data_5W7U # _model_server_result.job_id CHz6O0ZZXCJv7mD1hrmD4w _model_server_result.datetime_utc '2024-11-16 15:51:06' _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 5w7u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 5W7U # _exptl.entry_id 5W7U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 514.361 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-[(2S)-1-(3,5-dichloropyridine-4-carbonyl)pyrrolidin-2-yl]-N-(2,3-dihydro-1H-inden-2-yl)-5-hydroxy-6-oxo-1,6-dihydropy rimidine-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 5W7U _cell.length_a 90.746 _cell.length_b 90.746 _cell.length_c 135.256 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5W7U _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc2 A OE2 GLU 81 A GLU 80 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc3 A OD2 ASP 109 A ASP 108 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc4 A OD1 ASP 109 A ASP 108 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc5 A OE1 GLU 120 A GLU 119 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? metalc ? metalc6 A O ILE 121 A ILE 120 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc7 B MN MN . A MN 201 1_555 D O4 GY8 . A GY8 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? metalc ? metalc8 B MN MN . A MN 201 1_555 D O3 GY8 . A GY8 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc9 C MN MN . A MN 202 1_555 D O2 GY8 . A GY8 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc10 C MN MN . A MN 202 1_555 D O3 GY8 . A GY8 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.834 ? metalc ? metalc11 C MN MN . A MN 202 1_555 E O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.828 ? metalc ? metalc12 C MN MN . A MN 202 1_555 E O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? # _chem_comp.formula 'C24 H21 Cl2 N5 O4' _chem_comp.formula_weight 514.361 _chem_comp.id GY8 _chem_comp.mon_nstd_flag . _chem_comp.name '2-[(2S)-1-(3,5-dichloropyridine-4-carbonyl)pyrrolidin-2-yl]-N-(2,3-dihydro-1H-inden-2-yl)-5-hydroxy-6-oxo-1,6-dihydropy rimidine-4-carboxamide' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms SRI-29928 # 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 C14 C13 GY8 doub 129 n y C14 C15 GY8 sing 130 n y C13 C12 GY8 sing 131 n y C15 C10 GY8 doub 132 n y C12 C11 GY8 doub 133 n y C10 C11 GY8 sing 134 n y C10 C9 GY8 sing 135 n n C11 C16 GY8 sing 136 n n O1 C3 GY8 doub 137 n n C9 C8 GY8 sing 138 n n C16 C8 GY8 sing 139 n n CL2 C22 GY8 sing 140 n n C3 C2 GY8 sing 141 n n C3 N1 GY8 sing 142 n n C8 N3 GY8 sing 143 n n C22 C2 GY8 doub 144 n y C22 C23 GY8 sing 145 n y C2 C1 GY8 sing 146 n y C23 N5 GY8 doub 147 n y C21 N1 GY8 sing 148 n n C21 C20 GY8 sing 149 n n N3 C7 GY8 sing 150 n n C1 CL1 GY8 sing 151 n n C1 C24 GY8 doub 152 n y N1 C4 GY8 sing 153 n n N5 C24 GY8 sing 154 n y C7 O2 GY8 doub 155 n n C7 C6 GY8 sing 156 n n C20 C19 GY8 sing 157 n n N2 C6 GY8 sing 158 n n N2 C5 GY8 doub 159 n n C4 C5 GY8 sing 160 n n C4 C19 GY8 sing 161 n n C6 C17 GY8 doub 162 n n C5 N4 GY8 sing 163 n n C17 O3 GY8 sing 164 n n C17 C18 GY8 sing 165 n n N4 C18 GY8 sing 166 n n C18 O4 GY8 doub 167 n n C12 H1 GY8 sing 168 n n C13 H2 GY8 sing 169 n n C14 H3 GY8 sing 170 n n C15 H4 GY8 sing 171 n n C16 H5 GY8 sing 172 n n C16 H6 GY8 sing 173 n n C19 H7 GY8 sing 174 n n C19 H8 GY8 sing 175 n n C20 H9 GY8 sing 176 n n C20 H10 GY8 sing 177 n n C21 H11 GY8 sing 178 n n C21 H12 GY8 sing 179 n n C23 H13 GY8 sing 180 n n C24 H14 GY8 sing 181 n n C4 H15 GY8 sing 182 n n C8 H16 GY8 sing 183 n n C9 H17 GY8 sing 184 n n C9 H18 GY8 sing 185 n n N3 H19 GY8 sing 186 n n N4 H20 GY8 sing 187 n n O3 H21 GY8 sing 188 n n # _atom_sites.entry_id 5W7U _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] 0.007393 _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 GY8 A 1 203 1 GY8 GY8 . E 4 HOH A 1 301 5 HOH HOH . E 4 HOH A 2 302 6 HOH HOH . E 4 HOH A 3 303 7 HOH HOH . E 4 HOH A 4 304 3 HOH HOH . E 4 HOH A 5 305 4 HOH HOH . E 4 HOH A 6 306 10 HOH HOH . E 4 HOH A 7 307 8 HOH HOH . E 4 HOH A 8 308 1 HOH HOH . E 4 HOH A 9 309 9 HOH HOH . E 4 HOH A 10 310 11 HOH HOH . E 4 HOH A 11 311 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 GY8 . . . D 3 126.349 105.321 285.582 1 124.04 ? C1 GY8 203 A 1 HETATM 2 C C10 GY8 . . . D 3 132.989 105.219 282.573 1 90.67 ? C10 GY8 203 A 1 HETATM 3 C C11 GY8 . . . D 3 133.011 103.853 282.816 1 93.86 ? C11 GY8 203 A 1 HETATM 4 C C12 GY8 . . . D 3 132.265 102.987 282.03 1 94.69 ? C12 GY8 203 A 1 HETATM 5 C C13 GY8 . . . D 3 131.501 103.509 281 1 89.55 ? C13 GY8 203 A 1 HETATM 6 C C14 GY8 . . . D 3 131.476 104.87 280.76 1 86.79 ? C14 GY8 203 A 1 HETATM 7 C C15 GY8 . . . D 3 132.221 105.738 281.54 1 87.93 ? C15 GY8 203 A 1 HETATM 8 C C16 GY8 . . . D 3 133.921 103.562 283.981 1 94.56 ? C16 GY8 203 A 1 HETATM 9 C C17 GY8 . . . D 3 131.067 106.45 288.446 1 77.23 ? C17 GY8 203 A 1 HETATM 10 C C18 GY8 . . . D 3 129.824 106.348 289.08 1 79.17 ? C18 GY8 203 A 1 HETATM 11 C C19 GY8 . . . D 3 128.711 102.014 287.723 1 107.16 ? C19 GY8 203 A 1 HETATM 12 C C2 GY8 . . . D 3 127.649 105.248 285.074 1 116.49 ? C2 GY8 203 A 1 HETATM 13 C C20 GY8 . . . D 3 129.821 101.468 286.838 1 111.72 ? C20 GY8 203 A 1 HETATM 14 C C21 GY8 . . . D 3 129.325 101.822 285.451 1 114.1 ? C21 GY8 203 A 1 HETATM 15 C C22 GY8 . . . D 3 128.367 106.444 285.011 1 118.5 ? C22 GY8 203 A 1 HETATM 16 C C23 GY8 . . . D 3 127.763 107.625 285.422 1 118.64 ? C23 GY8 203 A 1 HETATM 17 C C24 GY8 . . . D 3 125.825 106.544 285.978 1 121.91 ? C24 GY8 203 A 1 HETATM 18 C C3 GY8 . . . D 3 128.253 103.932 284.676 1 109.3 ? C3 GY8 203 A 1 HETATM 19 C C4 GY8 . . . D 3 128.46 103.401 287.107 1 106.46 ? C4 GY8 203 A 1 HETATM 20 C C5 GY8 . . . D 3 129.36 104.507 287.615 1 98.63 ? C5 GY8 203 A 1 HETATM 21 C C6 GY8 . . . D 3 131.399 105.584 287.442 1 85.43 ? C6 GY8 203 A 1 HETATM 22 C C7 GY8 . . . D 3 132.711 105.656 286.709 1 90.9 ? C7 GY8 203 A 1 HETATM 23 C C8 GY8 . . . D 3 133.936 104.911 284.727 1 94.22 ? C8 GY8 203 A 1 HETATM 24 C C9 GY8 . . . D 3 133.88 105.921 283.563 1 92.82 ? C9 GY8 203 A 1 HETATM 25 N N1 GY8 . . . D 3 128.649 103.115 285.664 1 113.49 ? N1 GY8 203 A 1 HETATM 26 N N2 GY8 . . . D 3 130.548 104.638 287.02 1 91.23 ? N2 GY8 203 A 1 HETATM 27 N N3 GY8 . . . D 3 132.739 105.011 285.538 1 96.5 ? N3 GY8 203 A 1 HETATM 28 N N4 GY8 . . . D 3 128.984 105.351 288.632 1 89.91 ? N4 GY8 203 A 1 HETATM 29 N N5 GY8 . . . D 3 126.521 107.673 285.898 1 121.21 ? N5 GY8 203 A 1 HETATM 30 O O1 GY8 . . . D 3 128.402 103.627 283.493 1 99.87 ? O1 GY8 203 A 1 HETATM 31 O O2 GY8 . . . D 3 133.678 106.292 287.13 1 87.75 ? O2 GY8 203 A 1 HETATM 32 O O3 GY8 . . . D 3 131.88 107.417 288.89 1 77.98 ? O3 GY8 203 A 1 HETATM 33 O O4 GY8 . . . D 3 129.45 107.093 290.004 1 78.28 ? O4 GY8 203 A 1 HETATM 34 CL CL1 GY8 . . . D 3 125.379 103.902 285.71 1 130.14 ? CL1 GY8 203 A 1 HETATM 35 CL CL2 GY8 . . . D 3 129.984 106.478 284.411 1 119.84 ? CL2 GY8 203 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 35 #