data_5WB3 # _model_server_result.job_id 46DpuicflT-k04zcnNqRWw _model_server_result.datetime_utc '2024-11-16 13:31:03' _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 5wb3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":205}' # _entry.id 5WB3 # _exptl.entry_id 5WB3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 585.071 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-[(2S)-1-{[(2-chlorophenyl)sulfanyl]acetyl}pyrrolidin-2-yl]-N-(5,6-dimethoxy-2,3-dihydro-1H-inden-2-yl)-5-hydroxy-6-ox o-1,6-dihydropyrimidine-4-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 90 _cell.entry_id 5WB3 _cell.length_a 90.698 _cell.length_b 90.698 _cell.length_c 134.31 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WB3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 software_defined_assembly 1 PISA monomeric 1 software_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,D,E,F,G 1 1,2,3,4 A,B,C,D,E,F,G 2 1 # 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' 2_885 -x+3,-y+3,z -1 0 0 0 -1 0 0 0 1 272.094 272.094 0 3 'crystal symmetry operation' 3_855 -y+3,x,z 0 -1 0 1 0 0 0 0 1 272.094 0 0 4 'crystal symmetry operation' 4_585 y,-x+3,z 0 1 0 -1 0 0 0 0 1 0 272.094 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id F _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 61 A HIS 41 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc2 A OE1 GLU 81 A GLU 80 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc3 A OD2 ASP 109 A ASP 108 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc4 A OD1 ASP 109 A ASP 108 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc5 A OE1 GLU 120 A GLU 119 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc6 A O ILE 121 A ILE 120 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc7 B MN MN . A MN 201 1_555 F O1 GYA . A GYA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc8 B MN MN . A MN 201 1_555 F O2 GYA . A GYA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc9 C MN MN . A MN 202 1_555 F O5 GYA . A GYA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc10 C MN MN . A MN 202 1_555 F O2 GYA . A GYA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc11 C MN MN . A MN 202 1_555 G O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc12 C MN MN . A MN 202 1_555 G O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? # _chem_comp.formula 'C28 H29 Cl N4 O6 S' _chem_comp.formula_weight 585.071 _chem_comp.id GYA _chem_comp.mon_nstd_flag . _chem_comp.name '2-[(2S)-1-{[(2-chlorophenyl)sulfanyl]acetyl}pyrrolidin-2-yl]-N-(5,6-dimethoxy-2,3-dihydro-1H-inden-2-yl)-5-hydroxy-6-ox o-1,6-dihydropyrimidine-4-carboxamide' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms SRI-30026 # 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 CL1 C25 GYA sing 129 n n C24 C25 GYA doub 130 n y C24 C23 GYA sing 131 n y C25 C20 GYA sing 132 n y C10 O3 GYA sing 133 n n C23 C22 GYA doub 134 n y C20 S1 GYA sing 135 n n C20 C21 GYA doub 136 n y S1 C19 GYA sing 137 n n O3 C9 GYA sing 138 n n C22 C21 GYA sing 139 n y C8 C9 GYA doub 140 n y C8 C7 GYA sing 141 n y C9 C11 GYA sing 142 n y C19 C18 GYA sing 143 n n C6 C7 GYA sing 144 n n C6 C5 GYA sing 145 n n C7 C14 GYA doub 146 n y C12 O4 GYA sing 147 n n O6 C18 GYA doub 148 n n C11 O4 GYA sing 149 n n C11 C13 GYA doub 150 n y C18 N3 GYA sing 151 n n C14 C13 GYA sing 152 n y C14 C15 GYA sing 153 n n C5 N1 GYA sing 154 n n C5 C15 GYA sing 155 n n N1 C4 GYA sing 156 n n N3 C26 GYA sing 157 n n N3 C17 GYA sing 158 n n C4 O5 GYA doub 159 n n C4 C3 GYA sing 160 n n C26 C27 GYA sing 161 n n N2 C3 GYA sing 162 n n N2 C16 GYA doub 163 n n C3 C2 GYA doub 164 n n C17 C16 GYA sing 165 n n C17 C28 GYA sing 166 n n C16 N4 GYA sing 167 n n C2 O2 GYA sing 168 n n C2 C1 GYA sing 169 n n C27 C28 GYA sing 170 n n N4 C1 GYA sing 171 n n C1 O1 GYA doub 172 n n C10 H1 GYA sing 173 n n C10 H2 GYA sing 174 n n C10 H3 GYA sing 175 n n C12 H4 GYA sing 176 n n C12 H5 GYA sing 177 n n C12 H6 GYA sing 178 n n C13 H7 GYA sing 179 n n C15 H8 GYA sing 180 n n C15 H9 GYA sing 181 n n C17 H10 GYA sing 182 n n C19 H11 GYA sing 183 n n C19 H12 GYA sing 184 n n C21 H13 GYA sing 185 n n C22 H14 GYA sing 186 n n C23 H15 GYA sing 187 n n C24 H16 GYA sing 188 n n C26 H17 GYA sing 189 n n C26 H18 GYA sing 190 n n C27 H19 GYA sing 191 n n C27 H20 GYA sing 192 n n C28 H21 GYA sing 193 n n C28 H22 GYA sing 194 n n C5 H23 GYA sing 195 n n C6 H24 GYA sing 196 n n C6 H25 GYA sing 197 n n C8 H26 GYA sing 198 n n N1 H27 GYA sing 199 n n N4 H28 GYA sing 200 n n O2 H29 GYA sing 201 n n # _atom_sites.entry_id 5WB3 _atom_sites.fract_transf_matrix[1][1] 0.011026 _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] 0.011026 _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] 0.007445 _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 MN A 1 201 1 MN MN . C 2 MN A 1 202 2 MN MN . D 3 SO4 A 1 203 2 SO4 SO4 . E 3 SO4 A 1 204 3 SO4 SO4 . F 4 GYA A 1 205 1 GYA GYA . G 5 HOH A 1 301 2 HOH HOH . G 5 HOH A 2 302 4 HOH HOH . G 5 HOH A 3 303 14 HOH HOH . G 5 HOH A 4 304 6 HOH HOH . G 5 HOH A 5 305 1 HOH HOH . G 5 HOH A 6 306 5 HOH HOH . G 5 HOH A 7 307 10 HOH HOH . G 5 HOH A 8 308 3 HOH HOH . G 5 HOH A 9 309 8 HOH HOH . G 5 HOH A 10 310 7 HOH HOH . G 5 HOH A 11 311 15 HOH HOH . G 5 HOH A 12 312 13 HOH HOH . G 5 HOH A 13 313 12 HOH HOH . G 5 HOH A 14 314 11 HOH HOH . G 5 HOH A 15 315 16 HOH HOH . G 5 HOH A 16 316 9 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 GYA . . . F 4 130.403 106.263 286.962 1 63.1 ? C1 GYA 205 A 1 HETATM 2 C C10 GYA . . . F 4 133.213 99.845 279.646 1 104.27 ? C10 GYA 205 A 1 HETATM 3 C C11 GYA . . . F 4 134.817 99.834 282.923 1 102.31 ? C11 GYA 205 A 1 HETATM 4 C C12 GYA . . . F 4 135.822 97.68 282.873 1 112.27 ? C12 GYA 205 A 1 HETATM 5 C C13 GYA . . . F 4 135.392 100.689 283.85 1 97.04 ? C13 GYA 205 A 1 HETATM 6 C C14 GYA . . . F 4 135.479 102.041 283.543 1 90.79 ? C14 GYA 205 A 1 HETATM 7 C C15 GYA . . . F 4 136.046 103.177 284.351 1 86.45 ? C15 GYA 205 A 1 HETATM 8 C C16 GYA . . . F 4 130.238 104.115 285.91 1 70.2 ? C16 GYA 205 A 1 HETATM 9 C C17 GYA . . . F 4 129.492 102.824 285.651 1 77.76 ? C17 GYA 205 A 1 HETATM 10 C C18 GYA . . . F 4 129.893 102.257 283.274 1 90.31 ? C18 GYA 205 A 1 HETATM 11 C C19 GYA . . . F 4 130.668 101.438 282.262 1 98.12 ? C19 GYA 205 A 1 HETATM 12 C C2 GYA . . . F 4 131.646 106.396 286.349 1 57.7 ? C2 GYA 205 A 1 HETATM 13 C C20 GYA . . . F 4 131.024 103.452 280.248 1 102.16 ? C20 GYA 205 A 1 HETATM 14 C C21 GYA . . . F 4 131.533 104.212 281.302 1 99.95 ? C21 GYA 205 A 1 HETATM 15 C C22 GYA . . . F 4 132.081 105.457 281.055 1 97.96 ? C22 GYA 205 A 1 HETATM 16 C C23 GYA . . . F 4 132.131 105.953 279.77 1 96.27 ? C23 GYA 205 A 1 HETATM 17 C C24 GYA . . . F 4 131.637 105.214 278.718 1 97.2 ? C24 GYA 205 A 1 HETATM 18 C C25 GYA . . . F 4 131.085 103.971 278.958 1 101.13 ? C25 GYA 205 A 1 HETATM 19 C C26 GYA . . . F 4 130.969 100.961 285.121 1 86.91 ? C26 GYA 205 A 1 HETATM 20 C C27 GYA . . . F 4 130.958 101.231 286.61 1 87.75 ? C27 GYA 205 A 1 HETATM 21 C C28 GYA . . . F 4 129.571 101.821 286.813 1 84.64 ? C28 GYA 205 A 1 HETATM 22 C C3 GYA . . . F 4 132.126 105.395 285.561 1 64.99 ? C3 GYA 205 A 1 HETATM 23 C C4 GYA . . . F 4 133.469 105.529 284.903 1 68.34 ? C4 GYA 205 A 1 HETATM 24 C C5 GYA . . . F 4 135.286 104.386 283.77 1 82.64 ? C5 GYA 205 A 1 HETATM 25 C C6 GYA . . . F 4 135.221 104.019 282.277 1 84.08 ? C6 GYA 205 A 1 HETATM 26 C C7 GYA . . . F 4 134.991 102.532 282.337 1 90.13 ? C7 GYA 205 A 1 HETATM 27 C C8 GYA . . . F 4 134.415 101.687 281.402 1 95.22 ? C8 GYA 205 A 1 HETATM 28 C C9 GYA . . . F 4 134.321 100.333 281.696 1 101.91 ? C9 GYA 205 A 1 HETATM 29 N N1 GYA . . . F 4 133.943 104.434 284.314 1 77.4 ? N1 GYA 205 A 1 HETATM 30 N N2 GYA . . . F 4 131.438 104.264 285.342 1 69.15 ? N2 GYA 205 A 1 HETATM 31 N N3 GYA . . . F 4 130.114 102.027 284.579 1 84.5 ? N3 GYA 205 A 1 HETATM 32 N N4 GYA . . . F 4 129.717 105.093 286.717 1 63.31 ? N4 GYA 205 A 1 HETATM 33 O O1 GYA . . . F 4 129.9 107.128 287.694 1 67.19 ? O1 GYA 205 A 1 HETATM 34 O O2 GYA . . . F 4 132.314 107.531 286.593 1 58.33 ? O2 GYA 205 A 1 HETATM 35 O O3 GYA . . . F 4 133.776 99.388 280.872 1 106.49 ? O3 GYA 205 A 1 HETATM 36 O O4 GYA . . . F 4 134.665 98.483 283.089 1 107.84 ? O4 GYA 205 A 1 HETATM 37 O O5 GYA . . . F 4 134.101 106.583 284.926 1 68.63 ? O5 GYA 205 A 1 HETATM 38 O O6 GYA . . . F 4 129.082 103.103 282.91 1 91.03 ? O6 GYA 205 A 1 HETATM 39 S S1 GYA . . . F 4 130.317 101.855 280.529 1 105.57 ? S1 GYA 205 A 1 HETATM 40 CL CL1 GYA . . . F 4 130.468 103.068 277.616 1 105.14 ? CL1 GYA 205 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 40 #