data_5WDN # _model_server_result.job_id EiZA6z-u5vG0Edgytd0e1Q _model_server_result.datetime_utc '2024-11-13 20:39:27' _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 5wdn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 5WDN # _exptl.entry_id 5WDN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 359.333 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '5-hydroxy-6-oxo-2-[(2S)-1-(phenoxyacetyl)pyrrolidin-2-yl]-1,6-dihydropyrimidine-4-carboxylic acid' _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 120 _cell.entry_id 5WDN _cell.length_a 60.168 _cell.length_b 60.168 _cell.length_c 94.443 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WDN _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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 41 A HIS 41 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc2 A OE2 GLU 61 A GLU 80 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc3 A OD2 ASP 89 A ASP 108 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc4 A OD1 ASP 89 A ASP 108 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc5 A OE2 GLU 100 A GLU 119 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc6 A O ILE 101 A ILE 120 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc7 B MN MN . A MN 301 1_555 D O4 G1K . A G1K 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc8 B MN MN . A MN 301 1_555 D O2 G1K . A G1K 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc9 C MN MN . A MN 302 1_555 D O1 G1K . A G1K 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc10 C MN MN . A MN 302 1_555 D O2 G1K . A G1K 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc11 C MN MN . A MN 302 1_555 E O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc12 C MN MN . A MN 302 1_555 E O HOH . A HOH 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? # _chem_comp.formula 'C17 H17 N3 O6' _chem_comp.formula_weight 359.333 _chem_comp.id G1K _chem_comp.mon_nstd_flag . _chem_comp.name '5-hydroxy-6-oxo-2-[(2S)-1-(phenoxyacetyl)pyrrolidin-2-yl]-1,6-dihydropyrimidine-4-carboxylic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms SRI-29680 # 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 O4 C4 G1K doub 83 n n O2 C2 G1K sing 84 n n C4 O3 G1K sing 85 n n C4 C3 G1K sing 86 n n C2 C3 G1K doub 87 n n C2 C1 G1K sing 88 n n C3 N1 G1K sing 89 n n O1 C1 G1K doub 90 n n C1 N3 G1K sing 91 n n N1 C5 G1K doub 92 n n N3 C5 G1K sing 93 n n C5 C6 G1K sing 94 n n O6 C10 G1K doub 95 n n C13 C14 G1K doub 96 n y C13 C12 G1K sing 97 n y C14 C15 G1K sing 98 n y O5 C12 G1K sing 99 n n O5 C11 G1K sing 100 n n C10 C11 G1K sing 101 n n C10 N2 G1K sing 102 n n C6 N2 G1K sing 103 n n C6 C7 G1K sing 104 n n C12 C17 G1K doub 105 n y C15 C16 G1K doub 106 n y N2 C9 G1K sing 107 n n C17 C16 G1K sing 108 n y C7 C8 G1K sing 109 n n C9 C8 G1K sing 110 n n C11 H1 G1K sing 111 n n C11 H2 G1K sing 112 n n C13 H3 G1K sing 113 n n C14 H4 G1K sing 114 n n C15 H5 G1K sing 115 n n C16 H6 G1K sing 116 n n C17 H7 G1K sing 117 n n C6 H8 G1K sing 118 n n C7 H9 G1K sing 119 n n C7 H10 G1K sing 120 n n C8 H11 G1K sing 121 n n C8 H12 G1K sing 122 n n C9 H13 G1K sing 123 n n C9 H14 G1K sing 124 n n N3 H15 G1K sing 125 n n O2 H16 G1K sing 126 n n O3 H17 G1K sing 127 n n # _atom_sites.entry_id 5WDN _atom_sites.fract_transf_matrix[1][1] 0.01662 _atom_sites.fract_transf_matrix[1][2] 0.009596 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019191 _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] 0.010588 _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 1 301 201 MN MN . C 2 MN A 1 302 202 MN MN . D 3 G1K A 1 303 1 G1K G1K . E 4 HOH A 1 401 16 HOH HOH . E 4 HOH A 2 402 5 HOH HOH . E 4 HOH A 3 403 24 HOH HOH . E 4 HOH A 4 404 2 HOH HOH . E 4 HOH A 5 405 11 HOH HOH . E 4 HOH A 6 406 28 HOH HOH . E 4 HOH A 7 407 34 HOH HOH . E 4 HOH A 8 408 15 HOH HOH . E 4 HOH A 9 409 10 HOH HOH . E 4 HOH A 10 410 22 HOH HOH . E 4 HOH A 11 411 7 HOH HOH . E 4 HOH A 12 412 12 HOH HOH . E 4 HOH A 13 413 8 HOH HOH . E 4 HOH A 14 414 3 HOH HOH . E 4 HOH A 15 415 9 HOH HOH . E 4 HOH A 16 416 27 HOH HOH . E 4 HOH A 17 417 1 HOH HOH . E 4 HOH A 18 418 23 HOH HOH . E 4 HOH A 19 419 17 HOH HOH . E 4 HOH A 20 420 33 HOH HOH . E 4 HOH A 21 421 21 HOH HOH . E 4 HOH A 22 422 29 HOH HOH . E 4 HOH A 23 423 30 HOH HOH . E 4 HOH A 24 424 35 HOH HOH . E 4 HOH A 25 425 26 HOH HOH . E 4 HOH A 26 426 32 HOH HOH . E 4 HOH A 27 427 20 HOH HOH . E 4 HOH A 28 428 13 HOH HOH . E 4 HOH A 29 429 36 HOH HOH . E 4 HOH A 30 430 18 HOH HOH . E 4 HOH A 31 431 31 HOH HOH . E 4 HOH A 32 432 4 HOH HOH . E 4 HOH A 33 433 6 HOH HOH . E 4 HOH A 34 434 25 HOH HOH . E 4 HOH A 35 435 19 HOH HOH . E 4 HOH A 36 436 37 HOH HOH . E 4 HOH A 37 437 14 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 G1K . . . D 3 -21.869 16.026 8.29 1 50.13 ? C1 G1K 303 A 1 HETATM 2 C C10 G1K . . . D 3 -24.841 17.945 10.877 1 74.19 ? C10 G1K 303 A 1 HETATM 3 C C11 G1K . . . D 3 -25.81 16.915 11.403 1 80 ? C11 G1K 303 A 1 HETATM 4 C C12 G1K . . . D 3 -27.924 17.923 10.923 1 87.82 ? C12 G1K 303 A 1 HETATM 5 C C13 G1K . . . D 3 -29.158 17.893 10.293 1 89.75 ? C13 G1K 303 A 1 HETATM 6 C C14 G1K . . . D 3 -30.075 18.899 10.547 1 92.36 ? C14 G1K 303 A 1 HETATM 7 C C15 G1K . . . D 3 -29.773 19.919 11.417 1 93.62 ? C15 G1K 303 A 1 HETATM 8 C C16 G1K . . . D 3 -28.552 19.944 12.043 1 92.59 ? C16 G1K 303 A 1 HETATM 9 C C17 G1K . . . D 3 -27.62 18.949 11.806 1 89.88 ? C17 G1K 303 A 1 HETATM 10 C C2 G1K . . . D 3 -21.548 16.851 7.216 1 47.32 ? C2 G1K 303 A 1 HETATM 11 C C3 G1K . . . D 3 -21.547 18.205 7.376 1 50.74 ? C3 G1K 303 A 1 HETATM 12 C C4 G1K . . . D 3 -21.202 19.131 6.226 1 50.33 ? C4 G1K 303 A 1 HETATM 13 C C5 G1K . . . D 3 -22.152 18.017 9.591 1 56.98 ? C5 G1K 303 A 1 HETATM 14 C C6 G1K . . . D 3 -22.487 18.696 10.901 1 63.79 ? C6 G1K 303 A 1 HETATM 15 C C7 G1K . . . D 3 -21.417 18.496 11.991 1 65.49 ? C7 G1K 303 A 1 HETATM 16 C C8 G1K . . . D 3 -22.227 18.549 13.278 1 69.04 ? C8 G1K 303 A 1 HETATM 17 C C9 G1K . . . D 3 -23.42 17.698 12.92 1 69.07 ? C9 G1K 303 A 1 HETATM 18 N N1 G1K . . . D 3 -21.842 18.787 8.548 1 53.79 ? N1 G1K 303 A 1 HETATM 19 N N2 G1K . . . D 3 -23.682 18.109 11.535 1 68.86 ? N2 G1K 303 A 1 HETATM 20 N N3 G1K . . . D 3 -22.17 16.653 9.479 1 52.76 ? N3 G1K 303 A 1 HETATM 21 O O1 G1K . . . D 3 -21.894 14.787 8.226 1 47.47 ? O1 G1K 303 A 1 HETATM 22 O O2 G1K . . . D 3 -21.257 16.233 6.062 1 44.04 ? O2 G1K 303 A 1 HETATM 23 O O3 G1K . . . D 3 -21.284 20.354 6.436 1 53.78 -1 O3 G1K 303 A 1 HETATM 24 O O4 G1K . . . D 3 -20.855 18.604 5.152 1 45.88 ? O4 G1K 303 A 1 HETATM 25 O O5 G1K . . . D 3 -27.027 16.919 10.668 1 84.02 ? O5 G1K 303 A 1 HETATM 26 O O6 G1K . . . D 3 -25.11 18.634 9.897 1 74.35 ? O6 G1K 303 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 26 #