data_8DEY
#
_model_server_result.job_id            fZAmzIXPdqSQAMmYhsr8kQ 
_model_server_result.datetime_utc      '2025-01-11 07:05:02' 
_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          8dey 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":502}' 
#
_entry.id    8DEY 
#
_exptl.entry_id    8DEY 
_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    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          93.46 
_cell.angle_gamma         90 
_cell.entry_id            8DEY 
_cell.length_a            96.476 
_cell.length_b            96.227 
_cell.length_c            155.598 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DEY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
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 1 1 
D,E,F,K,L,M 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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             H 
_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
disulf ? disulf1 B SG CYS 18 B CYS 18 1_555 B SG CYS 313 B CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf2 E SG CYS 18 E CYS 18 1_555 E SG CYS 313 E CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
metalc ? metalc1 A SG CYS 254 A CYS 323 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.658 ? 
metalc ? metalc2 A SG CYS 257 A CYS 326 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc3 A SG CYS 322 A CYS 391 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? 
metalc ? metalc4 A SG CYS 325 A CYS 394 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc5 C SG CYS 7 C CYS 142 1_555 I ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? 
metalc ? metalc6 C SG CYS 10 C CYS 145 1_555 I ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? 
metalc ? metalc7 C NE2 HIS 23 C HIS 158 1_555 I ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? 
metalc ? metalc8 C NE2 HIS 27 C HIS 162 1_555 I ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? 
metalc ? metalc9 C SG CYS 35 C CYS 170 1_555 J ZN ZN . C ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? 
metalc ? metalc10 C SG CYS 38 C CYS 173 1_555 J ZN ZN . C ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? 
metalc ? metalc11 C NE2 HIS 51 C HIS 186 1_555 J ZN ZN . C ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc12 C NE2 HIS 55 C HIS 190 1_555 J ZN ZN . C ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
metalc ? metalc13 D SG CYS 254 D CYS 323 1_555 K ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? 
metalc ? metalc14 D SG CYS 257 D CYS 326 1_555 K ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? 
metalc ? metalc15 D SG CYS 322 D CYS 391 1_555 K ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? 
metalc ? metalc16 D SG CYS 325 D CYS 394 1_555 K ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? 
metalc ? metalc17 F SG CYS 7 F CYS 142 1_555 L ZN ZN . F ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? 
metalc ? metalc18 F SG CYS 10 F CYS 145 1_555 L ZN ZN . F ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? 
metalc ? metalc19 F NE2 HIS 23 F HIS 158 1_555 L ZN ZN . F ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? 
metalc ? metalc20 F NE2 HIS 27 F HIS 162 1_555 L ZN ZN . F ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? 
metalc ? metalc21 F SG CYS 35 F CYS 170 1_555 M ZN ZN . F ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? 
metalc ? metalc22 F SG CYS 38 F CYS 173 1_555 M ZN ZN . F ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? 
metalc ? metalc23 F NE2 HIS 51 F HIS 186 1_555 M ZN ZN . F ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? 
metalc ? metalc24 F NE2 HIS 55 F HIS 190 1_555 M ZN ZN . F ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? 
#
_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 192 n n 
C15 C14 LWK sing 193 n n 
C15 N16 LWK sing 194 n n 
C14 C13 LWK sing 195 n n 
C13 C11 LWK sing 196 n n 
N16 C17 LWK sing 197 n n 
C29 C28 LWK doub 198 n y 
C29 C30 LWK sing 199 n y 
C17 C11 LWK sing 200 n n 
C17 O18 LWK doub 201 n n 
C28 C27 LWK sing 202 n y 
C11 N8 LWK sing 203 n n 
C7 N8 LWK sing 204 n n 
C7 C4 LWK sing 205 n n 
C30 C31 LWK doub 206 n y 
N8 C9 LWK sing 207 n n 
C27 C26 LWK doub 208 n y 
C4 C3 LWK doub 209 n y 
C4 C5 LWK sing 210 n y 
C9 O12 LWK doub 211 n n 
C9 C5 LWK sing 212 n n 
C31 C26 LWK sing 213 n y 
C26 C25 LWK sing 214 n n 
C3 C2 LWK sing 215 n y 
C5 C6 LWK doub 216 n y 
C24 C23 LWK sing 217 n n 
C24 C10 LWK sing 218 n n 
C2 C10 LWK sing 219 n n 
C2 C1 LWK doub 220 n y 
N22 C25 LWK sing 221 n n 
N22 C23 LWK sing 222 n n 
N22 C21 LWK sing 223 n n 
C6 C1 LWK sing 224 n y 
C20 C10 LWK sing 225 n n 
C20 C21 LWK sing 226 n n 
C1 H1 LWK sing 227 n n 
C3 H2 LWK sing 228 n n 
C11 H3 LWK sing 229 n n 
C13 H4 LWK sing 230 n n 
C13 H5 LWK sing 231 n n 
C14 H6 LWK sing 232 n n 
C14 H7 LWK sing 233 n n 
C20 H8 LWK sing 234 n n 
C20 H9 LWK sing 235 n n 
C21 H10 LWK sing 236 n n 
C21 H11 LWK sing 237 n n 
C23 H12 LWK sing 238 n n 
C23 H13 LWK sing 239 n n 
C24 H14 LWK sing 240 n n 
C24 H15 LWK sing 241 n n 
C25 H16 LWK sing 242 n n 
C25 H17 LWK sing 243 n n 
C27 H18 LWK sing 244 n n 
C28 H19 LWK sing 245 n n 
C29 H20 LWK sing 246 n n 
C30 H21 LWK sing 247 n n 
C10 H22 LWK sing 248 n n 
C31 H23 LWK sing 249 n n 
C6 H24 LWK sing 250 n n 
C7 H25 LWK sing 251 n n 
C7 H26 LWK sing 252 n n 
N16 H27 LWK sing 253 n n 
#
_atom_sites.entry_id                     8DEY 
_atom_sites.fract_transf_matrix[1][1]    0.010365 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000627 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010392 
_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]    0.006439 
_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 4 ZN C 1 201 201 ZN ZN . 
J 4 ZN C 1 202 202 ZN ZN . 
K 4 ZN D 1 501 501 ZN ZN . 
L 4 ZN F 1 201 201 ZN ZN . 
M 4 ZN F 1 202 202 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 C C1 LWK . . . H 5 -23.7 -36.645 52.601 1 161.52 ? C1 LWK 502 A 1 
HETATM 2 C C2 LWK . . . H 5 -22.801 -37.556 53.066 1 165.72 ? C2 LWK 502 A 1 
HETATM 3 C C3 LWK . . . H 5 -21.714 -37.974 52.276 1 171.93 ? C3 LWK 502 A 1 
HETATM 4 C C11 LWK . . . H 5 -20.44 -36.573 47.58 1 151.76 ? C11 LWK 502 A 1 
HETATM 5 C C13 LWK . . . H 5 -19.289 -35.579 47.798 1 148.51 ? C13 LWK 502 A 1 
HETATM 6 C C14 LWK . . . H 5 -18.337 -35.558 46.625 1 154.41 ? C14 LWK 502 A 1 
HETATM 7 C C15 LWK . . . H 5 -17.805 -36.933 46.344 1 160.16 ? C15 LWK 502 A 1 
HETATM 8 C C17 LWK . . . H 5 -19.929 -37.939 47.122 1 162.78 ? C17 LWK 502 A 1 
HETATM 9 C C20 LWK . . . H 5 -23.855 -39.34 54.439 1 183.03 ? C20 LWK 502 A 1 
HETATM 10 C C21 LWK . . . H 5 -24.134 -39.689 55.901 1 189 ? C21 LWK 502 A 1 
HETATM 11 C C23 LWK . . . H 5 -21.863 -38.86 56.454 1 181.67 ? C23 LWK 502 A 1 
HETATM 12 C C24 LWK . . . H 5 -21.655 -38.427 55.012 1 178.83 ? C24 LWK 502 A 1 
HETATM 13 C C25 LWK . . . H 5 -23 -40.384 57.978 1 172.8 ? C25 LWK 502 A 1 
HETATM 14 C C26 LWK . . . H 5 -21.731 -41.102 58.313 1 172.39 ? C26 LWK 502 A 1 
HETATM 15 C C27 LWK . . . H 5 -21.463 -42.321 57.71 1 172.57 ? C27 LWK 502 A 1 
HETATM 16 C C28 LWK . . . H 5 -20.258 -42.959 57.953 1 172.92 ? C28 LWK 502 A 1 
HETATM 17 C C29 LWK . . . H 5 -19.323 -42.382 58.803 1 171.66 ? C29 LWK 502 A 1 
HETATM 18 C C30 LWK . . . H 5 -19.597 -41.165 59.419 1 170.81 ? C30 LWK 502 A 1 
HETATM 19 C C10 LWK . . . H 5 -22.998 -38.085 54.43 1 177.32 ? C10 LWK 502 A 1 
HETATM 20 C C31 LWK . . . H 5 -20.803 -40.522 59.18 1 173.26 ? C31 LWK 502 A 1 
HETATM 21 C C4 LWK . . . H 5 -21.61 -37.417 51.02 1 170.71 ? C4 LWK 502 A 1 
HETATM 22 C C5 LWK . . . H 5 -22.542 -36.488 50.57 1 168.1 ? C5 LWK 502 A 1 
HETATM 23 C C6 LWK . . . H 5 -23.562 -36.112 51.342 1 164.81 ? C6 LWK 502 A 1 
HETATM 24 C C7 LWK . . . H 5 -20.596 -37.644 49.946 1 158.49 ? C7 LWK 502 A 1 
HETATM 25 C C9 LWK . . . H 5 -22.233 -36.046 49.214 1 156.28 ? C9 LWK 502 A 1 
HETATM 26 N N16 LWK . . . H 5 -18.648 -38.034 46.578 1 164.19 ? N16 LWK 502 A 1 
HETATM 27 N N22 LWK . . . H 5 -22.827 -39.992 56.548 1 183.45 ? N22 LWK 502 A 1 
HETATM 28 N N8 LWK . . . H 5 -21.083 -36.742 48.86 1 148.65 ? N8 LWK 502 A 1 
HETATM 29 O O12 LWK . . . H 5 -22.802 -35.249 48.493 1 154.05 ? O12 LWK 502 A 1 
HETATM 30 O O18 LWK . . . H 5 -20.616 -38.952 47.192 1 163.37 ? O18 LWK 502 A 1 
HETATM 31 O O19 LWK . . . H 5 -16.675 -37.147 45.939 1 152.83 ? O19 LWK 502 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    31 
_model_server_stats.query_time_ms           260 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#