data_5W73 # _model_server_result.job_id DbbrcIbOqjcEFjUHQNgTIQ _model_server_result.datetime_utc '2024-11-24 21:24:19' _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 5w73 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":205}' # _entry.id 5W73 # _exptl.entry_id 5W73 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 512.942 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-{(2S)-1-[(2-chlorophenoxy)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 5W73 _cell.length_a 89.843 _cell.length_b 89.843 _cell.length_c 135.002 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5W73 _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,F,G _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 4 _struct_asym.id F _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc2 A OE1 GLU 81 A GLU 80 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc3 A OD2 ASP 109 A ASP 108 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc4 A OD1 ASP 109 A ASP 108 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc5 A OE2 GLU 120 A GLU 119 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc6 A O ILE 121 A ILE 120 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc7 B MN MN . A MN 201 1_555 F O1 GY9 . A GY9 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc8 B MN MN . A MN 201 1_555 F O2 GY9 . A GY9 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? metalc ? metalc9 C MN MN . A MN 202 1_555 F O3 GY9 . A GY9 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc10 C MN MN . A MN 202 1_555 F O1 GY9 . A GY9 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc11 C MN MN . A MN 202 1_555 G O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc12 C MN MN . A MN 202 1_555 G O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.822 ? # _chem_comp.formula 'C25 H25 Cl N4 O6' _chem_comp.formula_weight 512.942 _chem_comp.id GY9 _chem_comp.mon_nstd_flag . _chem_comp.name 2-{(2S)-1-[(2-chlorophenoxy)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 SRI-29835 # 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 GY9 doub 129 n y C20 C21 GY9 sing 130 n y C25 C24 GY9 sing 131 n y C21 C22 GY9 doub 132 n y C24 C23 GY9 doub 133 n y C22 C23 GY9 sing 134 n y C23 O6 GY9 sing 135 n n O6 C13 GY9 sing 136 n n C13 C12 GY9 sing 137 n n O5 C10 GY9 doub 138 n n C11 O4 GY9 sing 139 n n C11 C10 GY9 sing 140 n n CL1 C16 GY9 sing 141 n n C12 N3 GY9 sing 142 n n O4 C17 GY9 sing 143 n n C10 N4 GY9 sing 144 n n C16 C17 GY9 doub 145 n y C16 C15 GY9 sing 146 n y C17 C18 GY9 sing 147 n y N3 C5 GY9 sing 148 n n C15 C14 GY9 doub 149 n y C18 C19 GY9 doub 150 n y N4 C9 GY9 sing 151 n n N4 C8 GY9 sing 152 n n C14 C19 GY9 sing 153 n y C5 O3 GY9 doub 154 n n C5 C2 GY9 sing 155 n n C9 C6 GY9 sing 156 n n N1 C2 GY9 sing 157 n n N1 C1 GY9 doub 158 n n C2 C3 GY9 doub 159 n n C8 C1 GY9 sing 160 n n C8 C7 GY9 sing 161 n n C1 N2 GY9 sing 162 n n C3 O1 GY9 sing 163 n n C3 C4 GY9 sing 164 n n C6 C7 GY9 sing 165 n n N2 C4 GY9 sing 166 n n C4 O2 GY9 doub 167 n n C11 H1 GY9 sing 168 n n C11 H2 GY9 sing 169 n n C12 H3 GY9 sing 170 n n C12 H4 GY9 sing 171 n n C13 H5 GY9 sing 172 n n C13 H6 GY9 sing 173 n n C14 H7 GY9 sing 174 n n C15 H8 GY9 sing 175 n n C18 H9 GY9 sing 176 n n C19 H10 GY9 sing 177 n n C20 H11 GY9 sing 178 n n C21 H12 GY9 sing 179 n n C22 H13 GY9 sing 180 n n C24 H14 GY9 sing 181 n n C25 H15 GY9 sing 182 n n C6 H16 GY9 sing 183 n n C6 H17 GY9 sing 184 n n C7 H18 GY9 sing 185 n n C7 H19 GY9 sing 186 n n C8 H20 GY9 sing 187 n n C9 H21 GY9 sing 188 n n C9 H22 GY9 sing 189 n n N2 H23 GY9 sing 190 n n N3 H24 GY9 sing 191 n n O1 H25 GY9 sing 192 n n # _atom_sites.entry_id 5W73 _atom_sites.fract_transf_matrix[1][1] 0.011131 _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] 0.011131 _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] 0.007407 _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 SO4 A 1 203 2 SO4 SO4 . E 3 SO4 A 1 204 3 SO4 SO4 . F 4 GY9 A 1 205 1 GY9 GY9 . G 5 HOH A 1 301 24 HOH HOH . G 5 HOH A 2 302 61 HOH HOH . G 5 HOH A 3 303 63 HOH HOH . G 5 HOH A 4 304 16 HOH HOH . G 5 HOH A 5 305 62 HOH HOH . G 5 HOH A 6 306 19 HOH HOH . G 5 HOH A 7 307 64 HOH HOH . G 5 HOH A 8 308 68 HOH HOH . G 5 HOH A 9 309 65 HOH HOH . G 5 HOH A 10 310 67 HOH HOH . G 5 HOH A 11 311 66 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 GY9 . . . F 4 128.31 103.05 287.436 1 96.66 ? C1 GY9 205 A 1 HETATM 2 C C10 GY9 . . . F 4 127.696 101.442 284.731 1 106.38 ? C10 GY9 205 A 1 HETATM 3 C C11 GY9 . . . F 4 127.489 102.915 284.431 1 109.04 ? C11 GY9 205 A 1 HETATM 4 C C12 GY9 . . . F 4 132.887 103.066 284.531 1 94.89 ? C12 GY9 205 A 1 HETATM 5 C C13 GY9 . . . F 4 132.374 103.122 283.114 1 99.9 ? C13 GY9 205 A 1 HETATM 6 C C14 GY9 . . . F 4 123.875 105.506 286.761 1 114.94 ? C14 GY9 205 A 1 HETATM 7 C C15 GY9 . . . F 4 124.973 106.049 286.146 1 106.21 ? C15 GY9 205 A 1 HETATM 8 C C16 GY9 . . . F 4 125.722 105.281 285.264 1 118.99 ? C16 GY9 205 A 1 HETATM 9 C C17 GY9 . . . F 4 125.375 103.953 284.983 1 123.1 ? C17 GY9 205 A 1 HETATM 10 C C18 GY9 . . . F 4 124.252 103.429 285.619 1 117.84 ? C18 GY9 205 A 1 HETATM 11 C C19 GY9 . . . F 4 123.514 104.203 286.502 1 116.84 ? C19 GY9 205 A 1 HETATM 12 C C2 GY9 . . . F 4 130.272 104.19 287.001 1 90.97 ? C2 GY9 205 A 1 HETATM 13 C C20 GY9 . . . F 4 129.131 101.968 279.495 1 91.02 ? C20 GY9 205 A 1 HETATM 14 C C21 GY9 . . . F 4 129.099 100.916 280.38 1 101.93 ? C21 GY9 205 A 1 HETATM 15 C C22 GY9 . . . F 4 129.875 100.931 281.529 1 104.11 ? C22 GY9 205 A 1 HETATM 16 C C23 GY9 . . . F 4 130.697 102.019 281.782 1 100.58 ? C23 GY9 205 A 1 HETATM 17 C C24 GY9 . . . F 4 130.729 103.087 280.894 1 93.8 ? C24 GY9 205 A 1 HETATM 18 C C25 GY9 . . . F 4 129.945 103.047 279.752 1 90.53 ? C25 GY9 205 A 1 HETATM 19 C C3 GY9 . . . F 4 129.901 105.224 287.808 1 86.41 ? C3 GY9 205 A 1 HETATM 20 C C4 GY9 . . . F 4 128.671 105.179 288.468 1 82.94 ? C4 GY9 205 A 1 HETATM 21 C C5 GY9 . . . F 4 131.585 104.193 286.267 1 89.98 ? C5 GY9 205 A 1 HETATM 22 C C6 GY9 . . . F 4 128.794 99.976 287.854 1 103.55 ? C6 GY9 205 A 1 HETATM 23 C C7 GY9 . . . F 4 127.566 100.754 288.299 1 100.09 ? C7 GY9 205 A 1 HETATM 24 C C8 GY9 . . . F 4 127.454 101.823 287.198 1 97.57 ? C8 GY9 205 A 1 HETATM 25 C C9 GY9 . . . F 4 128.506 99.779 286.386 1 102.52 ? C9 GY9 205 A 1 HETATM 26 N N1 GY9 . . . F 4 129.489 103.117 286.818 1 98.53 ? N1 GY9 205 A 1 HETATM 27 N N2 GY9 . . . F 4 127.894 104.066 288.247 1 88.09 ? N2 GY9 205 A 1 HETATM 28 N N3 GY9 . . . F 4 131.775 103.146 285.463 1 90.77 ? N3 GY9 205 A 1 HETATM 29 N N4 GY9 . . . F 4 127.866 101.048 286.009 1 98.68 ? N4 GY9 205 A 1 HETATM 30 O O1 GY9 . . . F 4 130.663 106.305 288.02 1 85.17 ? O1 GY9 205 A 1 HETATM 31 O O2 GY9 . . . F 4 128.25 106.067 289.224 1 72.85 ? O2 GY9 205 A 1 HETATM 32 O O3 GY9 . . . F 4 132.399 105.108 286.384 1 87.1 ? O3 GY9 205 A 1 HETATM 33 O O4 GY9 . . . F 4 126.149 103.257 284.089 1 120 ? O4 GY9 205 A 1 HETATM 34 O O5 GY9 . . . F 4 127.713 100.615 283.824 1 112.22 ? O5 GY9 205 A 1 HETATM 35 O O6 GY9 . . . F 4 131.464 102.035 282.918 1 105.92 ? O6 GY9 205 A 1 HETATM 36 CL CL1 GY9 . . . F 4 127.104 106.011 284.503 1 128.79 ? CL1 GY9 205 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #