 A 1 601 601 NO3 NO3 . D 4 HOH A 1 2001 2001 HOH HOH . D 4 HOH A 2 2002 2002 HOH HOH . D 4 HOH A 3 2003 2003 HOH HOH . D 4 HOH A 4 2004 2004 HOH HOH . D 4 HOH A 5 2005 2005 HOH HOH . D 4 HOH A 6 2006 2006 HOH HOH . D 4 HOH A 7 2007 2007 HOH HOH . D 4 HOH A 8 2008 2008 HOH HOH . D 4 HOH A 9 2009 2009 HOH HOH . D 4 HOH A 10 2010 2010 HOH HOH . D 4 HOH A 11 2011 2011 HOH HOH . D 4 HOH A 12 2012 2012 HOH HOH . D 4 HOH A 13 2013 2013 HOH HOH . D 4 HOH A 14 2014 2014 HOH HOH . D 4 HOH A 15 2015 2015 HOH HOH . D 4 HOH A 16 2016 2016 HOH HOH . D 4 HOH A 17 2017 2017 HOH HOH . D 4 HOH A 18 2018 2018 HOH HOH . D 4 HOH A 19 2019 2019 HOH HOH . D 4 HOH A 20 2020 2020 HOH HOH . D 4 HOH A 21 2021 2021 HOH HOH . D 4 HOH A 22 2022 2022 HOH HOH . D 4 HOH A 23 2023 2023 HOH HOH . D 4 HOH A 24 2024 2024 HOH HOH . D 4 HOH A 25 2025 2025 HOH HOH . D 4 HOH A 26 2026 2026 HOH HOH . D 4 HOH A 27 2027 2027 HOH HOH . D 4 HOH A 28 2028 2028 HOH HOH . D 4 HOH A 29 2029 2029 HOH HOH . D 4 HOH A 30 2030 2030 HOH HOH . D 4 HOH A 31 2031 2031 HOH HOH . D 4 HOH A 32 2032 2032 HOH HOH . D 4 HOH A 33 2033 2033 HOH HOH . D 4 HOH A 34 2034 2034 HOH HOH . D 4 HOH A 35 2035 2035 HOH HOH . D 4 HOH A 36 2036 2036 HOH HOH . D 4 HOH A 37 2037 2037 HOH HOH . D 4 HOH A 38 2038 2038 HOH HOH . D 4 HOH A 39 2039 2039 HOH HOH . D 4 HOH A 40 2040 2040 HOH HOH . D 4 HOH A 41 2041 2041 HOH HOH . D 4 HOH A 42 2042 2042 HOH HOH . D 4 HOH A 43 2043 2043 HOH HOH . D 4 HOH A 44 2044 2044 HOH HOH . D 4 HOH A 45 2045 2045 HOH HOH . D 4 HOH A 46 2046 2046 HOH HOH . D 4 HOH A 47 2047 2047 HOH HOH . D 4 HOH A 48 2048 2048 HOH HOH . D 4 HOH A 49 2049 2049 HOH HOH . D 4 HOH A 50 2050 2050 HOH HOH . D 4 HOH A 51 2051 2051 HOH HOH . D 4 HOH A 52 2052 2052 HOH HOH . D 4 HOH A 53 2053 2053 HOH HOH . D 4 HOH A 54 2054 2054 HOH HOH . D 4 HOH A 55 2055 2055 HOH HOH . D 4 HOH A 56 2056 2056 HOH HOH . D 4 HOH A 57 2057 2057 HOH HOH . D 4 HOH A 58 2058 2058 HOH HOH . D 4 HOH A 59 2059 2059 HOH HOH . D 4 HOH A 60 2060 2060 HOH HOH . D 4 HOH A 61 2061 2061 HOH HOH . D 4 HOH A 62 2062 2062 HOH HOH . D 4 HOH A 63 2063 2063 HOH HOH . D 4 HOH A 64 2064 2064 HOH HOH . D 4 HOH A 65 2065 2065 HOH HOH . D 4 HOH A 66 2066 2066 HOH HOH . D 4 HOH A 67 2067 2067 HOH HOH . D 4 HOH A 68 2068 2068 HOH HOH . D 4 HOH A 69 2069 2069 HOH HOH . D 4 HOH A 70 2070 2070 HOH HOH . D 4 HOH A 71 2071 2071 HOH HOH . D 4 HOH A 72 2072 2072 HOH HOH . D 4 HOH A 73 2073 2073 HOH HOH . D 4 HOH A 74 2074 2074 HOH HOH . D 4 HOH A 75 2075 2075 HOH HOH . D 4 HOH A 76 2076 2076 HOH HOH . D 4 HOH A 77 2077 2077 HOH HOH . D 4 HOH A 78 2078 2078 HOH HOH . D 4 HOH A 79 2079 2079 HOH HOH . D 4 HOH A 80 2080 2080 HOH HOH . D 4 HOH A 81 2081 2081 HOH HOH . D 4 HOH A 82 2082 2082 HOH HOH . D 4 