data_1YOU # _model_server_result.job_id twOwFM4Nz5x3lFLkuhnpng _model_server_result.datetime_utc '2024-11-14 18:52:10' _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 1you # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":998}' # _entry.id 1YOU # _exptl.entry_id 1YOU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.373 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-(2-ETHOXYETHYL)-5-[4-(4-FLUOROPHENOXY)PHENOXY]PYRIMIDINE-2,4,6(1H,3H,5H)-TRIONE _entity.pdbx_number_of_molecules 2 _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 1YOU _cell.length_a 81.089 _cell.length_b 108.223 _cell.length_c 36.035 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YOU _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA,PQS tetrameric 4 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,N 1 1 B,I,J,K,L,M,O 2 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O 3 1,2 # 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' 2_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 81.089 108.223 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 H N N ? 5 M N 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 69 A HIS 172 1_555 D ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc2 A OD2 ASP 71 A ASP 174 1_555 D ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc3 A OD1 ASP 76 A ASP 179 1_555 E CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc4 A O GLY 77 A GLY 180 1_555 E CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc5 A O SER 79 A SER 182 1_555 E CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc6 A O LEU 81 A LEU 184 1_555 E CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc7 A NE2 HIS 84 A HIS 187 1_555 D ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc8 A ND1 HIS 97 A HIS 200 1_555 D ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.9 ? metalc ? metalc9 A OD2 ASP 99 A ASP 202 1_555 E CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc10 A OE2 GLU 102 A GLU 205 1_555 E CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc11 A NE2 HIS 119 A HIS 222 1_555 C ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc12 A NE2 HIS 123 A HIS 226 1_555 C ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc13 A NE2 HIS 129 A HIS 232 1_555 C ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc14 C ZN ZN . A ZN 301 1_555 H N9 PFD . A PFD 998 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc15 B NE2 HIS 69 B HIS 172 1_555 J ZN ZN . B ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.894 ? metalc ? metalc16 B OD2 ASP 71 B ASP 174 1_555 J ZN ZN . B ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? metalc ? metalc17 B OD1 ASP 76 B ASP 179 1_555 K CA CA . B CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc18 B O GLY 77 B GLY 180 1_555 K CA CA . B CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc19 B O SER 79 B SER 182 1_555 K CA CA . B CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc20 B O LEU 81 B LEU 184 1_555 K CA CA . B CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc21 B NE2 HIS 84 B HIS 187 1_555 J ZN ZN . B ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc22 B ND1 HIS 97 B HIS 200 1_555 J ZN ZN . B ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc23 B OD2 ASP 99 B ASP 202 1_555 K CA CA . B CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc24 B OE2 GLU 102 B GLU 205 1_555 K CA CA . B CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc25 B NE2 HIS 119 B HIS 222 1_555 I ZN ZN . B ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc26 B NE2 HIS 123 B HIS 226 1_555 I ZN ZN . B ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc27 B NE2 HIS 129 B HIS 232 1_555 I ZN ZN . B ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc28 I ZN ZN . B ZN 303 1_555 M N9 PFD . B PFD 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? # _chem_comp.formula 'C20 H19 F N2 O6' _chem_comp.formula_weight 402.373 _chem_comp.id PFD _chem_comp.mon_nstd_flag . _chem_comp.name 5-(2-ETHOXYETHYL)-5-[4-(4-FLUOROPHENOXY)PHENOXY]PYRIMIDINE-2,4,6(1H,3H,5H)-TRIONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 F29 C28 PFD sing 224 n n C28 C26 PFD doub 225 n y C28 C27 PFD sing 226 n y C26 C24 PFD sing 227 n y C26 H26 PFD sing 228 n n C24 C23 PFD doub 229 n y C24 H24 PFD sing 230 n n C27 C25 PFD doub 231 n y C27 H27 PFD sing 232 n n C25 C23 PFD sing 233 n y C25 H25 PFD sing 234 n n C23 O22 PFD sing 235 n n O22 C20 PFD sing 236 n n C20 C16 PFD doub 237 n y C20 C17 PFD sing 238 n y C16 C12 PFD sing 239 n y C16 H16 PFD sing 240 n n C12 C6 PFD doub 241 n y C12 H12 PFD sing 242 n n C17 C13 PFD doub 243 n y C17 H17 PFD sing 244 n n C13 C6 PFD sing 245 n y C13 H13 PFD sing 246 n n C6 O2 PFD sing 247 n n O2 C1 PFD sing 248 n n C1 C5 PFD sing 249 n n C1 C4 PFD sing 250 n n C1 C3 PFD sing 251 n n C5 C11 PFD sing 252 n n C5 H51 PFD sing 253 n n C5 H52 PFD sing 254 n n C11 O15 PFD sing 255 n n C11 H111 PFD sing 256 n n C11 H112 PFD sing 257 n n O15 C19 PFD sing 258 n n C19 C21 PFD sing 259 n n C19 H191 PFD sing 260 n n C19 H192 PFD sing 261 n n C21 H211 PFD sing 262 n n C21 H212 PFD sing 263 n n C21 H213 PFD sing 264 n n C4 O10 PFD doub 265 n n C4 N9 PFD sing 266 n n N9 C14 PFD sing 267 n n N9 HN9 PFD sing 268 n n C14 O18 PFD doub 269 n n C14 N7 PFD sing 270 n n N7 C3 PFD sing 271 n n N7 HN7 PFD sing 272 n n C3 O8 PFD doub 273 n n # _atom_sites.entry_id 1YOU _atom_sites.fract_transf_matrix[1][1] 0.012332 _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] 0.00924 _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] 0.027751 _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 C 2 ZN A 1 301 1 ZN ZN . D 2 ZN A 1 302 2 ZN ZN . E 3 CA A 1 401 1 CA CA . F 4 SO4 A 1 501 1 SO4 SO4 . G 4 SO4 A 1 502 2 SO4 SO4 . H 5 PFD A 1 998 998 PFD PFE . I 2 ZN B 1 303 3 ZN ZN . J 2 ZN B 1 304 4 ZN ZN . K 3 CA B 1 403 3 CA CA . L 4 SO4 B 1 503 3 SO4 SO4 . M 5 PFD B 1 999 999 PFD PFE . N 6 HOH A 1 1 1 HOH HOH . N 6 HOH A 2 3 3 HOH HOH . N 6 HOH A 3 4 4 HOH HOH . N 6 HOH A 4 6 6 HOH HOH . N 6 HOH A 5 7 7 HOH HOH . N 6 HOH A 6 10 10 HOH HOH . N 6 HOH A 7 12 12 HOH HOH . N 6 HOH A 8 13 13 HOH HOH . N 6 HOH A 9 14 14 HOH HOH . N 6 HOH A 10 16 16 HOH HOH . O 6 HOH B 1 2 2 HOH HOH . O 6 HOH B 2 5 5 HOH HOH . O 6 HOH B 3 8 8 HOH HOH . O 6 HOH B 4 9 9 HOH HOH . O 6 HOH B 5 11 11 HOH HOH . O 6 HOH B 6 15 15 HOH HOH . O 6 HOH B 7 17 17 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 F F29 PFD . . . H 5 42.089 29.535 -7.333 1 16.87 ? F29 PFD 998 A 1 HETATM 2 C C28 PFD . . . H 5 41.762 30.46 -6.43 1 19.83 ? C28 PFD 998 A 1 HETATM 3 C C26 PFD . . . H 5 40.411 30.768 -6.227 1 19.07 ? C26 PFD 998 A 1 HETATM 4 C C24 PFD . . . H 5 40.078 31.762 -5.314 1 22.62 ? C24 PFD 998 A 1 HETATM 5 C C27 PFD . . . H 5 42.786 31.133 -5.754 1 17.46 ? C27 PFD 998 A 1 HETATM 6 C C25 PFD . . . H 5 42.428 32.103 -4.823 1 21.7 ? C25 PFD 998 A 1 HETATM 7 C C23 PFD . . . H 5 41.083 32.413 -4.601 1 20.87 ? C23 PFD 998 A 1 HETATM 8 O O22 PFD . . . H 5 40.723 33.336 -3.688 1 24.66 ? O22 PFD 998 A 1 HETATM 9 C C20 PFD . . . H 5 41.06 34.671 -3.66 1 29.55 ? C20 PFD 998 A 1 HETATM 10 C C16 PFD . . . H 5 41.423 35.378 -4.797 1 30.31 ? C16 PFD 998 A 1 HETATM 11 C C12 PFD . . . H 5 41.74 36.746 -4.661 1 32.61 ? C12 PFD 998 A 1 HETATM 12 C C17 PFD . . . H 5 41.018 35.338 -2.423 1 29.96 ? C17 PFD 998 A 1 HETATM 13 C C13 PFD . . . H 5 41.346 36.693 -2.298 1 28.93 ? C13 PFD 998 A 1 HETATM 14 C C6 PFD . . . H 5 41.701 37.409 -3.43 1 30.61 ? C6 PFD 998 A 1 HETATM 15 O O2 PFD . . . H 5 42.124 38.73 -3.323 1 34.78 ? O2 PFD 998 A 1 HETATM 16 C C1 PFD . . . H 5 43.304 39.044 -2.432 1 38.34 ? C1 PFD 998 A 1 HETATM 17 C C5 PFD . . . H 5 44.303 40.141 -2.897 1 39.09 ? C5 PFD 998 A 1 HETATM 18 C C11 PFD . . . H 5 44.938 40.989 -1.755 1 41.15 ? C11 PFD 998 A 1 HETATM 19 O O15 PFD . . . H 5 46.166 40.468 -1.167 1 40.72 ? O15 PFD 998 A 1 HETATM 20 C C19 PFD . . . H 5 46.134 40.352 0.279 1 37.97 ? C19 PFD 998 A 1 HETATM 21 C C21 PFD . . . H 5 47.443 39.903 0.917 1 33.16 ? C21 PFD 998 A 1 HETATM 22 C C4 PFD . . . H 5 44.288 37.949 -1.987 1 36.62 ? C4 PFD 998 A 1 HETATM 23 O O10 PFD . . . H 5 45.057 37.415 -2.796 1 38.35 ? O10 PFD 998 A 1 HETATM 24 N N9 PFD . . . H 5 44.425 37.54 -0.702 1 35.03 ? N9 PFD 998 A 1 HETATM 25 C C14 PFD . . . H 5 43.644 38.078 0.246 1 35.08 ? C14 PFD 998 A 1 HETATM 26 O O18 PFD . . . H 5 43.787 37.632 1.492 1 38.43 ? O18 PFD 998 A 1 HETATM 27 N N7 PFD . . . H 5 42.743 39.039 -0.003 1 36.56 ? N7 PFD 998 A 1 HETATM 28 C C3 PFD . . . H 5 42.545 39.538 -1.245 1 36.36 ? C3 PFD 998 A 1 HETATM 29 O O8 PFD . . . H 5 41.703 40.406 -1.514 1 35.84 ? O8 PFD 998 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 29 #