data_5WDC # _model_server_result.job_id 2qikFEuLMtZKMuhSgcP1yw _model_server_result.datetime_utc '2025-06-28 14:52:42' _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 5wdc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":205}' # _entry.id 5WDC # _exptl.entry_id 5WDC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 496.943 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-{(2S)-1-[(2-chlorophenoxy)acetyl]pyrrolidin-2-yl}-5-hydroxy-6-oxo-N-(2-phenylethyl)-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 5WDC _cell.length_a 90.777 _cell.length_b 90.777 _cell.length_c 134.545 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WDC _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc2 A OE2 GLU 81 A GLU 80 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc3 A OD2 ASP 109 A ASP 108 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.873 ? metalc ? metalc4 A OD1 ASP 109 A ASP 108 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.819 ? metalc ? metalc5 A OE2 GLU 120 A GLU 119 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc6 A O ILE 121 A ILE 120 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc7 B MN MN . A MN 201 1_555 F O1 G2K . A G2K 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc8 B MN MN . A MN 201 1_555 F O2 G2K . A G2K 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc9 C MN MN . A MN 202 1_555 F O3 G2K . A G2K 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc10 C MN MN . A MN 202 1_555 F O2 G2K . A G2K 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc11 C MN MN . A MN 202 1_555 G O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc12 C MN MN . A MN 202 1_555 G O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? # _chem_comp.formula 'C25 H25 Cl N4 O5' _chem_comp.formula_weight 496.943 _chem_comp.id G2K _chem_comp.mon_nstd_flag . _chem_comp.name 2-{(2S)-1-[(2-chlorophenoxy)acetyl]pyrrolidin-2-yl}-5-hydroxy-6-oxo-N-(2-phenylethyl)-1,6-dihydropyrimidine-4-carboxamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms SRI-29843 # 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 G2K sing 83 n n C24 C25 G2K doub 84 n y C24 C23 G2K sing 85 n y C25 C20 G2K sing 86 n y C23 C22 G2K doub 87 n y C20 O4 G2K sing 88 n n C20 C21 G2K doub 89 n y O4 C19 G2K sing 90 n n C22 C21 G2K sing 91 n y C19 C18 G2K sing 92 n n C12 C11 G2K doub 93 n y C12 C7 G2K sing 94 n y C6 C7 G2K sing 95 n n C6 C5 G2K sing 96 n n C11 C10 G2K sing 97 n y O5 C18 G2K doub 98 n n C7 C8 G2K doub 99 n y C18 N3 G2K sing 100 n n C5 N1 G2K sing 101 n n N1 C4 G2K sing 102 n n C10 C9 G2K doub 103 n y C8 C9 G2K sing 104 n y N3 C17 G2K sing 105 n n N3 C14 G2K sing 106 n n C17 C16 G2K sing 107 n n C4 O3 G2K doub 108 n n C4 C3 G2K sing 109 n n N2 C3 G2K sing 110 n n N2 C13 G2K doub 111 n n C14 C13 G2K sing 112 n n C14 C15 G2K sing 113 n n C3 C2 G2K doub 114 n n C13 N4 G2K sing 115 n n C16 C15 G2K sing 116 n n C2 O2 G2K sing 117 n n C2 C1 G2K sing 118 n n N4 C1 G2K sing 119 n n C1 O1 G2K doub 120 n n C10 H1 G2K sing 121 n n C11 H2 G2K sing 122 n n C12 H3 G2K sing 123 n n C14 H4 G2K sing 124 n n C15 H5 G2K sing 125 n n C15 H6 G2K sing 126 n n C16 H7 G2K sing 127 n n C16 H8 G2K sing 128 n n C17 H9 G2K sing 129 n n C17 H10 G2K sing 130 n n C19 H11 G2K sing 131 n n C19 H12 G2K sing 132 n n C21 H13 G2K sing 133 n n C22 H14 G2K sing 134 n n C23 H15 G2K sing 135 n n C24 H16 G2K sing 136 n n C5 H17 G2K sing 137 n n C5 H18 G2K sing 138 n n C6 H19 G2K sing 139 n n C6 H20 G2K sing 140 n n C8 H21 G2K sing 141 n n C9 H22 G2K sing 142 n n N1 H23 G2K sing 143 n n N4 H24 G2K sing 144 n n O2 H25 G2K sing 145 n n # _atom_sites.entry_id 