data_5WA6 # _model_server_result.job_id F3QbU6eyPuvpMDjkbrHgqQ _model_server_result.datetime_utc '2024-11-16 15:47:24' _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 5wa6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 5WA6 # _exptl.entry_id 5WA6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 496.488 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-{(2S)-1-[(2-fluorophenoxy)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 5WA6 _cell.length_a 90.563 _cell.length_b 90.563 _cell.length_c 135.167 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WA6 _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 _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 3 _struct_asym.id D _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc2 A OE2 GLU 81 A GLU 80 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc3 A OD1 ASP 109 A ASP 108 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc4 A OD2 ASP 109 A ASP 108 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc5 A OD2 ASP 109 A ASP 108 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc6 A OE2 GLU 120 A GLU 119 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc7 A O ILE 121 A ILE 120 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc8 B MN MN . A MN 201 1_555 D O2 KU7 . A KU7 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc9 B MN MN . A MN 201 1_555 D O1 KU7 . A KU7 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc10 C MN MN . A MN 202 1_555 D O3 KU7 . A KU7 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc11 C MN MN . A MN 202 1_555 D O1 KU7 . A KU7 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc12 C MN MN . A MN 202 1_555 E O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc13 C MN MN . A MN 202 1_555 E O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? # _chem_comp.formula 'C25 H25 F N4 O6' _chem_comp.formula_weight 496.488 _chem_comp.id KU7 _chem_comp.mon_nstd_flag . _chem_comp.name 2-{(2S)-1-[(2-fluorophenoxy)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 ? # 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 KU7 doub 173 n y C20 C21 KU7 sing 174 n y C25 C24 KU7 sing 175 n y C21 C22 KU7 doub 176 n y C24 C23 KU7 doub 177 n y C22 C23 KU7 sing 178 n y C23 O4 KU7 sing 179 n n O4 C7 KU7 sing 180 n n C7 C6 KU7 sing 181 n n O6 C12 KU7 doub 182 n n C13 O5 KU7 sing 183 n n C13 C12 KU7 sing 184 n n O5 C17 KU7 sing 185 n n C6 N3 KU7 sing 186 n n F1 C16 KU7 sing 187 n n C12 N4 KU7 sing 188 n n C17 C16 KU7 doub 189 n y C17 C18 KU7 sing 190 n y C16 C15 KU7 sing 191 n y N3 C5 KU7 sing 192 n n C18 C19 KU7 doub 193 n y C15 C14 KU7 doub 194 n y C19 C14 KU7 sing 195 n y N4 C11 KU7 sing 196 n n N4 C10 KU7 sing 197 n n C5 O3 KU7 doub 198 n n C5 C2 KU7 sing 199 n n C11 C8 KU7 sing 200 n n N1 C2 KU7 sing 201 n n N1 C1 KU7 doub 202 n n C2 C3 KU7 doub 203 n n C10 C1 KU7 sing 204 n n C10 C9 KU7 sing 205 n n C1 N2 KU7 sing 206 n n C3 O1 KU7 sing 207 n n C3 C4 KU7 sing 208 n n C8 C9 KU7 sing 209 n n N2 C4 KU7 sing 210 n n C4 O2 KU7 doub 211 n n C10 H1 KU7 sing 212 n n C11 H2 KU7 sing 213 n n C11 H3 KU7 sing 214 n n C13 H4 KU7 sing 215 n n C13 H5 KU7 sing 216 n n C14 H6 KU7 sing 217 n n C15 H7 KU7 sing 218 n n C18 H8 KU7 sing 219 n n C19 H9 KU7 sing 220 n n C20 H10 KU7 sing 221 n n C21 H11 KU7 sing 222 n n C22 H12 KU7 sing 223 n n C24 H13 KU7 sing 224 n n C25 H14 KU7 sing 225 n n C6 H15 KU7 sing 226 n n C6 H16 KU7 sing 227 n n C7 H17 KU7 sing 228 n n C7 H18 KU7 sing 229 n n C8 H19 KU7 sing 230 n n C8 H20 KU7 sing 231 n n C9 H21 KU7 sing 232 n n C9 H22 KU7 sing 233 n n N2 H23 KU7 sing 234 n n N3 H24 KU7 sing 235 n n O1 H25 KU7 sing 236 n n # _atom_sites.entry_id 5WA6 _atom_sites.fract_transf_matrix[1][1] 0.011042 _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] 0.011042 _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 KU7 A 1 203 1 KU7 KU7 . E 4 HOH A 1 301 4 HOH HOH . E 4 HOH A 2 302 1 HOH HOH . E 4 HOH A 3 303 8 HOH HOH . E 4 HOH A 4 304 3 HOH HOH . E 4 HOH A 5 305 9 HOH HOH . E 4 HOH A 6 306 7 HOH HOH . E 4 HOH A 7 307 6 HOH HOH . E 4 HOH A 8 308 5 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 KU7 . . . D 3 491.977 194.444 558.183 1 86.93 ? C1 KU7 203 A 1 HETATM 2 C C10 KU7 . . . D 3 491.199 193.161 557.973 1 97.51 ? C10 KU7 203 A 1 HETATM 3 C C11 KU7 . . . D 3 492.6 191.241 557.435 1 109.19 ? C11 KU7 203 A 1 HETATM 4 C C12 KU7 . . . D 3 491.515 192.522 555.593 1 112.71 ? C12 KU7 203 A 1 HETATM 5 C C13 KU7 . . . D 3 490.512 193.578 555.217 1 120.83 ? C13 KU7 203 A 1 HETATM 6 C C14 KU7 . . . D 3 488.886 197.946 557.013 1 133.22 ? C14 KU7 203 A 1 HETATM 7 C C15 KU7 . . . D 3 490.174 198.165 556.558 1 135.63 ? C15 KU7 203 A 1 HETATM 8 C C16 KU7 . . . D 3 490.873 197.128 555.988 1 133.96 ? C16 KU7 203 A 1 HETATM 9 C C17 KU7 . . . D 3 490.326 195.858 555.85 1 136.71 ? C17 KU7 203 A 1 HETATM 10 C C18 KU7 . . . D 3 489.033 195.657 556.318 1 136.44 ? C18 KU7 203 A 1 HETATM 11 C C19 KU7 . . . D 3 488.32 196.701 556.893 1 132.4 ? C19 KU7 203 A 1 HETATM 12 C C2 KU7 . . . D 3 493.887 195.67 557.753 1 74.59 ? C2 KU7 203 A 1 HETATM 13 C C20 KU7 . . . D 3 492.761 193.778 550.377 1 107.35 ? C20 KU7 203 A 1 HETATM 14 C C21 KU7 . . . D 3 492.861 192.618 551.108 1 112.74 ? C21 KU7 203 A 1 HETATM 15 C C22 KU7 . . . D 3 493.701 192.547 552.207 1 114.51 ? C22 KU7 203 A 1 HETATM 16 C C23 KU7 . . . D 3 494.451 193.657 552.564 1 111.09 ? C23 KU7 203 A 1 HETATM 17 C C24 KU7 . . . D 3 494.348 194.831 551.832 1 106.11 ? C24 KU7 203 A 1 HETATM 18 C C25 KU7 . . . D 3 493.502 194.878 550.737 1 102.32 ? C25 KU7 203 A 1 HETATM 19 C C3 KU7 . . . D 3 493.45 196.706 558.523 1 70.43 ? C3 KU7 203 A 1 HETATM 20 C C4 KU7 . . . D 3 492.218 196.619 559.166 1 74.56 ? C4 KU7 203 A 1 HETATM 21 C C5 KU7 . . . D 3 495.21 195.731 557.036 1 80.06 ? C5 KU7 203 A 1 HETATM 22 C C6 KU7 . . . D 3 496.598 194.637 555.338 1 94.2 ? C6 KU7 203 A 1 HETATM 23 C C7 KU7 . . . D 3 496.159 194.695 553.897 1 102.6 ? C7 KU7 203 A 1 HETATM 24 C C8 KU7 . . . D 3 492.654 191.545 558.916 1 107.26 ? C8 KU7 203 A 1 HETATM 25 C C9 KU7 . . . D 3 491.294 192.182 559.154 1 102.69 ? C9 KU7 203 A 1 HETATM 26 F F1 KU7 . . . D 3 492.128 197.328 555.541 1 131.03 ? F1 KU7 203 A 1 HETATM 27 N N1 KU7 . . . D 3 493.164 194.554 557.583 1 82.02 ? N1 KU7 203 A 1 HETATM 28 N N2 KU7 . . . D 3 491.501 195.458 558.969 1 73.82 ? N2 KU7 203 A 1 HETATM 29 N N3 KU7 . . . D 3 495.466 194.689 556.249 1 88.48 ? N3 KU7 203 A 1 HETATM 30 N N4 KU7 . . . D 3 491.767 192.327 556.898 1 106.91 ? N4 KU7 203 A 1 HETATM 31 O O1 KU7 . . . D 3 494.142 197.838 558.72 1 68.48 ? O1 KU7 203 A 1 HETATM 32 O O2 KU7 . . . D 3 491.751 197.515 559.886 1 70.87 ? O2 KU7 203 A 1 HETATM 33 O O3 KU7 . . . D 3 495.957 196.701 557.158 1 72.81 ? O3 KU7 203 A 1 HETATM 34 O O4 KU7 . . . D 3 495.278 193.595 553.653 1 111.39 ? O4 KU7 203 A 1 HETATM 35 O O5 KU7 . . . D 3 491.089 194.875 555.282 1 132.88 ? O5 KU7 203 A 1 HETATM 36 O O6 KU7 . . . D 3 492.068 191.836 554.74 1 115.83 ? O6 KU7 203 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 36 #