data_8GNG # _model_server_result.job_id FIWHMtYbRaET0_S88zT1Uw _model_server_result.datetime_utc '2024-12-04 08:14:12' _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 8gng # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":401}' # _entry.id 8GNG # _exptl.entry_id 8GNG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.429 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 8-[(~{E})-2-(3,4-dimethoxyphenyl)ethenyl]-1,3-diethyl-7-methyl-purine-2,6-dione _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 97.72 _cell.angle_beta 91.44 _cell.angle_gamma 89.38 _cell.entry_id 8GNG _cell.length_a 74.59 _cell.length_b 134.84 _cell.length_c 42.15 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GNG _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? trimeric 3 author_defined_assembly 1 ? trimeric 3 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,B,C,G,H,I,J,K,L,M,N,O,W 1 1 D,E,F,P,Q,R,S,T,U,V 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 G N N ? 4 Q N 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 disulf ? disulf1 A SG CYS 78 A CYS 71 1_555 A SG CYS 166 A CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf2 A SG CYS 81 A CYS 74 1_555 A SG CYS 153 A CYS 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? disulf ? disulf3 A SG CYS 84 A CYS 77 1_555 A SG CYS 173 A CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? disulf ? disulf4 A SG CYS 266 A CYS 259 1_555 A SG CYS 269 A CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? disulf ? disulf5 B SG CYS 23 L CYS 23 1_555 B SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? disulf ? disulf6 B SG CYS 134 L CYS 134 1_555 B SG CYS 194 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? disulf ? disulf7 C SG CYS 22 H CYS 22 1_555 C SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? disulf ? disulf8 C SG CYS 151 H CYS 151 1_555 C SG CYS 206 H CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf9 D SG CYS 78 X CYS 71 1_555 D SG CYS 166 X CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? disulf ? disulf10 D SG CYS 81 X CYS 74 1_555 D SG CYS 153 X CYS 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf11 D SG CYS 84 X CYS 77 1_555 D SG CYS 173 X CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf12 D SG CYS 266 X CYS 259 1_555 D SG CYS 269 X CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf13 E SG CYS 23 Y CYS 23 1_555 E SG CYS 88 Y CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? disulf ? disulf14 E SG CYS 134 Y CYS 134 1_555 E SG CYS 194 Y CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? disulf ? disulf15 F SG CYS 22 Z CYS 22 1_555 F SG CYS 96 Z CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? disulf ? disulf16 F SG CYS 151 Z CYS 151 1_555 F SG CYS 206 Z CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc1 B OD1 ASP 56 L ASP 56 1_555 O K K . L K 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.203 ? metalc ? metalc2 E OD1 ASP 56 Y ASP 56 1_555 V K K . Y K 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.875 ? # _chem_comp.formula 'C20 H24 N4 O4' _chem_comp.formula_weight 384.429 _chem_comp.id JQ9 _chem_comp.mon_nstd_flag . _chem_comp.name 8-[(~{E})-2-(3,4-dimethoxyphenyl)ethenyl]-1,3-diethyl-7-methyl-purine-2,6-dione _chem_comp.type non-polymer _chem_comp.pdbx_synonyms istradefylline # 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 C22 C21 JQ9 sing 173 n n C12 C11 JQ9 sing 174 n n O2 C2 JQ9 doub 175 n n C21 N3 JQ9 sing 176 n n C2 N3 JQ9 sing 177 n n C2 N1 JQ9 sing 178 n n C11 N1 JQ9 sing 179 n n N3 C4 JQ9 sing 180 n n N1 C6 JQ9 sing 181 n n C4 N9 JQ9 sing 182 n y C4 C5 JQ9 doub 183 n y C6 C5 JQ9 sing 184 n n C6 O6 JQ9 doub 185 n n N9 C8 JQ9 doub 186 n y C5 N7 JQ9 sing 187 n y C8 N7 JQ9 sing 188 n y C8 CA JQ9 sing 189 n n N7 C7 JQ9 sing 190 n n CB CA JQ9 doub 191 e n CB C1' JQ9 sing 192 n n C2' C1' JQ9 doub 193 n y C2' C3' JQ9 sing 194 n y C9' O3' JQ9 sing 195 n n C1' C6' JQ9 sing 196 n y O3' C3' JQ9 sing 197 n n C3' C4' JQ9 doub 198 n y C6' C5' JQ9 doub 199 n y C4' C5' JQ9 sing 200 n y C4' O4' JQ9 sing 201 n n O4' C8' JQ9 sing 202 n n C12 H1 JQ9 sing 203 n n C12 H2 JQ9 sing 204 n n C12 H3 JQ9 sing 205 n n C21 H4 JQ9 sing 206 n n C21 H5 JQ9 sing 207 n n C22 H6 JQ9 sing 208 n n C22 H7 JQ9 sing 209 n n C22 H8 JQ9 sing 210 n n C7 H9 JQ9 sing 211 n n C7 H10 JQ9 sing 212 n n C7 H11 JQ9 sing 213 n n C11 H12 JQ9 sing 214 n n C11 H13 JQ9 sing 215 n n CA H14 JQ9 sing 216 n n CB H15 JQ9 sing 217 n n C6' H16 JQ9 sing 218 n n C5' H17 JQ9 sing 219 n n C8' H18 JQ9 sing 220 n n C8' H19 JQ9 sing 221 n n C8' H20 JQ9 sing 222 n n C2' H21 JQ9 sing 223 n n C9' H22 JQ9 sing 224 n n C9' H23 JQ9 sing 225 n n C9' H24 JQ9 sing 226 n n # _atom_sites.entry_id 8GNG _atom_sites.fract_transf_matrix[1][1] 0.013407 _atom_sites.fract_transf_matrix[1][2] -0.000144 _atom_sites.fract_transf_matrix[1][3] 0.000321 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007417 _atom_sites.fract_transf_matrix[2][3] 0.001003 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.023948 _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 G 4 JQ9 A 1 401 401 JQ9 KW2 . H 5 OLC A 1 402 402 OLC OLC . I 5 OLC A 1 403 403 OLC OLC . J 5 OLC A 1 404 404 OLC OLC . K 5 OLC A 1 405 406 OLC OLC . L 6 CL A 1 406 409 CL CL . M 5 OLC A 1 407 402 OLC OLC . N 5 OLC A 1 408 405 OLC OLC . O 7 K L 1 301 407 K K . P 5 OLC X 1 401 405 OLC OLC . Q 4 JQ9 X 1 402 401 JQ9 KW2 . R 5 OLC X 1 403 403 OLC OLC . S 5 OLC X 1 404 404 OLC OLC . T 5 OLC X 1 405 406 OLC OLC . U 6 CL X 1 406 410 CL CL . V 7 K Y 1 301 408 K K . W 8 HOH A 1 501 1 HOH HOH . W 8 HOH A 2 502 2 HOH HOH . W 8 HOH A 3 503 3 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 N1 JQ9 . . . G 4 14.797 84.231 9.444 1 55.38 ? N1 JQ9 401 A 1 HETATM 2 C C12 JQ9 . . . G 4 13.289 83.403 7.673 1 53.34 ? C12 JQ9 401 A 1 HETATM 3 O O2 JQ9 . . . G 4 16.401 83.41 7.977 1 56.75 ? O2 JQ9 401 A 1 HETATM 4 C C2 JQ9 . . . G 4 16.07 84.247 8.827 1 56.47 ? C2 JQ9 401 A 1 HETATM 5 N N3 JQ9 . . . G 4 16.996 85.228 9.184 1 57.85 ? N3 JQ9 401 A 1 HETATM 6 C C21 JQ9 . . . G 4 18.309 85.209 8.516 1 58.72 ? C21 JQ9 401 A 1 HETATM 7 C C22 JQ9 . . . G 4 18.221 85.346 6.99 1 58.49 ? C22 JQ9 401 A 1 HETATM 8 C C4 JQ9 . . . G 4 16.628 86.147 10.133 1 58.25 ? C4 JQ9 401 A 1 HETATM 9 N N9 JQ9 . . . G 4 17.398 87.159 10.601 1 59.67 ? N9 JQ9 401 A 1 HETATM 10 C C8 JQ9 . . . G 4 16.624 87.769 11.487 1 59.73 ? C8 JQ9 401 A 1 HETATM 11 N N7 JQ9 . . . G 4 15.366 87.147 11.603 1 58.56 ? N7 JQ9 401 A 1 HETATM 12 C C7 JQ9 . . . G 4 14.208 87.467 12.452 1 58.28 ? C7 JQ9 401 A 1 HETATM 13 C C5 JQ9 . . . G 4 15.388 86.101 10.721 1 57.49 ? C5 JQ9 401 A 1 HETATM 14 C C6 JQ9 . . . G 4 14.376 85.132 10.42 1 56 ? C6 JQ9 401 A 1 HETATM 15 O O6 JQ9 . . . G 4 13.257 85.105 10.947 1 55.38 ? O6 JQ9 401 A 1 HETATM 16 C C11 JQ9 . . . G 4 13.868 83.177 9.052 1 53.81 ? C11 JQ9 401 A 1 HETATM 17 C CA JQ9 . . . G 4 16.929 88.88 12.297 1 60.89 ? CA JQ9 401 A 1 HETATM 18 C CB JQ9 . . . G 4 18.036 89.601 12.158 1 62.02 ? CB JQ9 401 A 1 HETATM 19 C C1' JQ9 . . . G 4 18.3 90.731 13.043 1 63.46 ? C1' JQ9 401 A 1 HETATM 20 C C6' JQ9 . . . G 4 17.479 91.188 14.102 1 63.52 ? C6' JQ9 401 A 1 HETATM 21 C C5' JQ9 . . . G 4 17.827 92.292 14.909 1 65.18 ? C5' JQ9 401 A 1 HETATM 22 C C4' JQ9 . . . G 4 19.031 92.979 14.669 1 66.93 ? C4' JQ9 401 A 1 HETATM 23 O O4' JQ9 . . . G 4 19.534 94.093 15.354 1 68.65 ? O4' JQ9 401 A 1 HETATM 24 C C8' JQ9 . . . G 4 18.753 94.874 16.252 1 69.11 ? C8' JQ9 401 A 1 HETATM 25 C C3' JQ9 . . . G 4 19.831 92.484 13.593 1 66.82 ? C3' JQ9 401 A 1 HETATM 26 C C2' JQ9 . . . G 4 19.479 91.389 12.807 1 65.03 ? C2' JQ9 401 A 1 HETATM 27 O O3' JQ9 . . . G 4 20.997 93.13 13.343 1 68.78 ? O3' JQ9 401 A 1 HETATM 28 C C9' JQ9 . . . G 4 22.133 92.308 13.039 1 68.95 ? C9' JQ9 401 A 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #