data_5WAP # _model_server_result.job_id '_h8Uymyds4Gd9sEG3iOp9w' _model_server_result.datetime_utc '2024-11-28 13:31:29' _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 5wap # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":204}' # _entry.id 5WAP # _exptl.entry_id 5WAP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 525.019 _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-(2,3-dihydro-1H-inden-2-yl)-5-hydroxy-6-oxo-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 5WAP _cell.length_a 90.653 _cell.length_b 90.653 _cell.length_c 135.17 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WAP _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 _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 E _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 OE1 GLU 81 A GLU 80 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc2 A OD2 ASP 109 A ASP 108 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc3 A OD1 ASP 109 A ASP 108 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc4 A OE1 GLU 120 A GLU 119 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc5 A O ILE 121 A ILE 120 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc6 B MN MN . A MN 201 1_555 E O1 KU9 . A KU9 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.923 ? metalc ? metalc7 B MN MN . A MN 201 1_555 E O2 KU9 . A KU9 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc8 C MN MN . A MN 202 1_555 E O3 KU9 . A KU9 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc9 C MN MN . A MN 202 1_555 E O2 KU9 . A KU9 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc10 C MN MN . A MN 202 1_555 F O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc11 C MN MN . A MN 202 1_555 F O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? # _chem_comp.formula 'C26 H25 Cl N4 O4 S' _chem_comp.formula_weight 525.019 _chem_comp.id KU9 _chem_comp.mon_nstd_flag . _chem_comp.name 2-[(2S)-1-{[(2-chlorophenyl)sulfanyl]acetyl}pyrrolidin-2-yl]-N-(2,3-dihydro-1H-inden-2-yl)-5-hydroxy-6-oxo-1,6-dihydropyrimidine-4-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 C9 C10 KU9 doub 173 n y C9 C8 KU9 sing 174 n y C10 C11 KU9 sing 175 n y C8 C7 KU9 doub 176 n y C11 C12 KU9 doub 177 n y C7 C12 KU9 sing 178 n y C7 C6 KU9 sing 179 n n C12 C13 KU9 sing 180 n n S1 C17 KU9 sing 181 n n S1 C18 KU9 sing 182 n n C6 C5 KU9 sing 183 n n C13 C5 KU9 sing 184 n n O4 C16 KU9 doub 185 n n CL1 C23 KU9 sing 186 n n C17 C16 KU9 sing 187 n n C5 N1 KU9 sing 188 n n C18 C23 KU9 doub 189 n y C18 C19 KU9 sing 190 n y C16 N3 KU9 sing 191 n n C23 C22 KU9 sing 192 n y C19 C20 KU9 doub 193 n y N1 C4 KU9 sing 194 n n C22 C21 KU9 doub 195 n y C20 C21 KU9 sing 196 n y N3 C24 KU9 sing 197 n n N3 C15 KU9 sing 198 n n C4 O3 KU9 doub 199 n n C4 C3 KU9 sing 200 n n N2 C3 KU9 sing 201 n n N2 C14 KU9 doub 202 n n C24 C25 KU9 sing 203 n n C3 C2 KU9 doub 204 n n C15 C14 KU9 sing 205 n n C15 C26 KU9 sing 206 n n C14 N4 KU9 sing 207 n n C2 O2 KU9 sing 208 n n C2 C1 KU9 sing 209 n n C26 C25 KU9 sing 210 n n N4 C1 KU9 sing 211 n n C1 O1 KU9 doub 212 n n C10 H1 KU9 sing 213 n n C11 H2 KU9 sing 214 n n C13 H3 KU9 sing 215 n n C13 H4 KU9 sing 216 n n C15 H5 KU9 sing 217 n n C17 H6 KU9 sing 218 n n C17 H7 KU9 sing 219 n n C19 H8 KU9 sing 220 n n C20 H9 KU9 sing 221 n n C21 H10 KU9 sing 222 n n C22 H11 KU9 sing 223 n n C24 H12 KU9 sing 224 n n C24 H13 KU9 sing 225 n n C25 H14 KU9 sing 226 n n C25 H15 KU9 sing 227 n n C26 H16 KU9 sing 228 n n C26 H17 KU9 sing 229 n n C5 H18 KU9 sing 230 n n C6 H19 KU9 sing 231 n n C6 H20 KU9 sing 232 n n C8 H21 KU9 sing 233 n n C9 H22 KU9 sing 234 n n N1 H23 KU9 sing 235 n n N4 H24 KU9 sing 236 n n O2 H25 KU9 sing 237 n n # _atom_sites.entry_id 5WAP _atom_sites.fract_transf_matrix[1][1] 0.011031 _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] 0.011031 _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] 0.007398 _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 4 KU9 A 1 204 1 KU9 KU9 . F 5 HOH A 1 301 6 HOH HOH . F 5 HOH A 2 302 3 HOH HOH . F 5 HOH A 3 303 5 HOH HOH . F 5 HOH A 4 304 10 HOH HOH . F 5 HOH A 5 305 2 HOH HOH . F 5 HOH A 6 306 8 HOH HOH . F 5 HOH A 7 307 7 HOH HOH . F 5 HOH A 8 308 12 HOH HOH . F 5 HOH A 9 309 11 HOH HOH . F 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 C1 KU9 . . . E 4 -60.919 356.279 694.333 1 71.75 ? C1 KU9 204 A 1 HETATM 2 C C10 KU9 . . . E 4 -58.35 358.01 686.244 1 83.42 ? C10 KU9 204 A 1 HETATM 3 C C11 KU9 . . . E 4 -57.636 358.709 687.202 1 87.16 ? C11 KU9 204 A 1 HETATM 4 C C12 KU9 . . . E 4 -58.331 359.486 688.117 1 84.91 ? C12 KU9 204 A 1 HETATM 5 C C13 KU9 . . . E 4 -57.817 360.338 689.248 1 82.34 ? C13 KU9 204 A 1 HETATM 6 C C14 KU9 . . . E 4 -58.931 355.789 693.084 1 79.86 ? C14 KU9 204 A 1 HETATM 7 C C15 KU9 . . . E 4 -57.772 354.876 692.746 1 85.22 ? C15 KU9 204 A 1 HETATM 8 C C16 KU9 . . . E 4 -56.784 355.374 690.519 1 102.97 ? C16 KU9 204 A 1 HETATM 9 C C17 KU9 . . . E 4 -57.379 354.116 689.919 1 111.32 ? C17 KU9 204 A 1 HETATM 10 C C18 KU9 . . . E 4 -60.165 353.878 690.201 1 118.05 ? C18 KU9 204 A 1 HETATM 11 C C19 KU9 . . . E 4 -60.088 352.616 690.79 1 121.84 ? C19 KU9 204 A 1 HETATM 12 C C2 KU9 . . . E 4 -60.976 357.492 693.65 1 70.09 ? C2 KU9 204 A 1 HETATM 13 C C20 KU9 . . . E 4 -61.046 352.222 691.706 1 120.67 ? C20 KU9 204 A 1 HETATM 14 C C21 KU9 . . . E 4 -62.076 353.072 692.04 1 119.6 ? C21 KU9 204 A 1 HETATM 15 C C22 KU9 . . . E 4 -62.165 354.323 691.468 1 119.55 ? C22 KU9 204 A 1 HETATM 16 C C23 KU9 . . . E 4 -61.211 354.72 690.552 1 119.9 ? C23 KU9 204 A 1 HETATM 17 C C24 KU9 . . . E 4 -55.784 356.265 692.622 1 91.06 ? C24 KU9 204 A 1 HETATM 18 C C25 KU9 . . . E 4 -56.166 355.992 694.064 1 90.91 ? C25 KU9 204 A 1 HETATM 19 C C26 KU9 . . . E 4 -56.866 354.644 693.963 1 88.41 ? C26 KU9 204 A 1 HETATM 20 C C3 KU9 . . . E 4 -60.021 357.795 692.725 1 75.41 ? C3 KU9 204 A 1 HETATM 21 C C4 KU9 . . . E 4 -60.058 359.098 691.977 1 75.11 ? C4 KU9 204 A 1 HETATM 22 C C5 KU9 . . . E 4 -59.044 360.429 690.177 1 79.98 ? C5 KU9 204 A 1 HETATM 23 C C6 KU9 . . . E 4 -60.21 360.466 689.168 1 80.48 ? C6 KU9 204 A 1 HETATM 24 C C7 KU9 . . . E 4 -59.717 359.556 688.075 1 83.17 ? C7 KU9 204 A 1 HETATM 25 C C8 KU9 . . . E 4 -60.427 358.86 687.107 1 82.48 ? C8 KU9 204 A 1 HETATM 26 C C9 KU9 . . . E 4 -59.729 358.084 686.198 1 81.77 ? C9 KU9 204 A 1 HETATM 27 N N1 KU9 . . . E 4 -59.122 359.253 691.024 1 79.27 ? N1 KU9 204 A 1 HETATM 28 N N2 KU9 . . . E 4 -59.009 356.959 692.445 1 81.12 ? N2 KU9 204 A 1 HETATM 29 N N3 KU9 . . . E 4 -56.794 355.521 691.854 1 91.6 ? N3 KU9 204 A 1 HETATM 30 N N4 KU9 . . . E 4 -59.868 355.442 694.02 1 74.79 ? N4 KU9 204 A 1 HETATM 31 O O1 KU9 . . . E 4 -61.75 355.928 695.184 1 69.77 ? O1 KU9 204 A 1 HETATM 32 O O2 KU9 . . . E 4 -62.003 358.298 693.957 1 67.6 ? O2 KU9 204 A 1 HETATM 33 O O3 KU9 . . . E 4 -60.889 359.967 692.235 1 69.8 ? O3 KU9 204 A 1 HETATM 34 O O4 KU9 . . . E 4 -56.314 356.245 689.793 1 105.49 ? O4 KU9 204 A 1 HETATM 35 S S1 KU9 . . . E 4 -58.939 354.381 689.033 1 113.96 ? S1 KU9 204 A 1 HETATM 36 CL CL1 KU9 . . . E 4 -61.344 356.295 689.845 1 124.34 ? CL1 KU9 204 A 1 # _model_server_stats.io_time_ms 72 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 36 #