data_5V3O # _model_server_result.job_id du9mC7_Kr8nqSPYmRrL6BQ _model_server_result.datetime_utc '2024-12-03 14:06:28' _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 5v3o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5V3O # _exptl.entry_id 5V3O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 449.499 _entity.id 3 _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 5V3O _cell.length_a 111.029 _cell.length_b 126.886 _cell.length_c 172.487 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5V3O _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 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 3 _struct_asym.id C _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 A SG CYS 18 A CYS 18 1_555 A SG CYS 313 A CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc1 B SG CYS 287 C CYS 323 1_555 D ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc2 B SG CYS 290 C CYS 326 1_555 D ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc3 B SG CYS 358 C CYS 394 1_555 D ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? # _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 5V3O _atom_sites.fract_transf_matrix[1][1] 0.009007 _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] 0.007881 _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] 0.005798 _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 C 3 8W7 C 1 501 1 8W7 MOL . D 4 ZN C 1 502 1 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 . . . C 3 46.852 57.264 -37.745 1 86.55 ? C1 8W7 501 C 1 HETATM 2 C C2 8W7 . . . C 3 48.184 56.909 -37.929 1 89.71 ? C2 8W7 501 C 1 HETATM 3 C C3 8W7 . . . C 3 48.536 55.584 -38.181 1 90.04 ? C3 8W7 501 C 1 HETATM 4 C C4 8W7 . . . C 3 45.85 56.301 -37.811 1 82.76 ? C4 8W7 501 C 1 HETATM 5 C C5 8W7 . . . C 3 46.189 54.974 -38.067 1 85.85 ? C5 8W7 501 C 1 HETATM 6 C C6 8W7 . . . C 3 47.524 54.639 -38.246 1 88.07 ? C6 8W7 501 C 1 HETATM 7 N N1 8W7 . . . C 3 46.215 52.745 -38.429 1 84.07 ? N1 8W7 501 C 1 HETATM 8 N N2 8W7 . . . C 3 46.751 49.123 -37.876 1 76.68 ? N2 8W7 501 C 1 HETATM 9 N N3 8W7 . . . C 3 52.11 56.375 -31.64 1 156.93 ? N3 8W7 501 C 1 HETATM 10 O O1 8W7 . . . C 3 44.215 53.752 -38.073 1 82.86 ? O1 8W7 501 C 1 HETATM 11 C C7 8W7 . . . C 3 47.624 53.143 -38.5 1 89.01 ? C7 8W7 501 C 1 HETATM 12 C C8 8W7 . . . C 3 45.439 53.803 -38.188 1 85.74 ? C8 8W7 501 C 1 HETATM 13 C C9 8W7 . . . C 3 45.746 51.361 -38.589 1 79.34 ? C9 8W7 501 C 1 HETATM 14 C C10 8W7 . . . C 3 46.037 50.876 -40.006 1 78.72 ? C10 8W7 501 C 1 HETATM 15 C C11 8W7 . . . C 3 45.664 49.402 -40.156 1 78.33 ? C11 8W7 501 C 1 HETATM 16 C C12 8W7 . . . C 3 46.382 48.56 -39.103 1 75.17 ? C12 8W7 501 C 1 HETATM 17 C C13 8W7 . . . C 3 46.47 50.464 -37.579 1 77.38 ? C13 8W7 501 C 1 HETATM 18 C C14 8W7 . . . C 3 50.815 56.111 -37.893 1 110.21 ? C14 8W7 501 C 1 HETATM 19 C C15 8W7 . . . C 3 51.339 56.006 -36.606 1 116.25 ? C15 8W7 501 C 1 HETATM 20 O O2 8W7 . . . C 3 46.805 50.921 -36.488 1 76.08 ? O2 8W7 501 C 1 HETATM 21 C C22 8W7 . . . C 3 52.218 55.738 -30.316 1 162.92 ? C22 8W7 501 C 1 HETATM 22 C C23 8W7 . . . C 3 51.304 56.472 -29.328 1 167.58 ? C23 8W7 501 C 1 HETATM 23 O O5 8W7 . . . C 3 51.619 57.881 -29.265 1 166.88 ? O5 8W7 501 C 1 HETATM 24 C C24 8W7 . . . C 3 51.523 58.492 -30.565 1 158.51 ? C24 8W7 501 C 1 HETATM 25 C C25 8W7 . . . C 3 52.504 57.787 -31.504 1 157.68 ? C25 8W7 501 C 1 HETATM 26 C C21 8W7 . . . C 3 52.979 55.688 -32.615 1 142.17 ? C21 8W7 501 C 1 HETATM 27 C C20 8W7 . . . C 3 52.396 55.795 -34.032 1 124.23 ? C20 8W7 501 C 1 HETATM 28 C C19 8W7 . . . C 3 52.255 54.66 -34.824 1 118.04 ? C19 8W7 501 C 1 HETATM 29 C C17 8W7 . . . C 3 51.728 54.763 -36.107 1 117.37 ? C17 8W7 501 C 1 HETATM 30 C C18 8W7 . . . C 3 52.009 57.032 -34.539 1 121.75 ? C18 8W7 501 C 1 HETATM 31 C C16 8W7 . . . C 3 51.482 57.146 -35.82 1 118.47 ? C16 8W7 501 C 1 HETATM 32 O O4 8W7 . . . C 3 49.829 55.182 -38.371 1 98.13 ? O4 8W7 501 C 1 HETATM 33 O O3 8W7 . . . C 3 46.639 47.381 -39.333 1 75.95 ? O3 8W7 501 C 1 # _model_server_stats.io_time_ms 130 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 67 _model_server_stats.query_time_ms 470 _model_server_stats.encode_time_ms 108 _model_server_stats.element_count 33 #