data_8D80 # _model_server_result.job_id pavUph2AZDt24q8pxThlvw _model_server_result.datetime_utc '2025-02-05 10:46:57' _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 8d80 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":502}' # _entry.id 8D80 # _exptl.entry_id 8D80 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 449.499 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-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 90 _cell.angle_gamma 90 _cell.entry_id 8D80 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8D80 _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc2 B SG CYS 326 B CYS 326 1_555 D ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc3 B SG CYS 391 B CYS 391 1_555 D ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc4 B SG CYS 394 B CYS 394 1_555 D ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc5 C SG CYS 38 C CYS 147 1_555 F ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc6 C NE2 HIS 54 C HIS 163 1_555 F ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc7 C NE2 HIS 58 C HIS 167 1_555 F ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? # _chem_comp.formula 'C25 H27 N3 O5' _chem_comp.formula_weight 449.499 _chem_comp.id 8W7 _chem_comp.mon_nstd_flag . _chem_comp.name (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-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 C11 C10 8W7 sing 1 n n C11 C12 8W7 sing 2 n n C10 C9 8W7 sing 3 n n O3 C12 8W7 doub 4 n n C12 N2 8W7 sing 5 n n C9 N1 8W7 sing 6 n n C9 C13 8W7 sing 7 n n C7 N1 8W7 sing 8 n n C7 C6 8W7 sing 9 n n N1 C8 8W7 sing 10 n n O4 C3 8W7 sing 11 n n O4 C14 8W7 sing 12 n n C6 C3 8W7 doub 13 n y C6 C5 8W7 sing 14 n y C8 O1 8W7 doub 15 n n C8 C5 8W7 sing 16 n n C3 C2 8W7 sing 17 n y C5 C4 8W7 doub 18 n y C2 C1 8W7 doub 19 n y C14 C15 8W7 sing 20 n n N2 C13 8W7 sing 21 n n C4 C1 8W7 sing 22 n y C13 O2 8W7 doub 23 n n C15 C17 8W7 doub 24 n y C15 C16 8W7 sing 25 n y C17 C19 8W7 sing 26 n y C16 C18 8W7 doub 27 n y C19 C20 8W7 doub 28 n y C18 C20 8W7 sing 29 n y C20 C21 8W7 sing 30 n n C21 N3 8W7 sing 31 n n N3 C25 8W7 sing 32 n n N3 C22 8W7 sing 33 n n C25 C24 8W7 sing 34 n n C24 O5 8W7 sing 35 n n C22 C23 8W7 sing 36 n n C23 O5 8W7 sing 37 n n C1 H1 8W7 sing 38 n n C2 H2 8W7 sing 39 n n C4 H3 8W7 sing 40 n n N2 H4 8W7 sing 41 n n C7 H6 8W7 sing 42 n n C7 H7 8W7 sing 43 n n C9 H8 8W7 sing 44 n n C10 H9 8W7 sing 45 n n C10 H10 8W7 sing 46 n n C11 H11 8W7 sing 47 n n C11 H12 8W7 sing 48 n n C14 H13 8W7 sing 49 n n C14 H14 8W7 sing 50 n n C22 H15 8W7 sing 51 n n C22 H16 8W7 sing 52 n n C23 H17 8W7 sing 53 n n C23 H18 8W7 sing 54 n n C24 H19 8W7 sing 55 n n C24 H20 8W7 sing 56 n n C25 H21 8W7 sing 57 n n C25 H22 8W7 sing 58 n n C21 H23 8W7 sing 59 n n C21 H24 8W7 sing 60 n n C19 H25 8W7 sing 61 n n C17 H26 8W7 sing 62 n n C18 H27 8W7 sing 63 n n C16 H28 8W7 sing 64 n n # _atom_sites.entry_id 8D80 _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 8W7 B 1 502 502 8W7 8W7 . 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 C C1 8W7 . . . E 5 105.627 190.471 138.522 1 165.24 ? C1 8W7 502 B 1 HETATM 2 C C2 8W7 . . . E 5 105.794 191.477 139.469 1 165.24 ? C2 8W7 502 B 1 HETATM 3 C C3 8W7 . . . E 5 106.977 191.545 140.197 1 165.24 ? C3 8W7 502 B 1 HETATM 4 C C4 8W7 . . . E 5 106.615 189.531 138.281 1 165.24 ? C4 8W7 502 B 1 HETATM 5 C C5 8W7 . . . E 5 107.784 189.615 139.014 1 165.24 ? C5 8W7 502 B 1 HETATM 6 C C6 8W7 . . . E 5 107.971 190.605 139.96 1 165.24 ? C6 8W7 502 B 1 HETATM 7 N N1 8W7 . . . E 5 109.708 189.128 140.088 1 165.24 ? N1 8W7 502 B 1 HETATM 8 N N2 8W7 . . . E 5 111.134 187.191 142.861 1 165.24 ? N2 8W7 502 B 1 HETATM 9 N N3 8W7 . . . E 5 100.769 190.777 143.396 1 165.24 ? N3 8W7 502 B 1 HETATM 10 O O1 8W7 . . . E 5 109.325 187.926 138.166 1 165.24 ? O1 8W7 502 B 1 HETATM 11 C C7 8W7 . . . E 5 109.32 190.443 140.589 1 165.24 ? C7 8W7 502 B 1 HETATM 12 C C8 8W7 . . . E 5 108.991 188.775 138.988 1 165.24 ? C8 8W7 502 B 1 HETATM 13 C C9 8W7 . . . E 5 110.72 188.284 140.706 1 165.24 ? C9 8W7 502 B 1 HETATM 14 C C10 8W7 . . . E 5 112.001 189.063 140.954 1 165.24 ? C10 8W7 502 B 1 HETATM 15 C C11 8W7 . . . E 5 113.026 188.166 141.641 1 165.24 ? C11 8W7 502 B 1 HETATM 16 C C12 8W7 . . . E 5 112.486 187.461 142.843 1 165.24 ? C12 8W7 502 B 1 HETATM 17 C C13 8W7 . . . E 5 110.185 187.682 141.996 1 165.24 ? C13 8W7 502 B 1 HETATM 18 C C14 8W7 . . . E 5 106.293 193.548 141.307 1 165.24 ? C14 8W7 502 B 1 HETATM 19 C C15 8W7 . . . E 5 105.108 193.02 142.061 1 165.24 ? C15 8W7 502 B 1 HETATM 20 O O2 8W7 . . . E 5 109.005 187.622 142.264 1 165.24 ? O2 8W7 502 B 1 HETATM 21 C C22 8W7 . . . E 5 100.545 189.426 143.899 1 165.24 ? C22 8W7 502 B 1 HETATM 22 C C23 8W7 . . . E 5 99.391 188.78 143.178 1 165.24 ? C23 8W7 502 B 1 HETATM 23 O O5 8W7 . . . E 5 99.046 189.484 141.994 1 165.24 ? O5 8W7 502 B 1 HETATM 24 C C24 8W7 . . . E 5 98.582 190.784 142.327 1 165.24 ? C24 8W7 502 B 1 HETATM 25 C C25 8W7 . . . E 5 99.485 191.466 143.322 1 165.24 ? C25 8W7 502 B 1 HETATM 26 C C21 8W7 . . . E 5 101.717 191.506 144.235 1 165.24 ? C21 8W7 502 B 1 HETATM 27 C C20 8W7 . . . E 5 102.905 192.037 143.472 1 165.24 ? C20 8W7 502 B 1 HETATM 28 C C19 8W7 . . . E 5 104.154 192.088 144.062 1 165.24 ? C19 8W7 502 B 1 HETATM 29 C C17 8W7 . . . E 5 105.246 192.573 143.364 1 165.24 ? C17 8W7 502 B 1 HETATM 30 C C18 8W7 . . . E 5 102.767 192.481 142.169 1 165.24 ? C18 8W7 502 B 1 HETATM 31 C C16 8W7 . . . E 5 103.858 192.966 141.469 1 165.24 ? C16 8W7 502 B 1 HETATM 32 O O4 8W7 . . . E 5 107.246 192.492 141.151 1 165.24 ? O4 8W7 502 B 1 HETATM 33 O O3 8W7 . . . E 5 113.189 187.119 143.774 1 165.24 ? O3 8W7 502 B 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 237 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 33 #