data_1YOU
#
_model_server_result.job_id            GyTIR0XLRlIfGAxNuDSWtQ 
_model_server_result.datetime_utc      '2024-11-14 19:16:04' 
_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":"M","auth_seq_id":999}' 
#
_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 . . . M 5 69.66 55.552 24.989 1 29.31 ? F29 PFD 999 B 1 
HETATM 2 C C28 PFD . . . M 5 68.531 55.801 24.348 1 28.64 ? C28 PFD 999 B 1 
HETATM 3 C C26 PFD . . . M 5 68.276 57.077 23.863 1 27.36 ? C26 PFD 999 B 1 
HETATM 4 C C24 PFD . . . M 5 67.086 57.279 23.18 1 27.58 ? C24 PFD 999 B 1 
HETATM 5 C C27 PFD . . . M 5 67.638 54.748 24.186 1 28.47 ? C27 PFD 999 B 1 
HETATM 6 C C25 PFD . . . M 5 66.446 54.972 23.51 1 27.21 ? C25 PFD 999 B 1 
HETATM 7 C C23 PFD . . . M 5 66.18 56.233 23.012 1 27.34 ? C23 PFD 999 B 1 
HETATM 8 O O22 PFD . . . M 5 65.01 56.464 22.345 1 30.14 ? O22 PFD 999 B 1 
HETATM 9 C C20 PFD . . . M 5 63.779 56.291 22.913 1 30.87 ? C20 PFD 999 B 1 
HETATM 10 C C16 PFD . . . M 5 63.645 56.167 24.304 1 31.47 ? C16 PFD 999 B 1 
HETATM 11 C C12 PFD . . . M 5 62.35 55.986 24.845 1 33.42 ? C12 PFD 999 B 1 
HETATM 12 C C17 PFD . . . M 5 62.639 56.227 22.091 1 29.06 ? C17 PFD 999 B 1 
HETATM 13 C C13 PFD . . . M 5 61.36 56.056 22.662 1 31.83 ? C13 PFD 999 B 1 
HETATM 14 C C6 PFD . . . M 5 61.173 55.92 24.065 1 33.14 ? C6 PFD 999 B 1 
HETATM 15 O O2 PFD . . . M 5 59.893 55.686 24.674 1 35.69 ? O2 PFD 999 B 1 
HETATM 16 C C1 PFD . . . M 5 58.917 54.657 24.208 1 35.37 ? C1 PFD 999 B 1 
HETATM 17 C C5 PFD . . . M 5 57.753 54.232 25.15 1 37.42 ? C5 PFD 999 B 1 
HETATM 18 C C11 PFD . . . M 5 57.319 55.239 26.219 1 41.87 ? C11 PFD 999 B 1 
HETATM 19 O O15 PFD . . . M 5 56.78 54.619 27.399 1 45.19 ? O15 PFD 999 B 1 
HETATM 20 C C19 PFD . . . M 5 57.323 55.125 28.648 1 43.96 ? C19 PFD 999 B 1 
HETATM 21 C C21 PFD . . . M 5 57.311 54.09 29.773 1 43.32 ? C21 PFD 999 B 1 
HETATM 22 C C4 PFD . . . M 5 59.548 53.31 23.871 1 35.81 ? C4 PFD 999 B 1 
HETATM 23 O O10 PFD . . . M 5 60.088 52.617 24.751 1 32.84 ? O10 PFD 999 B 1 
HETATM 24 N N9 PFD . . . M 5 59.522 52.792 22.608 1 34.49 ? N9 PFD 999 B 1 
HETATM 25 C C14 PFD . . . M 5 58.91 53.45 21.618 1 32.3 ? C14 PFD 999 B 1 
HETATM 26 O O18 PFD . . . M 5 58.921 52.907 20.397 1 35.18 ? O18 PFD 999 B 1 
HETATM 27 N N7 PFD . . . M 5 58.354 54.643 21.784 1 32.15 ? N7 PFD 999 B 1 
HETATM 28 C C3 PFD . . . M 5 58.3 55.257 22.965 1 32.63 ? C3 PFD 999 B 1 
HETATM 29 O O8 PFD . . . M 5 57.724 56.358 23.027 1 31.6 ? O8 PFD 999 B 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           29 
#