data_8D7Z
#
_model_server_result.job_id            YUnew2-8L7AHYTPLMZbkyg 
_model_server_result.datetime_utc      '2025-08-02 05:13:50' 
_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          8d7z 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":502}' 
#
_entry.id    8D7Z 
#
_exptl.entry_id    8D7Z 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              567.61 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            Mezigdomide 
_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            8D7Z 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8D7Z 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_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    ? 
_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                      5 
_struct_asym.id                             E 
_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 B SG CYS 323 B CYS 323 1_555 D ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc2 B SG CYS 326 B CYS 326 1_555 D ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc3 B SG CYS 391 B CYS 391 1_555 D ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc4 B SG CYS 394 B CYS 394 1_555 D ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc5 C SG CYS 38 C CYS 147 1_555 F ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
metalc ? metalc6 C NE2 HIS 54 C HIS 163 1_555 F ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc7 C NE2 HIS 58 C HIS 167 1_555 F ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
#
_chem_comp.formula           'C32 H30 F N5 O4' 
_chem_comp.formula_weight    567.61 
_chem_comp.id                QFC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              Mezigdomide 
_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
C8 C9 QFC sing 275 n n 
C8 N1 QFC sing 276 n n 
C7 N1 QFC sing 277 n n 
C7 C6 QFC sing 278 n n 
C9 C10 QFC doub 279 n y 
C9 C28 QFC sing 280 n y 
C10 C11 QFC sing 281 n y 
C28 C27 QFC doub 282 n y 
C11 C12 QFC doub 283 n y 
C27 C12 QFC sing 284 n y 
C12 C13 QFC sing 285 n n 
N1 C29 QFC sing 286 n n 
C6 N QFC sing 287 n n 
C13 O QFC sing 288 n n 
C29 C30 QFC sing 289 n n 
N C5 QFC sing 290 n n 
N C30 QFC sing 291 n n 
C4 C5 QFC doub 292 n y 
C4 C3 QFC sing 293 n y 
O C14 QFC sing 294 n n 
C5 C QFC sing 295 n y 
C15 C14 QFC doub 296 n y 
C15 C16 QFC sing 297 n y 
C3 C2 QFC doub 298 n y 
C14 C21 QFC sing 299 n y 
C F QFC sing 300 n n 
C C1 QFC doub 301 n y 
C16 C17 QFC doub 302 n y 
C2 C1 QFC sing 303 n y 
C2 C31 QFC sing 304 n n 
C21 C20 QFC sing 305 n n 
C21 C18 QFC doub 306 n y 
C31 N4 QFC trip 307 n n 
C20 N2 QFC sing 308 n n 
C17 C18 QFC sing 309 n y 
C18 C19 QFC sing 310 n n 
N2 C19 QFC sing 311 n n 
N2 C22 QFC sing 312 n n 
C19 O1 QFC doub 313 n n 
C23 C22 QFC sing 314 n n 
C23 C24 QFC sing 315 n n 
O3 C26 QFC doub 316 n n 
C22 C26 QFC sing 317 n n 
C26 N3 QFC sing 318 n n 
N3 C25 QFC sing 319 n n 
C24 C25 QFC sing 320 n n 
C25 O2 QFC doub 321 n n 
N3 H2 QFC sing 322 n n 
C4 H3 QFC sing 323 n n 
C6 H4 QFC sing 324 n n 
C6 H5 QFC sing 325 n n 
C7 H6 QFC sing 326 n n 
C7 H7 QFC sing 327 n n 
C8 H8 QFC sing 328 n n 
C8 H9 QFC sing 329 n n 
C10 H10 QFC sing 330 n n 
C13 H11 QFC sing 331 n n 
C13 H12 QFC sing 332 n n 
C15 H13 QFC sing 333 n n 
C17 H14 QFC sing 334 n n 
C20 H15 QFC sing 335 n n 
C20 H16 QFC sing 336 n n 
C22 H17 QFC sing 337 n n 
C24 H18 QFC sing 338 n n 
C24 H19 QFC sing 339 n n 
C28 H20 QFC sing 340 n n 
C1 H21 QFC sing 341 n n 
C11 H22 QFC sing 342 n n 
C16 H23 QFC sing 343 n n 
C23 H24 QFC sing 344 n n 
C23 H25 QFC sing 345 n n 
C27 H26 QFC sing 346 n n 
C29 H27 QFC sing 347 n n 
C29 H28 QFC sing 348 n n 
C3 H29 QFC sing 349 n n 
C30 H30 QFC sing 350 n n 
C30 H31 QFC sing 351 n n 
#
_atom_sites.entry_id                     8D7Z 
_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
D 4 ZN B 1 501 501 ZN ZN . 
E 5 QFC B 1 502 502 QFC LIG . 
F 4 ZN C 1 201 201 ZN ZN . 
#
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 QFC . . . E 5 147.864 142.801 65.194 1 161.93 ? N1 QFC 502 B 1 
HETATM 2 N N3 QFC . . . E 5 136.723 141.653 71.182 1 161.93 ? N3 QFC 502 B 1 
HETATM 3 C C4 QFC . . . E 5 152.648 143.603 66.671 1 161.93 ? C4 QFC 502 B 1 
HETATM 4 C C5 QFC . . . E 5 151.439 144.292 66.721 1 161.93 ? C5 QFC 502 B 1 
HETATM 5 C C6 QFC . . . E 5 149.805 144.27 64.906 1 161.93 ? C6 QFC 502 B 1 
HETATM 6 C C7 QFC . . . E 5 148.878 143.272 64.244 1 161.93 ? C7 QFC 502 B 1 
HETATM 7 C C8 QFC . . . E 5 146.847 141.994 64.511 1 161.93 ? C8 QFC 502 B 1 
HETATM 8 C C10 QFC . . . E 5 145.117 143.828 64.612 1 161.93 ? C10 QFC 502 B 1 
HETATM 9 C C13 QFC . . . E 5 141.348 143.818 64.997 1 161.93 ? C13 QFC 502 B 1 
HETATM 10 C C15 QFC . . . E 5 141.954 145.782 66.988 1 161.93 ? C15 QFC 502 B 1 
HETATM 11 C C17 QFC . . . E 5 141.196 146.86 69.01 1 161.93 ? C17 QFC 502 B 1 
HETATM 12 C C20 QFC . . . E 5 139.01 143.916 68.637 1 161.93 ? C20 QFC 502 B 1 
HETATM 13 C C21 QFC . . . E 5 140.122 144.843 68.24 1 161.93 ? C21 QFC 502 B 1 
HETATM 14 C C22 QFC . . . E 5 137.507 143.95 70.726 1 161.93 ? C22 QFC 502 B 1 
HETATM 15 C C24 QFC . . . E 5 135.093 143.475 71.121 1 161.93 ? C24 QFC 502 B 1 
HETATM 16 C C26 QFC . . . E 5 137.793 142.477 70.939 1 161.93 ? C26 QFC 502 B 1 
HETATM 17 C C28 QFC . . . E 5 144.405 141.588 64.963 1 161.93 ? C28 QFC 502 B 1 
HETATM 18 N N QFC . . . E 5 150.238 143.767 66.209 1 161.93 ? N QFC 502 B 1 
HETATM 19 C C QFC . . . E 5 151.438 145.55 67.321 1 161.93 ? C QFC 502 B 1 
HETATM 20 O O QFC . . . E 5 140.845 143.712 66.334 1 161.93 ? O QFC 502 B 1 
HETATM 21 C C1 QFC . . . E 5 152.558 146.14 67.837 1 161.93 ? C1 QFC 502 B 1 
HETATM 22 C C11 QFC . . . E 5 143.809 144.263 64.73 1 161.93 ? C11 QFC 502 B 1 
HETATM 23 C C12 QFC . . . E 5 142.777 143.364 64.953 1 161.93 ? C12 QFC 502 B 1 
HETATM 24 C C14 QFC . . . E 5 140.993 144.796 67.155 1 161.93 ? C14 QFC 502 B 1 
HETATM 25 C C16 QFC . . . E 5 142.051 146.809 67.918 1 161.93 ? C16 QFC 502 B 1 
HETATM 26 C C18 QFC . . . E 5 140.23 145.868 69.156 1 161.93 ? C18 QFC 502 B 1 
HETATM 27 C C19 QFC . . . E 5 139.208 145.667 70.208 1 161.93 ? C19 QFC 502 B 1 
HETATM 28 C C2 QFC . . . E 5 153.753 145.428 67.797 1 161.93 ? C2 QFC 502 B 1 
HETATM 29 C C23 QFC . . . E 5 136.089 144.202 70.229 1 161.93 ? C23 QFC 502 B 1 
HETATM 30 C C25 QFC . . . E 5 135.408 142.02 71.281 1 161.93 ? C25 QFC 502 B 1 
HETATM 31 C C27 QFC . . . E 5 143.097 142.022 65.079 1 161.93 ? C27 QFC 502 B 1 
HETATM 32 C C29 QFC . . . E 5 148.513 142.025 66.26 1 161.93 ? C29 QFC 502 B 1 
HETATM 33 C C3 QFC . . . E 5 153.795 144.164 67.21 1 161.93 ? C3 QFC 502 B 1 
HETATM 34 C C30 QFC . . . E 5 150.003 142.329 66.335 1 161.93 ? C30 QFC 502 B 1 
HETATM 35 C C31 QFC . . . E 5 154.925 145.975 68.433 1 161.93 ? C31 QFC 502 B 1 
HETATM 36 C C9 QFC . . . E 5 145.433 142.483 64.717 1 161.93 ? C9 QFC 502 B 1 
HETATM 37 F F QFC . . . E 5 150.259 146.167 67.496 1 161.93 ? F QFC 502 B 1 
HETATM 38 N N2 QFC . . . E 5 138.542 144.526 69.884 1 161.93 ? N2 QFC 502 B 1 
HETATM 39 N N4 QFC . . . E 5 155.833 146.433 68.95 1 161.93 ? N4 QFC 502 B 1 
HETATM 40 O O1 QFC . . . E 5 138.975 146.358 71.182 1 161.93 ? O1 QFC 502 B 1 
HETATM 41 O O2 QFC . . . E 5 134.541 141.178 71.492 1 161.93 ? O2 QFC 502 B 1 
HETATM 42 O O3 QFC . . . E 5 138.942 142.048 70.911 1 161.93 ? O3 QFC 502 B 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           218 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           42 
#