HOH A 83 2083 2083 HOH HOH . D 4 HOH A 84 2084 2084 HOH HOH . D 4 HOH A 85 2085 2085 HOH HOH . D 4 HOH A 86 2086 2086 HOH HOH . D 4 HOH A 87 2087 2087 HOH HOH . D 4 HOH A 88 2088 2088 HOH HOH . D 4 HOH A 89 2089 2089 HOH HOH . D 4 HOH A 90 2090 2090 HOH HOH . D 4 HOH A 91 2091 2091 HOH HOH . D 4 HOH A 92 2092 2092 HOH HOH . D 4 HOH A 93 2093 2093 HOH HOH . D 4 HOH A 94 2094 2094 HOH HOH . D 4 HOH A 95 2095 2095 HOH HOH . D 4 HOH A 96 2096 2096 HOH HOH . D 4 HOH A 97 2097 2097 HOH HOH . D 4 HOH A 98 2098 2098 HOH HOH . D 4 HOH A 99 2099 2099 HOH HOH . D 4 HOH A 100 2100 2100 HOH HOH . D 4 HOH A 101 2101 2101 HOH HOH . D 4 HOH A 102 2102 2102 HOH HOH . D 4 HOH A 103 2103 2103 HOH HOH . D 4 HOH A 104 2104 2104 HOH HOH . D 4 HOH A 105 2105 2105 HOH HOH . D 4 HOH A 106 2106 2106 HOH HOH . D 4 HOH A 107 2107 2107 HOH HOH . D 4 HOH A 108 2108 2108 HOH HOH . D 4 HOH A 109 2109 2109 HOH HOH . D 4 HOH A 110 2110 2110 HOH HOH . D 4 HOH A 111 2111 2111 HOH HOH . D 4 HOH A 112 2112 2112 HOH HOH . D 4 HOH A 113 2113 2113 HOH HOH . D 4 HOH A 114 2114 2114 HOH HOH . D 4 HOH A 115 2115 2115 HOH HOH . D 4 HOH A 116 2116 2116 HOH HOH . D 4 HOH A 117 2117 2117 HOH HOH . D 4 HOH A 118 2118 2118 HOH HOH . D 4 HOH A 119 2119 2119 HOH HOH . D 4 HOH A 120 2120 2120 HOH HOH . D 4 HOH A 121 2121 2121 HOH HOH . D 4 HOH A 122 2122 2122 HOH HOH . D 4 HOH A 123 2123 2123 HOH HOH . D 4 HOH A 124 2124 2124 HOH HOH . D 4 HOH A 125 2125 2125 HOH HOH . D 4 HOH A 126 2126 2126 HOH HOH . D 4 HOH A 127 2127 2127 HOH HOH . D 4 HOH A 128 2128 2128 HOH HOH . D 4 HOH A 129 2129 2129 HOH HOH . D 4 HOH A 130 2130 2130 HOH HOH . D 4 HOH A 131 2131 2131 HOH HOH . D 4 HOH A 132 2132 2132 HOH HOH . D 4 HOH A 133 2133 2133 HOH HOH . D 4 HOH A 134 2134 2134 HOH HOH . D 4 HOH A 135 2135 2135 HOH HOH . D 4 HOH A 136 2136 2136 HOH HOH . D 4 HOH A 137 2137 2137 HOH HOH . D 4 HOH A 138 2138 2138 HOH HOH . D 4 HOH A 139 2139 2139 HOH HOH . D 4 HOH A 140 2140 2140 HOH HOH . D 4 HOH A 141 2141 2141 HOH HOH . D 4 HOH A 142 2142 2142 HOH HOH . D 4 HOH A 143 2143 2143 HOH HOH . D 4 HOH A 144 2144 2144 HOH HOH . D 4 HOH A 145 2145 2145 HOH HOH . D 4 HOH A 146 2146 2146 HOH HOH . D 4 HOH A 147 2147 2147 HOH HOH . D 4 HOH A 148 2148 2148 HOH HOH . D 4 HOH A 149 2149 2149 HOH HOH . D 4 HOH A 150 2150 2150 HOH HOH . D 4 HOH A 151 2151 2151 HOH HOH . D 4 HOH A 152 2152 2152 HOH HOH . D 4 HOH A 153 2153 2153 HOH HOH . D 4 HOH A 154 2154 2154 HOH HOH . D 4 HOH A 155 2155 2155 HOH HOH . D 4 HOH A 156 2156 2156 HOH HOH . D 4 HOH A 157 2157 2157 HOH HOH . D 4 HOH A 158 2158 2158 HOH HOH . D 4 HOH A 159 2159 2159 HOH HOH . D 4 HOH A 160 2160 2160 HOH HOH . D 4 HOH A 161 2161 2161 HOH HOH . D 4 HOH A 162 2162 2162 HOH HOH . D 4 HOH A 163 2163 2163 HOH