data_5WCS # _model_server_result.job_id bGtmyDhB5PY27NlHVMD-Kw _model_server_result.datetime_utc '2024-11-24 20:37:32' _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 5wcs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 5WCS # _exptl.entry_id 5WCS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 409.392 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '5-hydroxy-2-[(2S)-1-{[(naphthalen-1-yl)oxy]acetyl}pyrrolidin-2-yl]-6-oxo-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 5WCS _cell.length_a 74.666 _cell.length_b 74.666 _cell.length_c 125.722 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WCS _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 software_defined_assembly 1 PISA monomeric 1 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E 1 1,2 A,B,C,D,E 2 1 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 8_675 x-y+1,-y+2,-z 1 0 0 0 -1 0 0 0 -1 0 129.325306 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 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc2 A OE1 GLU 61 A GLU 80 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc3 A OD2 ASP 89 A ASP 108 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc4 A OD1 ASP 89 A ASP 108 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc5 A OE1 GLU 100 A GLU 119 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc6 A O ILE 101 A ILE 120 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc7 B MN MN . A MN 301 1_555 D O1 9KU . A 9KU 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc8 B MN MN . A MN 301 1_555 D O2 9KU . A 9KU 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc9 B MN MN . A MN 301 1_555 E O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.607 ? metalc ? metalc10 B MN MN . A MN 301 1_555 E O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc11 C MN MN . A MN 302 1_555 D O2 9KU . A 9KU 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc12 C MN MN . A MN 302 1_555 D O4 9KU . A 9KU 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? # _chem_comp.formula 'C21 H19 N3 O6' _chem_comp.formula_weight 409.392 _chem_comp.id 9KU _chem_comp.mon_nstd_flag . _chem_comp.name '5-hydroxy-2-[(2S)-1-{[(naphthalen-1-yl)oxy]acetyl}pyrrolidin-2-yl]-6-oxo-1,6-dihydropyrimidine-4-carboxylic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms SRI-29789 # 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 C19 9KU sing 1 n n C20 C21 9KU sing 2 n n O1 C1 9KU doub 3 n n C19 N2 9KU sing 4 n n C21 C6 9KU sing 5 n n C1 N3 9KU sing 6 n n C1 C2 9KU sing 7 n n N3 C5 9KU sing 8 n n O2 C2 9KU sing 9 n n C2 C3 9KU doub 10 n n C5 C6 9KU sing 11 n n C5 N1 9KU doub 12 n n N2 C6 9KU sing 13 n n N2 C7 9KU sing 14 n n C8 C7 9KU sing 15 n n C8 O5 9KU sing 16 n n C3 N1 9KU sing 17 n n C3 C4 9KU sing 18 n n C7 O6 9KU doub 19 n n O4 C4 9KU doub 20 n n C4 O3 9KU sing 21 n n O5 C9 9KU sing 22 n n C10 C9 9KU doub 23 n y C10 C11 9KU sing 24 n y C9 C14 9KU sing 25 n y C11 C12 9KU doub 26 n y C14 C15 9KU doub 27 n y C14 C13 9KU sing 28 n y C15 C16 9KU sing 29 n y C12 C13 9KU sing 30 n y C13 C18 9KU doub 31 n y C16 C17 9KU doub 32 n y C18 C17 9KU sing 33 n y C10 H1 9KU sing 34 n n C11 H2 9KU sing 35 n n C12 H3 9KU sing 36 n n C15 H4 9KU sing 37 n n C16 H5 9KU sing 38 n n C17 H6 9KU sing 39 n n C18 H7 9KU sing 40 n n C19 H8 9KU sing 41 n n C19 H9 9KU sing 42 n n C20 H10 9KU sing 43 n n C20 H11 9KU sing 44 n n C21 H12 9KU sing 45 n n C21 H13 9KU sing 46 n n C6 H14 9KU sing 47 n n C8 H15 9KU sing 48 n n C8 H16 9KU sing 49 n n N3 H17 9KU sing 50 n n O2 H18 9KU sing 51 n n O3 H19 9KU sing 52 n n # _atom_sites.entry_id 5WCS _atom_sites.fract_transf_matrix[1][1] 0.013393 _atom_sites.fract_transf_matrix[1][2] 0.007732 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015465 _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] 0.007954 _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 1 MN MN . C 2 MN A 1 302 2 MN MN . D 3 9KU A 1 303 1 9KU 9KU . E 4 HOH A 1 401 11 HOH HOH . E 4 HOH A 2 402 2 HOH HOH . E 4 HOH A 3 403 8 HOH HOH . E 4 HOH A 4 404 1 HOH HOH . E 4 HOH A 5 405 18 HOH HOH . E 4 HOH A 6 406 19 HOH HOH . E 4 HOH A 7 407 24 HOH HOH . E 4 HOH A 8 408 12 HOH HOH . E 4 HOH A 9 409 5 HOH HOH . E 4 HOH A 10 410 15 HOH HOH . E 4 HOH A 11 411 6 HOH HOH . E 4 HOH A 12 412 17 HOH HOH . E 4 HOH A 13 413 22 HOH HOH . E 4 HOH A 14 414 20 HOH HOH . E 4 HOH A 15 415 10 HOH HOH . E 4 HOH A 16 416 14 HOH HOH . E 4 HOH A 17 417 3 HOH HOH . E 4 HOH A 18 418 9 HOH HOH . E 4 HOH A 19 419 4 HOH HOH . E 4 HOH A 20 420 13 HOH HOH . E 4 HOH A 21 421 7 HOH HOH . E 4 HOH A 22 422 21 HOH HOH . E 4 HOH A 23 423 23 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 9KU . . . D 3 65.065 80.498 3.064 1 95.27 ? C1 9KU 303 A 1 HETATM 2 C C10 9KU . . . D 3 71.838 81.471 6.759 1 120.77 ? C10 9KU 303 A 1 HETATM 3 C C11 9KU . . . D 3 72.634 81.995 7.79 1 121.97 ? C11 9KU 303 A 1 HETATM 4 C C12 9KU . . . D 3 72.914 81.266 8.903 1 121.33 ? C12 9KU 303 A 1 HETATM 5 C C13 9KU . . . D 3 72.409 79.953 9.056 1 119.07 ? C13 9KU 303 A 1 HETATM 6 C C14 9KU . . . D 3 71.601 79.41 8.023 1 117.57 ? C14 9KU 303 A 1 HETATM 7 C C15 9KU . . . D 3 71.09 78.098 8.164 1 114.07 ? C15 9KU 303 A 1 HETATM 8 C C16 9KU . . . D 3 71.374 77.365 9.283 1 113.67 ? C16 9KU 303 A 1 HETATM 9 C C17 9KU . . . D 3 72.173 77.902 10.304 1 115.17 ? C17 9KU 303 A 1 HETATM 10 C C18 9KU . . . D 3 72.677 79.159 10.196 1 117.61 ? C18 9KU 303 A 1 HETATM 11 C C19 9KU . . . D 3 69.542 82.373 2.779 1 108.21 ? C19 9KU 303 A 1 HETATM 12 C C2 9KU . . . D 3 64.029 80.876 3.913 1 93.31 ? C2 9KU 303 A 1 HETATM 13 C C20 9KU . . . D 3 68.551 83.151 1.946 1 109.36 ? C20 9KU 303 A 1 HETATM 14 C C21 9KU . . . D 3 67.902 84.044 2.992 1 110.41 ? C21 9KU 303 A 1 HETATM 15 C C3 9KU . . . D 3 64.205 81.915 4.777 1 91.16 ? C3 9KU 303 A 1 HETATM 16 C C4 9KU . . . D 3 63.093 82.345 5.713 1 82.94 ? C4 9KU 303 A 1 HETATM 17 C C5 9KU . . . D 3 66.36 82.264 4.039 1 102.04 ? C5 9KU 303 A 1 HETATM 18 C C6 9KU . . . D 3 67.64 83.063 4.148 1 107.57 ? C6 9KU 303 A 1 HETATM 19 C C7 9KU . . . D 3 69.14 81.327 5.027 1 112.06 ? C7 9KU 303 A 1 HETATM 20 C C8 9KU . . . D 3 70.227 80.318 4.762 1 113.89 ? C8 9KU 303 A 1 HETATM 21 C C9 9KU . . . D 3 71.327 80.205 6.872 1 118.34 ? C9 9KU 303 A 1 HETATM 22 N N1 9KU . . . D 3 65.352 82.605 4.843 1 97.87 ? N1 9KU 303 A 1 HETATM 23 N N2 9KU . . . D 3 68.818 82.183 4.044 1 108.82 ? N2 9KU 303 A 1 HETATM 24 N N3 9KU . . . D 3 66.232 81.224 3.156 1 99.44 ? N3 9KU 303 A 1 HETATM 25 O O1 9KU . . . D 3 64.983 79.564 2.252 1 91.34 ? O1 9KU 303 A 1 HETATM 26 O O2 9KU . . . D 3 62.895 80.167 3.82 1 92.24 ? O2 9KU 303 A 1 HETATM 27 O O3 9KU . . . D 3 63.338 83.28 6.496 1 90.22 -1 O3 9KU 303 A 1 HETATM 28 O O4 9KU . . . D 3 62.013 81.734 5.631 1 68.44 ? O4 9KU 303 A 1 HETATM 29 O O5 9KU . . . D 3 70.55 79.589 5.939 1 115.77 ? O5 9KU 303 A 1 HETATM 30 O O6 9KU . . . D 3 68.568 81.38 6.112 1 113.1 ? O6 9KU 303 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 30 #