5WDC _atom_sites.fract_transf_matrix[1][1] 0.011016 _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] 0.011016 _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] 0.007432 _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 G2K A 1 205 1 G2K G2K . G 5 HOH A 1 301 2 HOH HOH . G 5 HOH A 2 302 15 HOH HOH . G 5 HOH A 3 303 1 HOH HOH . G 5 HOH A 4 304 13 HOH HOH . G 5 HOH A 5 305 9 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 16 HOH HOH . G 5 HOH A 9 309 3 HOH HOH . G 5 HOH A 10 310 18 HOH HOH . G 5 HOH A 11 311 17 HOH HOH . G 5 HOH A 12 312 14 HOH HOH . G 5 HOH A 13 313 7 HOH HOH . G 5 HOH A 14 314 5 HOH HOH . G 5 HOH A 15 315 12 HOH HOH . G 5 HOH A 16 316 4 HOH HOH . G 5 HOH A 17 317 6 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 G2K . . . F 4 493.42 197.215 556.52 1 69.86 ? C1 G2K 205 A 1 HETATM 2 C C10 G2K . . . F 4 497.4 190.252 553.603 1 112.11 ? C10 G2K 205 A 1 HETATM 3 C C11 G2K . . . F 4 497.108 190.504 552.284 1 106.75 ? C11 G2K 205 A 1 HETATM 4 C C12 G2K . . . F 4 497.335 191.763 551.749 1 107.14 ? C12 G2K 205 A 1 HETATM 5 C C13 G2K . . . F 4 493.118 195.151 555.345 1 64.86 ? C13 G2K 205 A 1 HETATM 6 C C14 G2K . . . F 4 492.296 193.926 555.007 1 68.55 ? C14 G2K 205 A 1 HETATM 7 C C15 G2K . . . F 4 492.27 192.869 556.122 1 79.78 ? C15 G2K 205 A 1 HETATM 8 C C16 G2K . . . F 4 493.597 192.157 555.911 1 85.67 ? C16 G2K 205 A 1 HETATM 9 C C17 G2K . . . F 4 493.6 191.951 554.412 1 84.05 ? C17 G2K 205 A 1 HETATM 10 C C18 G2K . . . F 4 492.827 193.52 552.626 1 89.94 ? C18 G2K 205 A 1 HETATM 11 C C19 G2K . . . F 4 493.596 192.704 551.611 1 97.66 ? C19 G2K 205 A 1 HETATM 12 C C2 G2K . . . F 4 494.675 197.297 555.921 1 60.37 ? C2 G2K 205 A 1 HETATM 13 C C20 G2K . . . F 4 494.139 194.35 549.954 1 103.54 ? C20 G2K 205 A 1 HETATM 14 C C21 G2K . . . F 4 494.871 195.143 550.837 1 89.86 ? C21 G2K 205 A 1 HETATM 15 C C22 G2K . . . F 4 495.515 196.281 550.384 1 95.2 ? C22 G2K 205 A 1 HETATM 16 C C23 G2K . . . F 4 495.454 196.642 549.056 1 92.37 ? C23 G2K 205 A 1 HETATM 17 C C24 G2K . . . F 4 494.746 195.874 548.167 1 92.38 ? C24 G2K 205 A 1 HETATM 18 C C25 G2K . . . F 4 494.096 194.736 548.616 1 106.19 ? C25 G2K 205 A 1 HETATM 19 C C3 G2K . . . F 4 495.095 196.313 555.077 1 66.96 ? C3 G2K 205 A 1 HETATM 20 C C4 G2K . . . F 4 496.448 196.383 554.415 1 74.99 ? C4 G2K 205 A 1 HETATM 21 C C5 G2K . . . F 4 498.054 195.255 552.975 1 84.37 ? C5 G2K 205 A 1 HETATM 22 C C6 G2K . . . F 4 498.104 194.153 551.945 1 91.24 ? C6 G2K 205 A 1 HETATM 23 C C7 G2K . . . F 4 497.854 192.783 552.531 1 98.88 ? C7 G2K 205 A 1 HETATM 24 C C8 G2K . . . F 4 498.147 192.51 553.858 1 106.8 ? C8 G2K 205 A 1 HETATM 25 C C9 G2K . . . F 4 497.917 191.251 554.39 1 107.1 ? C9 G2K 205 A 1 HETATM 26 N N1 G2K . . . F 4 496.738 195.374 553.597 1 80.03 ? N1 G2K 205 A 1 HETATM 27 N N2 G2K . . . F 4 494.329 195.25 554.792 1 66.48 ? N2 G2K 205 A 1 HETATM 28 N N3 G2K . . . F 4 492.906 193.147 553.914 1 81.28 ? N3 G2K 205 A 1 HETATM 29 N N4 G2K . . . F 4 492.657 196.112 556.204 1 63.42 ? N4 G2K 205 A 1 HETATM 30 O O1 G2K . . . F 4 492.975 198.069 557.3 1 67.02 ? O1 G2K 205 A 1 HETATM 31 O O2 G2K . . . F 4 495.403 198.376 556.237 1 65.52 ? O2 G2K 205 A 1 HETATM 32 O O3 G2K . . . F 4 497.212 197.321 554.636 1 72.44 ? O3 G2K 205 A 1 HETATM 33 O O4 G2K . . . F 4 493.468 193.211 550.286 1 107.89 ? O4 G2K 205 A 1 HETATM 34 O O5 G2K . . . F 4 492.153 194.493 552.297 1 91.03 ? O5 G2K 205 A 1 HETATM 35 CL CL1 G2K . . . F 4 493.201 193.768 547.482 1 123.89 ? CL1 G2K 205 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 33 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 35 #