data_3B0Q # _model_server_result.job_id ZGth1EnVn0HvAfFjJynS4A _model_server_result.datetime_utc '2025-09-07 21:33:53' _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 3b0q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1}' # _entry.id 3B0Q # _exptl.entry_id 3B0Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 381.42 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (5S)-5-({6-[(2-fluorobenzyl)oxy]naphthalen-2-yl}methyl)-1,3-thiazolidine-2,4-dione _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 103.89 _cell.angle_gamma 90 _cell.entry_id 3B0Q _cell.length_a 93.252 _cell.length_b 59.812 _cell.length_c 117.846 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3B0Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C21 H16 F N O3 S' _chem_comp.formula_weight 381.42 _chem_comp.id MC5 _chem_comp.mon_nstd_flag . _chem_comp.name (5S)-5-({6-[(2-fluorobenzyl)oxy]naphthalen-2-yl}methyl)-1,3-thiazolidine-2,4-dione _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Netoglitazone # 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 F C20 MC5 sing 218 n n N C14 MC5 sing 219 n n N C16 MC5 sing 220 n n S C13 MC5 sing 221 n n S C16 MC5 sing 222 n n C1 C2 MC5 doub 223 n y C1 C3 MC5 sing 224 n y C1 C4 MC5 sing 225 n y O1 C7 MC5 sing 226 n n O1 C18 MC5 sing 227 n n C2 C6 MC5 sing 228 n y C2 C8 MC5 sing 229 n y O2 C14 MC5 doub 230 n n C3 C9 MC5 doub 231 n y O3 C16 MC5 doub 232 n n C4 C5 MC5 doub 233 n y C5 C11 MC5 sing 234 n y C5 C12 MC5 sing 235 n n C6 C7 MC5 doub 236 n y C7 C9 MC5 sing 237 n y C8 C11 MC5 doub 238 n y C10 C15 MC5 doub 239 n y C10 C21 MC5 sing 240 n y C12 C13 MC5 sing 241 n n C13 C14 MC5 sing 242 n n C15 C17 MC5 sing 243 n y C17 C20 MC5 doub 244 n y C18 C19 MC5 sing 245 n n C19 C20 MC5 sing 246 n y C19 C21 MC5 doub 247 n y N HN MC5 sing 248 n n C3 H3 MC5 sing 249 n n C4 H4 MC5 sing 250 n n C6 H6 MC5 sing 251 n n C8 H8 MC5 sing 252 n n C9 H9 MC5 sing 253 n n C10 H10 MC5 sing 254 n n C11 H11 MC5 sing 255 n n C12 H12 MC5 sing 256 n n C12 H12A MC5 sing 257 n n C13 H13 MC5 sing 258 n n C15 H15 MC5 sing 259 n n C17 H17 MC5 sing 260 n n C18 H18 MC5 sing 261 n n C18 H18A MC5 sing 262 n n C21 H21 MC5 sing 263 n n # _atom_sites.entry_id 3B0Q _atom_sites.fract_transf_matrix[1][1] 0.010724 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002651 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016719 _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] 0.008741 _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 MC5 A 1 1 1 MC5 MCC . D 3 HOH A 1 3 3 HOH HOH . D 3 HOH A 2 4 4 HOH HOH . D 3 HOH A 3 5 5 HOH HOH . D 3 HOH A 4 10 10 HOH HOH . D 3 HOH A 5 11 11 HOH HOH . D 3 HOH A 6 12 12 HOH HOH . D 3 HOH A 7 13 13 HOH HOH . D 3 HOH A 8 15 15 HOH HOH . D 3 HOH A 9 17 17 HOH HOH . D 3 HOH A 10 19 19 HOH HOH . D 3 HOH A 11 20 20 HOH HOH . D 3 HOH A 12 21 21 HOH HOH . D 3 HOH A 13 22 22 HOH HOH . D 