data_9DJX # _model_server_result.job_id LHT-Lagw33b7RrkhgfdNPg _model_server_result.datetime_utc '2025-01-10 14:21:05' _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 9djx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":503}' # _entry.id 9DJX # _exptl.entry_id 9DJX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 385.457 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3S)-3-(5-{[(3R,6S)-1-ethyl-6-methylpiperidin-3-yl]oxy}-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 90 _cell.entry_id 9DJX _cell.length_a 109.114 _cell.length_b 145.029 _cell.length_c 191.895 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DJX _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_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,P,Q,R 1 1 D,E,F,K,L,M,N,O,S,T 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 ? 6 I N N ? 6 M 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 disulf ? disulf1 B SG CYS 18 B CYS 18 1_555 B SG CYS 313 B CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? disulf ? disulf2 E SG CYS 18 E CYS 18 1_555 E SG CYS 313 E CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc1 A SG CYS 254 A CYS 323 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc2 A SG CYS 257 A CYS 326 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc3 A SG CYS 322 A CYS 391 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc4 A SG CYS 325 A CYS 394 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc5 C SG CYS 7 C CYS 872 1_555 J ZN ZN . C ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc6 C SG CYS 10 C CYS 875 1_555 J ZN ZN . C ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc7 C NE2 HIS 23 C HIS 888 1_555 J ZN ZN . C ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc8 C NE2 HIS 27 C HIS 892 1_555 J ZN ZN . C ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc9 D SG CYS 254 D CYS 323 1_555 K ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc10 D SG CYS 257 D CYS 326 1_555 K ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc11 D SG CYS 322 D CYS 391 1_555 K ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc12 D SG CYS 325 D CYS 394 1_555 K ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc13 F SG CYS 7 F CYS 872 1_555 O ZN ZN . F ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc14 F SG CYS 10 F CYS 875 1_555 O ZN ZN . F ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc15 F NE2 HIS 23 F HIS 888 1_555 O ZN ZN . F ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? metalc ? metalc16 F NE2 HIS 27 F HIS 892 1_555 O ZN ZN . F ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? # _chem_comp.formula 'C21 H27 N3 O4' _chem_comp.formula_weight 385.457 _chem_comp.id A1A5I _chem_comp.mon_nstd_flag . _chem_comp.name (3S)-3-(5-{[(3R,6S)-1-ethyl-6-methylpiperidin-3-yl]oxy}-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 C26 C27 A1A5I sing 1 n n C26 N24 A1A5I sing 2 n n C28 C23 A1A5I sing 3 n n N24 C23 A1A5I sing 4 n n N24 C25 A1A5I sing 5 n n C23 C22 A1A5I sing 6 n n C25 C20 A1A5I sing 7 n n C22 C21 A1A5I sing 8 n n O10 C20 A1A5I sing 9 n n O10 C2 A1A5I sing 10 n n C20 C21 A1A5I sing 11 n n C2 C1 A1A5I doub 12 n y C2 C3 A1A5I sing 13 n y C1 C6 A1A5I sing 14 n y C3 C4 A1A5I doub 15 n y C6 C5 A1A5I doub 16 n y C4 C5 A1A5I sing 17 n y C4 C7 A1A5I sing 18 n n C5 C9 A1A5I sing 19 n n C7 N8 A1A5I sing 20 n n C9 N8 A1A5I sing 21 n n C9 O11 A1A5I doub 22 n n N8 C12 A1A5I sing 23 n n C13 C12 A1A5I sing 24 n n C13 C14 A1A5I sing 25 n n C12 C17 A1A5I sing 26 n n C14 C15 A1A5I sing 27 n n C17 O18 A1A5I doub 28 n n C17 N16 A1A5I sing 29 n n C15 N16 A1A5I sing 30 n n C15 O19 A1A5I doub 31 n n C1 H1 A1A5I sing 32 n n C3 H2 A1A5I sing 33 n n C12 H3 A1A5I sing 34 n n C13 H4 A1A5I sing 35 n n C13 H5 A1A5I sing 36 n n C14 H6 A1A5I sing 37 n n C14 H7 A1A5I sing 38 n n C20 H8 A1A5I sing 39 n n C21 H9 A1A5I sing 40 n n C21 H10 A1A5I sing 41 n n C22 H11 A1A5I sing 42 n n C22 H12 A1A5I sing 43 n n C23 H13 A1A5I sing 44 n n C25 H14 A1A5I sing 45 n n C25 H15 A1A5I sing 46 n n C26 H16 A1A5I sing 47 n n C26 H17 A1A5I sing 48 n n C27 H18 A1A5I sing 49 n n C27 H19 A1A5I sing 50 n n C27 H20 A1A5I sing 51 n n C28 H21 A1A5I sing 52 n n C28 H22 A1A5I sing 53 n n C28 H23 A1A5I sing 54 n n C6 H24 A1A5I sing 55 n n C7 H25 A1A5I sing 56 n n C7 H26 A1A5I sing 57 n n N16 H27 A1A5I sing 58 n n # _atom_sites.entry_id 9DJX _atom_sites.fract_transf_matrix[1][1] 0.009165 _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] 0.006895 _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] 0.005211 _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 SO4 A 1 502 502 SO4 SO4 . I 6 A1A5I A 1 503 1 A1A5I LI1 . J 4 ZN C 1 900 900 ZN ZN . K 4 ZN D 1 501 501 ZN ZN . L 5 SO4 D 1 502 502 SO4 SO4 . M 6 A1A5I D 1 503 1 A1A5I LI1 . N 5 SO4 E 1 1201 1201 SO4 SO4 . O 4 ZN F 1 900 900 ZN ZN . P 7 HOH A 1 601 4 HOH HOH . P 7 HOH A 2 602 2 HOH HOH . P 7 HOH A 3 603 16 HOH HOH . P 7 HOH A 4 604 1 HOH HOH . Q 7 HOH B 1 1201 6 HOH HOH . Q 7 HOH B 2 1202 17 HOH HOH . Q 7 HOH B 3 1203 5 HOH HOH . Q 7 HOH B 4 1204 7 HOH HOH . Q 7 HOH B 5 1205 3 HOH HOH . R 7 HOH C 1 1001 21 HOH HOH . R 7 HOH C 2 1002 18 HOH HOH . R 7 HOH C 3 1003 22 HOH HOH . S 7 HOH D 1 601 20 HOH HOH . S 7 HOH D 2 602 8 HOH HOH . S 7 HOH D 3 603 10 HOH HOH . S 7 HOH D 4 604 9 HOH HOH . T 7 HOH E 1 1301 12 HOH HOH . T 7 HOH E 2 1302 11 HOH HOH . T 7 HOH E 3 1303 13 HOH HOH . T 7 HOH E 4 1304 19 HOH HOH . T 7 HOH E 5 1305 15 HOH HOH . T 7 HOH E 6 1306 14 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 A1A5I . . . I 6 19.531 16.824 -62.019 1 97.27 ? C1 A1A5I 503 A 1 HETATM 2 C C2 A1A5I . . . I 6 18.547 15.89 -62.315 1 102.63 ? C2 A1A5I 503 A 1 HETATM 3 C C3 A1A5I . . . I 6 17.367 15.856 -61.59 1 102.17 ? C3 A1A5I 503 A 1 HETATM 4 C C12 A1A5I . . . I 6 15.691 18.582 -57.673 1 92.59 ? C12 A1A5I 503 A 1 HETATM 5 C C13 A1A5I . . . I 6 14.337 19.134 -58.072 1 92.8 ? C13 A1A5I 503 A 1 HETATM 6 C C14 A1A5I . . . I 6 13.566 19.564 -56.836 1 98.24 ? C14 A1A5I 503 A 1 HETATM 7 C C15 A1A5I . . . I 6 13.446 18.458 -55.837 1 100.15 ? C15 A1A5I 503 A 1 HETATM 8 C C17 A1A5I . . . I 6 15.591 17.541 -56.574 1 105.06 ? C17 A1A5I 503 A 1 HETATM 9 C C20 A1A5I . . . I 6 18.354 13.584 -63.035 1 104.98 ? C20 A1A5I 503 A 1 HETATM 10 C C21 A1A5I . . . I 6 19.627 12.82 -62.755 1 104.59 ? C21 A1A5I 503 A 1 HETATM 11 C C22 A1A5I . . . I 6 20.497 12.739 -64.004 1 110.52 ? C22 A1A5I 503 A 1 HETATM 12 C C23 A1A5I . . . I 6 19.72 12.252 -65.218 1 112.82 ? C23 A1A5I 503 A 1 HETATM 13 C C25 A1A5I . . . I 6 17.627 13.015 -64.233 1 108.91 ? C25 A1A5I 503 A 1 HETATM 14 C C26 A1A5I . . . I 6 17.766 12.697 -66.629 1 120.29 ? C26 A1A5I 503 A 1 HETATM 15 C C27 A1A5I . . . I 6 16.323 13.121 -66.601 1 118.78 ? C27 A1A5I 503 A 1 HETATM 16 C C28 A1A5I . . . I 6 20.573 12.192 -66.47 1 115.96 ? C28 A1A5I 503 A 1 HETATM 17 C C4 A1A5I . . . I 6 17.178 16.763 -60.558 1 95.67 ? C4 A1A5I 503 A 1 HETATM 18 C C5 A1A5I . . . I 6 18.147 17.705 -60.267 1 97.79 ? C5 A1A5I 503 A 1 HETATM 19 C C6 A1A5I . . . I 6 19.334 17.732 -60.993 1 93.79 ? C6 A1A5I 503 A 1 HETATM 20 C C7 A1A5I . . . I 6 16.042 16.895 -59.589 1 94.71 ? C7 A1A5I 503 A 1 HETATM 21 C C9 A1A5I . . . I 6 17.655 18.566 -59.169 1 102.06 ? C9 A1A5I 503 A 1 HETATM 22 N N16 A1A5I . . . I 6 14.471 17.558 -55.786 1 105.47 ? N16 A1A5I 503 A 1 HETATM 23 N N24 A1A5I . . . I 6 18.501 13.047 -65.409 1 113.73 ? N24 A1A5I 503 A 1 HETATM 24 N N8 A1A5I . . . I 6 16.457 18.048 -58.786 1 96.37 ? N8 A1A5I 503 A 1 HETATM 25 O O10 A1A5I . . . I 6 18.713 14.959 -63.312 1 104.05 ? O10 A1A5I 503 A 1 HETATM 26 O O11 A1A5I . . . I 6 18.161 19.568 -58.705 1 101.11 ? O11 A1A5I 503 A 1 HETATM 27 O O18 A1A5I . . . I 6 16.496 16.739 -56.37 1 109.7 ? O18 A1A5I 503 A 1 HETATM 28 O O19 A1A5I . . . I 6 12.482 18.345 -55.089 1 94.91 ? O19 A1A5I 503 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #