data_5WF3 # _model_server_result.job_id 8LbtGYJNkOGPkrhnu7jBLw _model_server_result.datetime_utc '2024-11-28 19:04:44' _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 5wf3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":205}' # _entry.id 5WF3 # _exptl.entry_id 5WF3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 529.008 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-[(2S)-1-{[(2-chlorophenyl)sulfanyl]acetyl}pyrrolidin-2-yl]-5-hydroxy-6-oxo-N-(2-phenoxyethyl)-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 5WF3 _cell.length_a 90.679 _cell.length_b 90.679 _cell.length_c 133.752 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WF3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # _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,F,G _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 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc2 A OE1 GLU 81 A GLU 80 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc3 A OD1 ASP 109 A ASP 108 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc4 A OD2 ASP 109 A ASP 108 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc5 A OD1 ASP 120 A ASP 119 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc6 A O ILE 121 A ILE 120 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc7 B MN MN . A MN 201 1_555 F O2 KU2 . A KU2 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc8 B MN MN . A MN 201 1_555 F O1 KU2 . A KU2 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc9 C MN MN . A MN 202 1_555 F O3 KU2 . A KU2 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc10 C MN MN . A MN 202 1_555 F O1 KU2 . A KU2 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc11 C MN MN . A MN 202 1_555 G O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc12 C MN MN . A MN 202 1_555 G O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? # _chem_comp.formula 'C25 H25 Cl N4 O5 S' _chem_comp.formula_weight 529.008 _chem_comp.id KU2 _chem_comp.mon_nstd_flag . _chem_comp.name '2-[(2S)-1-{[(2-chlorophenyl)sulfanyl]acetyl}pyrrolidin-2-yl]-5-hydroxy-6-oxo-N-(2-phenoxyethyl)-1,6-dihydropyrimidine-4 -carboxamide' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms SRI-30023 # 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 C20 C25 KU2 doub 173 n y C20 C21 KU2 sing 174 n y C25 C24 KU2 sing 175 n y C21 C22 KU2 doub 176 n y C24 C23 KU2 doub 177 n y C22 C23 KU2 sing 178 n y C23 O5 KU2 sing 179 n n O5 C13 KU2 sing 180 n n C13 C12 KU2 sing 181 n n C18 C19 KU2 doub 182 n y C18 C17 KU2 sing 183 n y C19 C14 KU2 sing 184 n y S1 C17 KU2 sing 185 n n S1 C11 KU2 sing 186 n n O4 C10 KU2 doub 187 n n C17 C16 KU2 doub 188 n y C14 C15 KU2 doub 189 n y C12 N3 KU2 sing 190 n n C10 C11 KU2 sing 191 n n C10 N4 KU2 sing 192 n n C16 C15 KU2 sing 193 n y C16 CL1 KU2 sing 194 n n N3 C5 KU2 sing 195 n n N4 C9 KU2 sing 196 n n N4 C8 KU2 sing 197 n n C9 C6 KU2 sing 198 n n C5 O3 KU2 doub 199 n n C5 C2 KU2 sing 200 n n N1 C2 KU2 sing 201 n n N1 C1 KU2 doub 202 n n C2 C3 KU2 doub 203 n n C8 C1 KU2 sing 204 n n C8 C7 KU2 sing 205 n n C1 N2 KU2 sing 206 n n C6 C7 KU2 sing 207 n n C3 O1 KU2 sing 208 n n C3 C4 KU2 sing 209 n n N2 C4 KU2 sing 210 n n C4 O2 KU2 doub 211 n n C13 H1 KU2 sing 212 n n C13 H2 KU2 sing 213 n n C14 H3 KU2 sing 214 n n C18 H4 KU2 sing 215 n n C19 H5 KU2 sing 216 n n C20 H6 KU2 sing 217 n n C21 H7 KU2 sing 218 n n C22 H8 KU2 sing 219 n n C24 H9 KU2 sing 220 n n C25 H10 KU2 sing 221 n n C11 H11 KU2 sing 222 n n C11 H12 KU2 sing 223 n n C12 H13 KU2 sing 224 n n C12 H14 KU2 sing 225 n n C15 H15 KU2 sing 226 n n C6 H16 KU2 sing 227 n n C6 H17 KU2 sing 228 n n C7 H18 KU2 sing 229 n n C7 H19 KU2 sing 230 n n C8 H20 KU2 sing 231 n n C9 H21 KU2 sing 232 n n C9 H22 KU2 sing 233 n n N2 H23 KU2 sing 234 n n N3 H24 KU2 sing 235 n n O1 H25 KU2 sing 236 n n # _atom_sites.entry_id 5WF3 _atom_sites.fract_transf_matrix[1][1] 0.011028 _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] 0.011028 _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] 0.007477 _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 1 SO4 SO4 . E 3 SO4 A 1 204 2 SO4 SO4 . F 4 KU2 A 1 205 1 KU2 KU3 . G 5 HOH A 1 301 2 HOH HOH . G 5 HOH A 2 302 1 HOH HOH . G 5 HOH A 3 303 4 HOH HOH . G 5 HOH A 4 304 12 HOH HOH . G 5 HOH A 5 305 7 HOH HOH . G 5 HOH A 6 306 8 HOH HOH . G 5 HOH A 7 307 11 HOH HOH . G 5 HOH A 8 308 3 HOH HOH . G 5 HOH A 9 309 5 HOH HOH . G 5 HOH A 10 310 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 C10 KU2 . . . F 4 128.662 193.089 282.344 1 118 ? C10 KU2 205 A 1 HETATM 2 C C13 KU2 . . . F 4 133.855 195.273 280.628 1 100.28 ? C13 KU2 205 A 1 HETATM 3 C C14 KU2 . . . F 4 130.361 198.328 282.004 1 120.58 ? C14 KU2 205 A 1 HETATM 4 C C17 KU2 . . . F 4 128.442 196.377 281.495 1 127.67 ? C17 KU2 205 A 1 HETATM 5 C C18 KU2 . . . F 4 129.68 196.324 280.885 1 125.85 ? C18 KU2 205 A 1 HETATM 6 C C19 KU2 . . . F 4 130.634 197.294 281.139 1 122.56 ? C19 KU2 205 A 1 HETATM 7 C C20 KU2 . . . F 4 130.589 194.113 276.951 1 101.8 ? C20 KU2 205 A 1 HETATM 8 C C21 KU2 . . . F 4 130.688 193.026 277.788 1 107.01 ? C21 KU2 205 A 1 HETATM 9 C C22 KU2 . . . F 4 131.415 193.111 278.964 1 107.15 ? C22 KU2 205 A 1 HETATM 10 C C24 KU2 . . . F 4 131.942 195.389 278.461 1 99.92 ? C24 KU2 205 A 1 HETATM 11 C C25 KU2 . . . F 4 131.213 195.291 277.287 1 97.86 ? C25 KU2 205 A 1 HETATM 12 C C1 KU2 . . . F 4 129.804 194.728 285.05 1 87.06 ? C1 KU2 205 A 1 HETATM 13 C C11 KU2 . . . F 4 127.391 193.908 282.482 1 126.41 ? C11 KU2 205 A 1 HETATM 14 C C12 KU2 . . . F 4 134.346 195.132 282.045 1 94.64 ? C12 KU2 205 A 1 HETATM 15 C C15 KU2 . . . F 4 129.134 198.405 282.624 1 123.19 ? C15 KU2 205 A 1 HETATM 16 C C16 KU2 . . . F 4 128.177 197.44 282.371 1 128 ? C16 KU2 205 A 1 HETATM 17 C C2 KU2 . . . F 4 131.71 196.014 284.604 1 80.22 ? C2 KU2 205 A 1 HETATM 18 C C23 KU2 . . . F 4 132.041 194.295 279.295 1 105.34 ? C23 KU2 205 A 1 HETATM 19 C C3 KU2 . . . F 4 131.302 196.992 285.462 1 75.16 ? C3 KU2 205 A 1 HETATM 20 C C4 KU2 . . . F 4 130.06 196.82 286.159 1 71.05 ? C4 KU2 205 A 1 HETATM 21 C C5 KU2 . . . F 4 132.982 196.109 283.835 1 84.9 ? C5 KU2 205 A 1 HETATM 22 C C6 KU2 . . . F 4 130.797 191.888 285.068 1 98.9 ? C6 KU2 205 A 1 HETATM 23 C C7 KU2 . . . F 4 129.457 192.277 285.679 1 96.95 ? C7 KU2 205 A 1 HETATM 24 C C8 KU2 . . . F 4 129.042 193.449 284.779 1 94.82 ? C8 KU2 205 A 1 HETATM 25 C C9 KU2 . . . F 4 130.496 191.905 283.578 1 101.07 ? C9 KU2 205 A 1 HETATM 26 N N1 KU2 . . . F 4 130.966 194.916 284.411 1 83.52 ? N1 KU2 205 A 1 HETATM 27 N N2 KU2 . . . F 4 129.336 195.666 285.925 1 80.31 ? N2 KU2 205 A 1 HETATM 28 N N3 KU2 . . . F 4 133.231 195.117 282.98 1 89.22 ? N3 KU2 205 A 1 HETATM 29 N N4 KU2 . . . F 4 129.364 192.851 283.469 1 104.34 ? N4 KU2 205 A 1 HETATM 30 O O1 KU2 . . . F 4 132.048 198.092 285.646 1 70.08 ? O1 KU2 205 A 1 HETATM 31 O O2 KU2 . . . F 4 129.645 197.671 286.955 1 60.38 ? O2 KU2 205 A 1 HETATM 32 O O3 KU2 . . . F 4 133.768 197.049 283.953 1 85.15 ? O3 KU2 205 A 1 HETATM 33 O O4 KU2 . . . F 4 129.015 192.61 281.259 1 119.37 ? O4 KU2 205 A 1 HETATM 34 O O5 KU2 . . . F 4 132.756 194.373 280.463 1 106.3 ? O5 KU2 205 A 1 HETATM 35 S S1 KU2 . . . F 4 127.216 195.157 281.171 1 131.05 ? S1 KU2 205 A 1 HETATM 36 CL CL1 KU2 . . . F 4 126.642 197.562 283.166 1 134.64 ? CL1 KU2 205 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 241 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 36 #