3 HOH A 14 23 23 HOH HOH . D 3 HOH A 15 24 24 HOH HOH . D 3 HOH A 16 25 25 HOH HOH . D 3 HOH A 17 26 26 HOH HOH . D 3 HOH A 18 28 28 HOH HOH . D 3 HOH A 19 29 29 HOH HOH . D 3 HOH A 20 32 32 HOH HOH . D 3 HOH A 21 34 34 HOH HOH . D 3 HOH A 22 35 35 HOH HOH . D 3 HOH A 23 36 36 HOH HOH . D 3 HOH A 24 39 39 HOH HOH . D 3 HOH A 25 40 40 HOH HOH . D 3 HOH A 26 42 42 HOH HOH . D 3 HOH A 27 43 43 HOH HOH . D 3 HOH A 28 45 45 HOH HOH . D 3 HOH A 29 46 46 HOH HOH . D 3 HOH A 30 47 47 HOH HOH . D 3 HOH A 31 48 48 HOH HOH . D 3 HOH A 32 49 49 HOH HOH . D 3 HOH A 33 50 50 HOH HOH . D 3 HOH A 34 55 55 HOH HOH . D 3 HOH A 35 56 56 HOH HOH . D 3 HOH A 36 57 57 HOH HOH . D 3 HOH A 37 60 60 HOH HOH . D 3 HOH A 38 62 62 HOH HOH . D 3 HOH A 39 66 66 HOH HOH . D 3 HOH A 40 71 71 HOH HOH . D 3 HOH A 41 73 73 HOH HOH . D 3 HOH A 42 75 75 HOH HOH . D 3 HOH A 43 77 77 HOH HOH . D 3 HOH A 44 80 80 HOH HOH . D 3 HOH A 45 82 82 HOH HOH . D 3 HOH A 46 83 83 HOH HOH . D 3 HOH A 47 87 87 HOH HOH . D 3 HOH A 48 88 88 HOH HOH . D 3 HOH A 49 92 92 HOH HOH . D 3 HOH A 50 95 95 HOH HOH . D 3 HOH A 51 98 98 HOH HOH . D 3 HOH A 52 99 99 HOH HOH . D 3 HOH A 53 101 101 HOH HOH . D 3 HOH A 54 106 106 HOH HOH . D 3 HOH A 55 109 109 HOH HOH . D 3 HOH A 56 110 110 HOH HOH . D 3 HOH A 57 112 112 HOH HOH . D 3 HOH A 58 113 113 HOH HOH . D 3 HOH A 59 114 114 HOH HOH . D 3 HOH A 60 117 117 HOH HOH . D 3 HOH A 61 118 118 HOH HOH . D 3 HOH A 62 120 120 HOH HOH . D 3 HOH A 63 126 126 HOH HOH . D 3 HOH A 64 129 129 HOH HOH . D 3 HOH A 65 130 130 HOH HOH . D 3 HOH A 66 131 131 HOH HOH . D 3 HOH A 67 132 132 HOH HOH . D 3 HOH A 68 133 133 HOH HOH . D 3 HOH A 69 134 134 HOH HOH . D 3 HOH A 70 136 136 HOH HOH . D 3 HOH A 71 137 137 HOH HOH . D 3 HOH A 72 138 138 HOH HOH . D 3 HOH A 73 139 139 HOH HOH . D 3 HOH A 74 140 140 HOH HOH . D 3 HOH A 75 141 141 HOH HOH . D 3 HOH A 76 144 144 HOH HOH . D 3 HOH A 77 146 146 HOH HOH . D 3 HOH A 78 149 149 HOH HOH . D 3 HOH A 79 151 151 HOH HOH . D 3 HOH A 80 153 153 HOH HOH . D 3 HOH A 81 154 154 HOH HOH . D 3 HOH A 82 477 1 HOH HOH . E 3 HOH B 1 2 2 HOH HOH . E 3 HOH B 2 7 7 HOH HOH . E 3 HOH B 3 8 8 HOH HOH . E 3 HOH B 4 9 9 HOH HOH . E 3 HOH B 5 14 14 HOH HOH . E 3 HOH B 6 16 16 HOH HOH . E 3 HOH B 7 18 18 HOH HOH . E 3 HOH B 8 27 27 HOH HOH . E 3 HOH B 9 31 31 HOH HOH . E 3 HOH B 10 33 33 HOH HOH . E 3 HOH B 11 37 37 HOH HOH . E 3 HOH B 12 38 38 HOH HOH . E 3 HOH B 13 41 41 HOH HOH . E 3 HOH B 14 44 44 HOH HOH . E 3 HOH B 15 53 53 HOH HOH . E 3 HOH B 16 54 54 HOH HOH . E 3 HOH B 17 58 58 HOH HOH . E 3 HOH B 18 59 59 HOH HOH . E 3 HOH B 19 63 63 HOH HOH . E 3 HOH B 20 64 64 HOH HOH . E 3 HOH B 21 65 65 HOH HOH . E 3 HOH B 22 67 67 HOH HOH . E 3 HOH B 23 68 68 HOH HOH . E 3 HOH B 24 72 72 HOH HOH . E 3 HOH B 25 74 74 HOH HOH . E 3 HOH B 26 76 76 HOH HOH . E 3 HOH B 27 78 78 HOH HOH . E 3 HOH B 28 79 79 HOH HOH . E 3 HOH B 29 81 81 HOH HOH . E 3 HOH B 30 86 86 HOH HOH . E 3 HOH B 31 89 89 HOH HOH . E 3 HOH B 32 90 90 HOH HOH . E 3 HOH B 33 91 91 HOH HOH . E 3 HOH B 34 93 93 HOH HOH . E 3 HOH B 35 94 94 HOH HOH . E 3 HOH B 36 96 96 HOH HOH . E 3 HOH B 37 97 97 HOH HOH . E 3 HOH B 38 102 102 HOH HOH . E 3 HOH B 39 104 104 HOH HOH . E 3 HOH B 40 108 108 HOH HOH . E 3 HOH B 41 111 111 HOH HOH . E 3 HOH B 42 115 115 HOH HOH . E 3 HOH B 43 119 119 HOH HOH . E 3 HOH B 44 123 123 HOH HOH . E 3 HOH B 45 124 124 HOH HOH . E 3 HOH B 46 127 127 HOH HOH . E 3 HOH B 47 128 128 HOH HOH . E 3 HOH B 48 135 135 HOH HOH . E 3 HOH B 49 143 143 HOH HOH . E 3 HOH B 50 145 145 HOH HOH . E 3 HOH B 51 148 148 HOH HOH . E 3 HOH B 52 152 152 HOH HOH . E 3 HOH B 53 158 158 HOH HOH . E 3 HOH B 54 159 159 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 F F MC5 . . . C 2 -19.323 18.064 -8.649 1 43.31 ? F MC5 1 A 1 HETATM 2 N N MC5 . . . C 2 -19.863 19.354 -20.512 1 34.98 ? N MC5 1 A 1 HETATM 3 S S MC5 . . . C 2 -20.244 19.593 -18.056 1 37.37 ? S MC5 1 A 1 HETATM 4 C C1 MC5 . . . C 2 -16.849 17.246 -14.878 1 37.14 ? C1 MC5 1 A 1 HETATM 5 O O1 MC5 . . . C 2 -15.922 17.12 -10.829 1 39.57 ? O1 MC5 1 A 1 HETATM 6 C C2 MC5 . . . C 2 -17.879 17.117 -13.95 1 37.92 ? C2 MC5 1 A 1 HETATM 7 O O2 MC5 . . . C 2 -17.753 18.533 -20.642 1 34.59 ? O2 MC5 1 A 1 HETATM 8 C C3 MC5 . . . C 2 -15.531 17.32 -14.455 1 38.44 ? C3 MC5 1 A 1 HETATM 9 O O3 MC5 . . . C 2 -21.855 20.224 -19.901 1 36.87 ? O3 MC5 1 A 1 HETATM 10 C C4 MC5 . . . C 2 -17.146 17.287 -16.231 1 36.9 ? C4 MC5 1 A 1 HETATM 11 C C5 MC5 . . . C 2 -18.468 17.202 -16.651 1 36.61 ? C5 MC5 1 A 1 HETATM 12 C C6 MC5 . . . C 2 -17.589 17.075 -12.595 1 37.87 ? C6 MC5 1 A 1 HETATM 13 C C7 MC5 . . . C 2 -16.263 17.154 -12.16 1 38.6 ? C7 MC5 1 A 1 HETATM 14 C C8 MC5 . . . C 2 -19.204 17.037 -14.375 1 37.61 ? C8 MC5 1 A 1 HETATM 15 C C9 MC5 . . . C 2 -15.235 17.275 -13.095 1 38.88 ? C9 MC5 1 A 1 HETATM 16 C C10 MC5 . . . C 2 -16.888 21.116 -9.971 1 39.57 ? C10 MC5 1 A 1 HETATM 17 C C11 MC5 . . . C 2 -19.502 17.086 -15.729 1 38.14 ? C11 MC5 1 A 1 HETATM 18 C C12 MC5 . . . C 2 -18.785 17.276 -18.112 1 36.04 ? C12 MC5 1 A 1 HETATM 19 C C13 MC5 . . . C 2 -18.762 18.75 -18.507 1 36.26 ? C13 MC5 1 A 1 HETATM 20 C C14 MC5 . . . C 2 -18.734 18.856 -20.001 1 34.84 ? C14 MC5 1 A 1 HETATM 21 C C15 MC5 . . . C 2 -18.124 21.403 -9.402 1 40.94 ? C15 MC5 1 A 1 HETATM 22 C C16 MC5 . . . C 2 -20.76 19.777 -19.622 1 35.44 ? C16 MC5 1 A 1 HETATM 23 C C17 MC5 . . . C 2 -18.945 20.371 -8.961 1 40.49 ? C17 MC5 1 A 1 HETATM 24 C C18 MC5 . . . C 2 -16.857 17.327 -9.769 1 39.26 ? C18 MC5 1 A 1 HETATM 25 C C19 MC5 . . . C 2 -17.297 18.766 -9.659 1 39.75 ? C19 MC5 1 A 1 HETATM 26 C C20 MC5 . . . C 2 -18.526 19.054 -9.086 1 40.93 ? C20 MC5 1 A 1 HETATM 27 C C21 MC5 . . . C 2 -16.475 19.803 -10.099 1 39.31 ? C21 MC5 1 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #