data_8W28
#
_model_server_result.job_id            m8BVr2Y702Jte2vgxnhkQw 
_model_server_result.datetime_utc      '2025-07-16 22:37:02' 
_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          8w28 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":1201}' 
#
_entry.id    8W28 
#
_exptl.entry_id    8W28 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              312.31 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-[4-(trifluoromethyl)phenyl]-7,8-dihydro-5H-thiopyrano[4,3-d]pyrimidin-4-ol 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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,H 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 E 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 SG CYS 644 D CYS 1081 1_555 D ZN ZN . D ZN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc2 A ND1 HIS 647 D HIS 1084 1_555 D ZN ZN . D ZN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
metalc ? metalc3 A SG CYS 652 D CYS 1089 1_555 D ZN ZN . D ZN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? 
metalc ? metalc4 A SG CYS 655 D CYS 1092 1_555 D ZN ZN . D ZN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? 
metalc ? metalc5 B SG CYS 644 Q CYS 1081 1_555 F ZN ZN . Q ZN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? 
metalc ? metalc6 B ND1 HIS 647 Q HIS 1084 1_555 F ZN ZN . Q ZN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
metalc ? metalc7 B SG CYS 652 Q CYS 1089 1_555 F ZN ZN . Q ZN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? 
metalc ? metalc8 B SG CYS 655 Q CYS 1092 1_555 F ZN ZN . Q ZN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
#
_chem_comp.formula           'C14 H11 F3 N2 O S' 
_chem_comp.formula_weight    312.31 
_chem_comp.id                XAV 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-[4-(trifluoromethyl)phenyl]-7,8-dihydro-5H-thiopyrano[4,3-d]pyrimidin-4-ol 
_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
N1 C2 XAV sing 376 n y 
N1 C6 XAV doub 377 n y 
C2 N3 XAV doub 378 n y 
C2 CAP XAV sing 379 n y 
N3 C4 XAV sing 380 n y 
C4 C5 XAV doub 381 n y 
C4 CAJ XAV sing 382 n n 
C5 C6 XAV sing 383 n y 
C5 CAK XAV sing 384 n n 
C6 O6 XAV sing 385 n n 
FAB CAU XAV sing 386 n n 
FAC CAU XAV sing 387 n n 
FAD CAU XAV sing 388 n n 
CAE CAG XAV doub 389 n y 
CAE CAP XAV sing 390 n y 
CAF CAH XAV sing 391 n y 
CAF CAP XAV doub 392 n y 
CAG CAQ XAV sing 393 n y 
CAH CAQ XAV doub 394 n y 
CAI CAJ XAV sing 395 n n 
CAI SAN XAV sing 396 n n 
CAK SAN XAV sing 397 n n 
CAQ CAU XAV sing 398 n n 
O6 HO6 XAV sing 399 n n 
CAE HAE XAV sing 400 n n 
CAF HAF XAV sing 401 n n 
CAG HAG XAV sing 402 n n 
CAH HAH XAV sing 403 n n 
CAI HAI XAV sing 404 n n 
CAI HAIA XAV sing 405 n n 
CAJ HAJ XAV sing 406 n n 
CAJ HAJA XAV sing 407 n n 
CAK HAK XAV sing 408 n n 
CAK HAKA XAV sing 409 n n 
#
_atom_sites.entry_id                     8W28 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 XAV D 1 1201 1163 XAV XAV . 
D 3 ZN D 1 1202 1201 ZN ZN . 
E 2 XAV Q 1 1201 1163 XAV XAV . 
F 3 ZN Q 1 1202 1201 ZN ZN . 
G 4 HOH D 1 1301 44 HOH HOH . 
G 4 HOH D 2 1302 65 HOH HOH . 
G 4 HOH D 3 1303 71 HOH HOH . 
G 4 HOH D 4 1304 45 HOH HOH . 
G 4 HOH D 5 1305 14 HOH HOH . 
G 4 HOH D 6 1306 35 HOH HOH . 
G 4 HOH D 7 1307 40 HOH HOH . 
G 4 HOH D 8 1308 56 HOH HOH . 
G 4 HOH D 9 1309 53 HOH HOH . 
G 4 HOH D 10 1310 48 HOH HOH . 
G 4 HOH D 11 1311 69 HOH HOH . 
G 4 HOH D 12 1312 60 HOH HOH . 
G 4 HOH D 13 1313 70 HOH HOH . 
G 4 HOH D 14 1314 46 HOH HOH . 
G 4 HOH D 15 1315 6 HOH HOH . 
G 4 HOH D 16 1316 55 HOH HOH . 
G 4 HOH D 17 1317 47 HOH HOH . 
G 4 HOH D 18 1318 13 HOH HOH . 
H 4 HOH Q 1 1301 43 HOH HOH . 
H 4 HOH Q 2 1302 59 HOH HOH . 
H 4 HOH Q 3 1303 67 HOH HOH . 
H 4 HOH Q 4 1304 49 HOH HOH . 
H 4 HOH Q 5 1305 62 HOH HOH . 
H 4 HOH Q 6 1306 50 HOH HOH . 
H 4 HOH Q 7 1307 19 HOH HOH . 
H 4 HOH Q 8 1308 41 HOH HOH . 
H 4 HOH Q 9 1309 15 HOH HOH . 
H 4 HOH Q 10 1310 1 HOH HOH . 
H 4 HOH Q 11 1311 66 HOH HOH . 
H 4 HOH Q 12 1312 20 HOH HOH . 
H 4 HOH Q 13 1313 68 HOH HOH . 
H 4 HOH Q 14 1314 63 HOH HOH . 
H 4 HOH Q 15 1315 64 HOH HOH . 
H 4 HOH Q 16 1316 51 HOH HOH . 
H 4 HOH Q 17 1317 57 HOH HOH . 
H 4 HOH Q 18 1318 58 HOH HOH . 
H 4 HOH Q 19 1319 61 HOH HOH . 
H 4 HOH Q 20 1320 42 HOH HOH . 
H 4 HOH Q 21 1321 54 HOH HOH . 
H 4 HOH Q 22 1322 52 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 N N1 XAV . . . E 2 104.388 165.38 170.157 1 21.4 ? N1 XAV 1201 Q 1 
HETATM 2 C C2 XAV . . . E 2 103.492 166.11 170.812 1 19.46 ? C2 XAV 1201 Q 1 
HETATM 3 N N3 XAV . . . E 2 102.521 165.628 171.553 1 22.77 ? N3 XAV 1201 Q 1 
HETATM 4 C C4 XAV . . . E 2 102.422 164.303 171.676 1 22.27 ? C4 XAV 1201 Q 1 
HETATM 5 C C5 XAV . . . E 2 103.302 163.443 171.038 1 22.68 ? C5 XAV 1201 Q 1 
HETATM 6 C C6 XAV . . . E 2 104.292 164.077 170.272 1 18.86 ? C6 XAV 1201 Q 1 
HETATM 7 O O6 XAV . . . E 2 105.175 163.33 169.633 1 17.72 ? O6 XAV 1201 Q 1 
HETATM 8 F FAB XAV . . . E 2 103.266 172.476 171.209 1 32.78 ? FAB XAV 1201 Q 1 
HETATM 9 F FAC XAV . . . E 2 105.203 172.242 170.298 1 24.73 ? FAC XAV 1201 Q 1 
HETATM 10 F FAD XAV . . . E 2 103.432 172.223 169.084 1 22.78 ? FAD XAV 1201 Q 1 
HETATM 11 C CAE XAV . . . E 2 104.789 168.149 170.237 1 20.21 ? CAE XAV 1201 Q 1 
HETATM 12 C CAF XAV . . . E 2 102.519 168.402 170.981 1 21.86 ? CAF XAV 1201 Q 1 
HETATM 13 C CAG XAV . . . E 2 104.902 169.52 170.101 1 21.43 ? CAG XAV 1201 Q 1 
HETATM 14 C CAH XAV . . . E 2 102.626 169.774 170.846 1 19.44 ? CAH XAV 1201 Q 1 
HETATM 15 C CAI XAV . . . E 2 100.984 162.367 172.486 1 21.04 ? CAI XAV 1201 Q 1 
HETATM 16 C CAJ XAV . . . E 2 101.289 163.846 172.546 1 21.33 ? CAJ XAV 1201 Q 1 
HETATM 17 C CAK XAV . . . E 2 103.253 161.947 171.133 1 20.7 ? CAK XAV 1201 Q 1 
HETATM 18 S SAN XAV . . . E 2 102.493 161.385 172.67 1 24.63 ? SAN XAV 1201 Q 1 
HETATM 19 C CAP XAV . . . E 2 103.6 167.576 170.676 1 19.51 ? CAP XAV 1201 Q 1 
HETATM 20 C CAQ XAV . . . E 2 103.819 170.335 170.407 1 20.15 ? CAQ XAV 1201 Q 1 
HETATM 21 C CAU XAV . . . E 2 103.937 171.817 170.253 1 25.61 ? CAU XAV 1201 Q 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    25 
_model_server_stats.query_time_ms           330 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           21 
#