data_7U8F
#
_model_server_result.job_id            CGmd0wAy0Ib5RiI9u2Z1Vw 
_model_server_result.datetime_utc      '2025-01-11 05:00:33' 
_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          7u8f 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":502}' 
#
_entry.id    7U8F 
#
_exptl.entry_id    7U8F 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              417.5 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione 
_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         120 
_cell.entry_id            7U8F 
_cell.length_a            180.892 
_cell.length_b            180.892 
_cell.length_c            555.884 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7U8F 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 2 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
? trimeric 3 author_defined_assembly 1 
? trimeric 3 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,G,H,I,J,K,L,M,V,W,X 1 1 
D,E,F,N,O,P,Q,R,S,T,U,Y,Z,AA 2 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
? 5 H N N 
? 5 O 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 286 A CYS 323 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? 
metalc ? metalc2 A SG CYS 289 A CYS 326 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? 
metalc ? metalc3 A SG CYS 354 A CYS 391 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? 
metalc ? metalc4 A SG CYS 357 A CYS 394 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc5 C SG CYS 7 C CYS 142 1_555 M ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? 
metalc ? metalc6 C SG CYS 10 C CYS 145 1_555 M ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
metalc ? metalc7 C NE2 HIS 23 C HIS 158 1_555 M ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
metalc ? metalc8 C NE2 HIS 27 C HIS 162 1_555 M ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? 
metalc ? metalc9 D SG CYS 286 D CYS 323 1_555 N ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc10 D SG CYS 289 D CYS 326 1_555 N ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? 
metalc ? metalc11 D SG CYS 354 D CYS 391 1_555 N ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc12 D SG CYS 357 D CYS 394 1_555 N ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc13 F SG CYS 7 F CYS 142 1_555 U ZN ZN . F ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? 
metalc ? metalc14 F SG CYS 10 F CYS 145 1_555 U ZN ZN . F ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
metalc ? metalc15 F NE2 HIS 23 F HIS 158 1_555 U ZN ZN . F ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? 
metalc ? metalc16 F NE2 HIS 27 F HIS 162 1_555 U ZN ZN . F ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? 
#
_chem_comp.formula           'C25 H27 N3 O3' 
_chem_comp.formula_weight    417.5 
_chem_comp.id                LWK 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione 
_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
O19 C15 LWK doub 227 n n 
C15 C14 LWK sing 228 n n 
C15 N16 LWK sing 229 n n 
C14 C13 LWK sing 230 n n 
C13 C11 LWK sing 231 n n 
N16 C17 LWK sing 232 n n 
C29 C28 LWK doub 233 n y 
C29 C30 LWK sing 234 n y 
C17 C11 LWK sing 235 n n 
C17 O18 LWK doub 236 n n 
C28 C27 LWK sing 237 n y 
C11 N8 LWK sing 238 n n 
C7 N8 LWK sing 239 n n 
C7 C4 LWK sing 240 n n 
C30 C31 LWK doub 241 n y 
N8 C9 LWK sing 242 n n 
C27 C26 LWK doub 243 n y 
C4 C3 LWK doub 244 n y 
C4 C5 LWK sing 245 n y 
C9 O12 LWK doub 246 n n 
C9 C5 LWK sing 247 n n 
C31 C26 LWK sing 248 n y 
C26 C25 LWK sing 249 n n 
C3 C2 LWK sing 250 n y 
C5 C6 LWK doub 251 n y 
C24 C23 LWK sing 252 n n 
C24 C10 LWK sing 253 n n 
C2 C10 LWK sing 254 n n 
C2 C1 LWK doub 255 n y 
N22 C25 LWK sing 256 n n 
N22 C23 LWK sing 257 n n 
N22 C21 LWK sing 258 n n 
C6 C1 LWK sing 259 n y 
C20 C10 LWK sing 260 n n 
C20 C21 LWK sing 261 n n 
C1 H1 LWK sing 262 n n 
C3 H2 LWK sing 263 n n 
C11 H3 LWK sing 264 n n 
C13 H4 LWK sing 265 n n 
C13 H5 LWK sing 266 n n 
C14 H6 LWK sing 267 n n 
C14 H7 LWK sing 268 n n 
C20 H8 LWK sing 269 n n 
C20 H9 LWK sing 270 n n 
C21 H10 LWK sing 271 n n 
C21 H11 LWK sing 272 n n 
C23 H12 LWK sing 273 n n 
C23 H13 LWK sing 274 n n 
C24 H14 LWK sing 275 n n 
C24 H15 LWK sing 276 n n 
C25 H16 LWK sing 277 n n 
C25 H17 LWK sing 278 n n 
C27 H18 LWK sing 279 n n 
C28 H19 LWK sing 280 n n 
C29 H20 LWK sing 281 n n 
C30 H21 LWK sing 282 n n 
C10 H22 LWK sing 283 n n 
C31 H23 LWK sing 284 n n 
C6 H24 LWK sing 285 n n 
C7 H25 LWK sing 286 n n 
C7 H26 LWK sing 287 n n 
N16 H27 LWK sing 288 n n 
#
_atom_sites.entry_id                     7U8F 
_atom_sites.fract_transf_matrix[1][1]    0.005528 
_atom_sites.fract_transf_matrix[1][2]    0.003192 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006383 
_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]    0.001799 
_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
G 4 ZN A 1 501 501 ZN ZN . 
H 5 LWK A 1 502 1 LWK LI1 . 
I 6 SO4 B 1 1201 1 SO4 SO4 . 
J 6 SO4 B 1 1202 4 SO4 SO4 . 
K 6 SO4 B 1 1203 6 SO4 SO4 . 
L 6 SO4 B 1 1204 8 SO4 SO4 . 
M 4 ZN C 1 201 201 ZN ZN . 
N 4 ZN D 1 501 501 ZN ZN . 
O 5 LWK D 1 502 1 LWK LI1 . 
P 6 SO4 D 1 503 7 SO4 SO4 . 
Q 7 EPE E 1 1201 1201 EPE EPE . 
R 6 SO4 E 1 1202 2 SO4 SO4 . 
S 6 SO4 E 1 1203 3 SO4 SO4 . 
T 6 SO4 E 1 1204 5 SO4 SO4 . 
U 4 ZN F 1 201 201 ZN ZN . 
V 8 HOH A 1 601 13 HOH HOH . 
V 8 HOH A 2 602 17 HOH HOH . 
W 8 HOH B 1 1301 5 HOH HOH . 
W 8 HOH B 2 1302 7 HOH HOH . 
W 8 HOH B 3 1303 15 HOH HOH . 
W 8 HOH B 4 1304 9 HOH HOH . 
W 8 HOH B 5 1305 8 HOH HOH . 
W 8 HOH B 6 1306 12 HOH HOH . 
W 8 HOH B 7 1307 1 HOH HOH . 
W 8 HOH B 8 1308 10 HOH HOH . 
X 8 HOH C 1 301 2 HOH HOH . 
Y 8 HOH D 1 601 18 HOH HOH . 
Z 8 HOH E 1 1301 6 HOH HOH . 
Z 8 HOH E 2 1302 14 HOH HOH . 
Z 8 HOH E 3 1303 4 HOH HOH . 
Z 8 HOH E 4 1304 16 HOH HOH . 
Z 8 HOH E 5 1305 11 HOH HOH . 
Z 8 HOH E 6 1306 19 HOH HOH . 
AA 8 HOH F 1 301 3 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 LWK . . . O 5 43.872 15.764 21.349 1 97.95 ? C1 LWK 502 D 1 
HETATM 2 C C2 LWK . . . O 5 44.126 16.588 22.423 1 94.29 ? C2 LWK 502 D 1 
HETATM 3 C C3 LWK . . . O 5 43.44 16.383 23.636 1 98.72 ? C3 LWK 502 D 1 
HETATM 4 C C11 LWK . . . O 5 39.532 13.472 24.996 1 96.78 ? C11 LWK 502 D 1 
HETATM 5 C C13 LWK . . . O 5 39.955 12.609 26.208 1 87.08 ? C13 LWK 502 D 1 
HETATM 6 C C14 LWK . . . O 5 38.769 12.24 27.072 1 77.56 ? C14 LWK 502 D 1 
HETATM 7 C C15 LWK . . . O 5 38.081 13.486 27.558 1 90.75 ? C15 LWK 502 D 1 
HETATM 8 C C17 LWK . . . O 5 38.679 14.683 25.427 1 104.06 ? C17 LWK 502 D 1 
HETATM 9 C C20 LWK . . . O 5 44.688 18.78 23.401 1 95.82 ? C20 LWK 502 D 1 
HETATM 10 C C21 LWK . . . O 5 45.632 19.97 23.346 1 82.22 ? C21 LWK 502 D 1 
HETATM 11 C C23 LWK . . . O 5 47.395 18.596 22.427 1 100.32 ? C23 LWK 502 D 1 
HETATM 12 C C24 LWK . . . O 5 46.483 17.365 22.416 1 108.61 ? C24 LWK 502 D 1 
HETATM 13 C C25 LWK . . . O 5 48.012 20.44 24.135 1 143.5 ? C25 LWK 502 D 1 
HETATM 14 C C26 LWK . . . O 5 48.983 19.884 25.221 1 132.37 ? C26 LWK 502 D 1 
HETATM 15 C C27 LWK . . . O 5 48.566 19.421 26.487 1 126.25 ? C27 LWK 502 D 1 
HETATM 16 C C28 LWK . . . O 5 49.484 18.893 27.407 1 140.27 ? C28 LWK 502 D 1 
HETATM 17 C C29 LWK . . . O 5 50.839 18.816 27.088 1 139.79 ? C29 LWK 502 D 1 
HETATM 18 C C30 LWK . . . O 5 51.265 19.278 25.846 1 139.78 ? C30 LWK 502 D 1 
HETATM 19 C C10 LWK . . . O 5 45.026 17.787 22.288 1 91.47 ? C10 LWK 502 D 1 
HETATM 20 C C31 LWK . . . O 5 50.349 19.81 24.921 1 127.06 ? C31 LWK 502 D 1 
HETATM 21 C C4 LWK . . . O 5 42.484 15.388 23.724 1 97.87 ? C4 LWK 502 D 1 
HETATM 22 C C5 LWK . . . O 5 42.199 14.579 22.635 1 89.97 ? C5 LWK 502 D 1 
HETATM 23 C C6 LWK . . . O 5 42.906 14.755 21.446 1 99.59 ? C6 LWK 502 D 1 
HETATM 24 C C7 LWK . . . O 5 41.596 15.037 24.887 1 83.67 ? C7 LWK 502 D 1 
HETATM 25 C C9 LWK . . . O 5 41.049 13.686 22.988 1 90.16 ? C9 LWK 502 D 1 
HETATM 26 N N16 LWK . . . O 5 38.047 14.613 26.69 1 102.63 ? N16 LWK 502 D 1 
HETATM 27 N N22 LWK . . . O 5 46.989 19.413 23.607 1 125.05 ? N22 LWK 502 D 1 
HETATM 28 N N8 LWK . . . O 5 40.702 14.015 24.308 1 83.57 ? N8 LWK 502 D 1 
HETATM 29 O O12 LWK . . . O 5 40.477 12.806 22.353 1 95.98 ? O12 LWK 502 D 1 
HETATM 30 O O18 LWK . . . O 5 38.528 15.701 24.7 1 91.91 ? O18 LWK 502 D 1 
HETATM 31 O O19 LWK . . . O 5 37.556 13.585 28.657 1 89.32 ? O19 LWK 502 D 1 
#
_model_server_stats.io_time_ms              68 
_model_server_stats.parse_time_ms           26 
_model_server_stats.create_model_time_ms    64 
_model_server_stats.query_time_ms           551 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           31 
#