HOH . D 4 HOH A 164 2164 2164 HOH HOH . D 4 HOH A 165 2165 2165 HOH HOH . D 4 HOH A 166 2166 2166 HOH HOH . D 4 HOH A 167 2167 2167 HOH HOH . D 4 HOH A 168 2168 2168 HOH HOH . D 4 HOH A 169 2169 2169 HOH HOH . D 4 HOH A 170 2170 2170 HOH HOH . D 4 HOH A 171 2171 2171 HOH HOH . D 4 HOH A 172 2172 2172 HOH HOH . D 4 HOH A 173 2173 2173 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 N NAA YIR . . . B 2 49.117 16.744 -11.851 1 63.6 ? NAA YIR 600 A 1 HETATM 2 N NAB YIR . . . B 2 48.268 15.775 -9.198 1 55.44 ? NAB YIR 600 A 1 HETATM 3 N NAC YIR . . . B 2 47.139 14.66 -5.888 1 51.54 ? NAC YIR 600 A 1 HETATM 4 N NAD YIR . . . B 2 47.191 12.211 -0.103 1 51.33 ? NAD YIR 600 A 1 HETATM 5 N NAE YIR . . . B 2 47.288 11.659 1.007 1 52.25 ? NAE YIR 600 A 1 HETATM 6 N NAF YIR . . . B 2 46.254 13.485 1.942 1 53.4 ? NAF YIR 600 A 1 HETATM 7 N NAG YIR . . . B 2 46.907 11.776 3.298 1 53.83 ? NAG YIR 600 A 1 HETATM 8 C CAH YIR . . . B 2 47.519 18.561 -11.764 1 60.41 ? CAH YIR 600 A 1 HETATM 9 C CAI YIR . . . B 2 46.551 19.143 -10.947 1 59.81 ? CAI YIR 600 A 1 HETATM 10 C CAJ YIR . . . B 2 46.212 18.647 -9.695 1 58.44 ? CAJ YIR 600 A 1 HETATM 11 C CAK YIR . . . B 2 46.818 17.508 -9.168 1 56.95 ? CAK YIR 600 A 1 HETATM 12 C CAL YIR . . . B 2 47.821 16.84 -9.873 1 58.39 ? CAL YIR 600 A 1 HETATM 13 C CAM YIR . . . B 2 48.176 17.342 -11.127 1 60.42 ? CAM YIR 600 A 1 HETATM 14 C CAN YIR . . . B 2 46.591 16.774 -7.87 1 54.39 ? CAN YIR 600 A 1 HETATM 15 C CAO YIR . . . B 2 47.624 15.699 -8.028 1 54.65 ? CAO YIR 600 A 1 HETATM 16 C CAP YIR . . . B 2 47.927 14.65 -6.971 1 52.57 ? CAP YIR 600 A 1 HETATM 17 C CAQ YIR . . . B 2 47.266 13.898 -4.796 1 50.63 ? CAQ YIR 600 A 1 HETATM 18 C CAR YIR . . . B 2 48.269 12.926 -4.645 1 49.95 ? CAR YIR 600 A 1 HETATM 19 C CAS YIR . . . B 2 48.372 12.195 -3.453 1 51.31 ? CAS YIR 600 A 1 HETATM 20 C CAT YIR . . . B 2 47.481 12.441 -2.41 1 50.27 ? CAT YIR 600 A 1 HETATM 21 C CAU YIR . . . B 2 46.495 13.432 -2.554 1 49.79 ? CAU YIR 600 A 1 HETATM 22 C CAV YIR . . . B 2 46.388 14.155 -3.74 1 48.24 ? CAV YIR 600 A 1 HETATM 23 C CAW YIR . . . B 2 49.475 11.128 -3.33 1 52.06 ? CAW YIR 600 A 1 HETATM 24 C CAX YIR . . . B 2 49.025 9.933 -2.48 1 53.32 ? CAX YIR 600 A 1 HETATM 25 C CAY YIR . . . B 2 48.402 10.353 -1.154 1 52.37 ? CAY YIR 600 A 1 HETATM 26 C CAZ YIR . . . B 2 47.642 11.691 -1.24 1 50.22 ? CAZ YIR 600 A 1 HETATM 27 C CBA YIR . . . B 2 46.826 12.301 2.079 1 52.6 ? CBA YIR 600 A 1 HETATM 28 O OBB YIR . . . B 2 49.796 15.58 -11.423 1 66.29 ? OBB YIR 600 A 1 HETATM 29 O OBC YIR . . . B 2 49.444 17.253 -13.121 1 67.78 ? OBC YIR 600 A 1 HETATM 30 O OBD YIR . . . B 2 48.892 13.748 -7.229 1 54.19 ? OBD YIR 600 A 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 30 #