data_7U8F # _model_server_result.job_id 3C27sfuP1KjUNoateCBNJw _model_server_result.datetime_utc '2025-01-11 04:44:13' _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":"H","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 . . . H 5 -81.438 -97.862 77.168 1 108.56 ? C1 LWK 502 A 1 HETATM 2 C C2 LWK . . . H 5 -82.569 -97.364 76.532 1 95.43 ? C2 LWK 502 A 1 HETATM 3 C C3 LWK . . . H 5 -82.449 -96.556 75.392 1 94.08 ? C3 LWK 502 A 1 HETATM 4 C C11 LWK . . . H 5 -78.346 -94.574 73.12 1 99.04 ? C11 LWK 502 A 1 HETATM 5 C C13 LWK . . . H 5 -78.277 -95.217 71.73 1 97.13 ? C13 LWK 502 A 1 HETATM 6 C C14 LWK . . . H 5 -77.578 -94.307 70.733 1 93.63 ? C14 LWK 502 A 1 HETATM 7 C C15 LWK . . . H 5 -78.305 -92.988 70.624 1 93.99 ? C15 LWK 502 A 1 HETATM 8 C C17 LWK . . . H 5 -78.915 -93.151 73.015 1 98.78 ? C17 LWK 502 A 1 HETATM 9 C C20 LWK . . . H 5 -84.944 -96.646 76.834 1 87.46 ? C20 LWK 502 A 1 HETATM 10 C C21 LWK . . . H 5 -86.302 -97.12 77.38 1 108.77 ? C21 LWK 502 A 1 HETATM 11 C C23 LWK . . . H 5 -85.731 -99.389 76.904 1 115.99 ? C23 LWK 502 A 1 HETATM 12 C C24 LWK . . . H 5 -84.341 -99.001 76.411 1 96.79 ? C24 LWK 502 A 1 HETATM 13 C C25 LWK . . . H 5 -88.125 -98.737 76.742 1 132.55 ? C25 LWK 502 A 1 HETATM 14 C C26 LWK . . . H 5 -88.728 -99.131 75.375 1 144.96 ? C26 LWK 502 A 1 HETATM 15 C C27 LWK . . . H 5 -88.905 -98.181 74.352 1 148.64 ? C27 LWK 502 A 1 HETATM 16 C C28 LWK . . . H 5 -89.402 -98.54 73.086 1 123.11 ? C28 LWK 502 A 1 HETATM 17 C C29 LWK . . . H 5 -89.732 -99.858 72.817 1 125.41 ? C29 LWK 502 A 1 HETATM 18 C C30 LWK . . . H 5 -89.569 -100.816 73.826 1 134.19 ? C30 LWK 502 A 1 HETATM 19 C C10 LWK . . . H 5 -83.897 -97.715 77.088 1 83.05 ? C10 LWK 502 A 1 HETATM 20 C C31 LWK . . . H 5 -89.074 -100.464 75.099 1 136.19 ? C31 LWK 502 A 1 HETATM 21 C C4 LWK . . . H 5 -81.16 -96.25 74.964 1 99.54 ? C4 LWK 502 A 1 HETATM 22 C C5 LWK . . . H 5 -80.02 -96.719 75.644 1 100.89 ? C5 LWK 502 A 1 HETATM 23 C C6 LWK . . . H 5 -80.148 -97.542 76.738 1 100.22 ? C6 LWK 502 A 1 HETATM 24 C C7 LWK . . . H 5 -80.727 -95.434 73.782 1 88.16 ? C7 LWK 502 A 1 HETATM 25 C C9 LWK . . . H 5 -78.795 -96.13 75.027 1 99.95 ? C9 LWK 502 A 1 HETATM 26 N N16 LWK . . . H 5 -78.893 -92.476 71.786 1 84.85 ? N16 LWK 502 A 1 HETATM 27 N N22 LWK . . . H 5 -86.673 -98.299 76.557 1 125.27 ? N22 LWK 502 A 1 HETATM 28 N N8 LWK . . . H 5 -79.247 -95.362 73.956 1 96.09 ? N8 LWK 502 A 1 HETATM 29 O O12 LWK . . . H 5 -77.61 -96.199 75.335 1 103.41 ? O12 LWK 502 A 1 HETATM 30 O O18 LWK . . . H 5 -79.367 -92.566 73.988 1 108.61 ? O18 LWK 502 A 1 HETATM 31 O O19 LWK . . . H 5 -78.433 -92.35 69.588 1 93.27 ? O19 LWK 502 A 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 31 #