data_5WDW # _model_server_result.job_id lPkcthfl-B9wfwiG5M-S_Q _model_server_result.datetime_utc '2024-11-24 20:28:00' _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 5wdw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 5WDW # _exptl.entry_id 5WDW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 541.018 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-[(2S)-1-{[(2-chlorophenyl)sulfanyl]acetyl}pyrrolidin-2-yl]-N-{[(2S)-2,3-dihydro-1-benzofuran-2-yl]methyl}-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 5WDW _cell.length_a 90.744 _cell.length_b 90.744 _cell.length_c 135.876 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WDW _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc2 A OE2 GLU 81 A GLU 80 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc3 A OD2 ASP 109 A ASP 108 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc4 A OD1 ASP 109 A ASP 108 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? metalc ? metalc5 A OE1 GLU 120 A GLU 119 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc6 A O ILE 121 A ILE 120 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc7 B MN MN . A MN 201 1_555 D O1 8KU . A 8KU 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc8 B MN MN . A MN 201 1_555 D O2 8KU . A 8KU 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc9 C MN MN . A MN 202 1_555 D O4 8KU . A 8KU 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc10 C MN MN . A MN 202 1_555 D O2 8KU . A 8KU 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc11 C MN MN . A MN 202 1_555 E O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc12 C MN MN . A MN 202 1_555 E O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.914 ? # _chem_comp.formula 'C26 H25 Cl N4 O5 S' _chem_comp.formula_weight 541.018 _chem_comp.id 8KU _chem_comp.mon_nstd_flag . _chem_comp.name 2-[(2S)-1-{[(2-chlorophenyl)sulfanyl]acetyl}pyrrolidin-2-yl]-N-{[(2S)-2,3-dihydro-1-benzofuran-2-yl]methyl}-5-hydroxy-6-oxo-1,6-dihydropyrimidine-4-carboxamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms SRI-30027 # 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 C10 C9 8KU doub 1 n y C10 C11 8KU sing 2 n y C9 C8 8KU sing 3 n y C11 C12 8KU doub 4 n y C8 C7 8KU doub 5 n y C12 C7 8KU sing 6 n y C12 C13 8KU sing 7 n n C7 O3 8KU sing 8 n n C13 C6 8KU sing 9 n n O3 C6 8KU sing 10 n n S1 C17 8KU sing 11 n n S1 C18 8KU sing 12 n n C6 C5 8KU sing 13 n n O5 C16 8KU doub 14 n n C17 C16 8KU sing 15 n n C18 C19 8KU doub 16 n y C18 C23 8KU sing 17 n y CL1 C23 8KU sing 18 n n C16 N3 8KU sing 19 n n C19 C20 8KU sing 20 n y C5 N1 8KU sing 21 n n C23 C22 8KU doub 22 n y N1 C4 8KU sing 23 n n N3 C24 8KU sing 24 n n N3 C15 8KU sing 25 n n C20 C21 8KU doub 26 n y C22 C21 8KU sing 27 n y C24 C25 8KU sing 28 n n C4 O4 8KU doub 29 n n C4 C3 8KU sing 30 n n N2 C3 8KU sing 31 n n N2 C14 8KU doub 32 n n C15 C14 8KU sing 33 n n C15 C26 8KU sing 34 n n C3 C2 8KU doub 35 n n C14 N4 8KU sing 36 n n C25 C26 8KU sing 37 n n C2 O2 8KU sing 38 n n C2 C1 8KU sing 39 n n N4 C1 8KU sing 40 n n C1 O1 8KU doub 41 n n C10 H1 8KU sing 42 n n C11 H2 8KU sing 43 n n C13 H3 8KU sing 44 n n C13 H4 8KU sing 45 n n C15 H5 8KU sing 46 n n C17 H6 8KU sing 47 n n C17 H7 8KU sing 48 n n C19 H8 8KU sing 49 n n C20 H9 8KU sing 50 n n C21 H10 8KU sing 51 n n C22 H11 8KU sing 52 n n C24 H12 8KU sing 53 n n C24 H13 8KU sing 54 n n C25 H14 8KU sing 55 n n C25 H15 8KU sing 56 n n C26 H16 8KU sing 57 n n C26 H17 8KU sing 58 n n C5 H18 8KU sing 59 n n C5 H19 8KU sing 60 n n C6 H20 8KU sing 61 n n C8 H21 8KU sing 62 n n C9 H22 8KU sing 63 n n N1 H23 8KU sing 64 n n N4 H24 8KU sing 65 n n O2 H25 8KU sing 66 n n # _atom_sites.entry_id 5WDW _atom_sites.fract_transf_matrix[1][1] 0.01102 _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] 0.01102 _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] 0.00736 _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 8KU A 1 203 1 8KU 8KU . E 4 HOH A 1 301 4 HOH HOH . E 4 HOH A 2 302 3 HOH HOH . E 4 HOH A 3 303 1 HOH HOH . E 4 HOH A 4 304 2 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 8KU . . . D 3 29.835 447.41 697.657 1 83.58 ? C1 8KU 203 A 1 HETATM 2 C C10 8KU . . . D 3 31.564 448.761 689.271 1 90.49 ? C10 8KU 203 A 1 HETATM 3 C C11 8KU . . . D 3 30.712 449.478 690.1 1 89.61 ? C11 8KU 203 A 1 HETATM 4 C C12 8KU . . . D 3 31.279 450.222 691.125 1 89.48 ? C12 8KU 203 A 1 HETATM 5 C C13 8KU . . . D 3 30.662 451.096 692.184 1 88.81 ? C13 8KU 203 A 1 HETATM 6 C C14 8KU . . . D 3 31.933 447.101 696.535 1 85.65 ? C14 8KU 203 A 1 HETATM 7 C C15 8KU . . . D 3 33.144 446.246 696.224 1 90.65 ? C15 8KU 203 A 1 HETATM 8 C C16 8KU . . . D 3 33.761 446.391 693.783 1 115.35 ? C16 8KU 203 A 1 HETATM 9 C C17 8KU . . . D 3 32.412 446.667 693.151 1 126.53 ? C17 8KU 203 A 1 HETATM 10 C C18 8KU . . . D 3 30.453 444.634 693.687 1 132.96 ? C18 8KU 203 A 1 HETATM 11 C C19 8KU . . . D 3 30.548 443.308 694.115 1 130.79 ? C19 8KU 203 A 1 HETATM 12 C C2 8KU . . . D 3 29.805 448.692 697.116 1 88.13 ? C2 8KU 203 A 1 HETATM 13 C C20 8KU . . . D 3 29.687 442.829 695.085 1 127.88 ? C20 8KU 203 A 1 HETATM 14 C C21 8KU . . . D 3 28.728 443.653 695.631 1 126.55 ? C21 8KU 203 A 1 HETATM 15 C C22 8KU . . . D 3 28.617 444.962 695.218 1 128.67 ? C22 8KU 203 A 1 HETATM 16 C C23 8KU . . . D 3 29.472 445.448 694.248 1 133.68 ? C23 8KU 203 A 1 HETATM 17 C C24 8KU . . . D 3 35.094 447.472 695.575 1 95.12 ? C24 8KU 203 A 1 HETATM 18 C C25 8KU . . . D 3 35.507 446.6 696.726 1 93.23 ? C25 8KU 203 A 1 HETATM 19 C C26 8KU . . . D 3 34.168 446.274 697.38 1 89.63 ? C26 8KU 203 A 1 HETATM 20 C C3 8KU . . . D 3 30.833 449.119 696.325 1 87.72 ? C3 8KU 203 A 1 HETATM 21 C C4 8KU . . . D 3 30.81 450.502 695.733 1 87.65 ? C4 8KU 203 A 1 HETATM 22 C C5 8KU . . . D 3 31.922 452.064 694.219 1 89.87 ? C5 8KU 203 A 1 HETATM 23 C C6 8KU . . . D 3 31.892 451.838 692.72 1 89.78 ? C6 8KU 203 A 1 HETATM 24 C C7 8KU . . . D 3 32.653 450.242 691.289 1 91.11 ? C7 8KU 203 A 1 HETATM 25 C C8 8KU . . . D 3 33.515 449.525 690.483 1 92.55 ? C8 8KU 203 A 1 HETATM 26 C C9 8KU . . . D 3 32.939 448.788 689.464 1 91.65 ? C9 8KU 203 A 1 HETATM 27 N N1 8KU . . . D 3 31.849 450.816 694.963 1 90.54 ? N1 8KU 203 A 1 HETATM 28 N N2 8KU . . . D 3 31.89 448.342 696.043 1 91.34 ? N2 8KU 203 A 1 HETATM 29 N N3 8KU . . . D 3 33.957 446.697 695.079 1 100.34 ? N3 8KU 203 A 1 HETATM 30 N N4 8KU . . . D 3 30.931 446.633 697.347 1 77.41 ? N4 8KU 203 A 1 HETATM 31 O O1 8KU . . . D 3 28.94 446.951 698.382 1 78.89 ? O1 8KU 203 A 1 HETATM 32 O O2 8KU . . . D 3 28.737 449.44 697.42 1 87.98 ? O2 8KU 203 A 1 HETATM 33 O O3 8KU . . . D 3 33.049 451.009 692.344 1 92.3 ? O3 8KU 203 A 1 HETATM 34 O O4 8KU . . . D 3 29.87 451.269 695.935 1 79.32 ? O4 8KU 203 A 1 HETATM 35 O O5 8KU . . . D 3 34.664 445.891 693.117 1 119.24 ? O5 8KU 203 A 1 HETATM 36 S S1 8KU . . . D 3 31.56 445.227 692.442 1 136.53 ? S1 8KU 203 A 1 HETATM 37 CL CL1 8KU . . . D 3 29.296 447.098 693.753 1 140.02 ? CL1 8KU 203 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 37 #