data_5DSY # _model_server_result.job_id WwIteE5gbksgGvJE3Tap4Q _model_server_result.datetime_utc '2024-11-05 08:02:31' _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 5dsy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1001}' # _entry.id 5DSY # _exptl.entry_id 5DSY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 537.528 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide _entity.pdbx_number_of_molecules 4 _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 5DSY _cell.length_a 92.163 _cell.length_b 119.9 _cell.length_c 120.739 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DSY _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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I 1 1 B,F,J 2 1 C,G,K 3 1 D,H,L 4 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 ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N # _chem_comp.formula 'C24 H27 N9 O6' _chem_comp.formula_weight 537.528 _chem_comp.id UHB _chem_comp.mon_nstd_flag . _chem_comp.name 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide _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 C01 C02 UHB doub 358 n y C01 C06 UHB sing 359 n y C02 C03 UHB sing 360 n y C03 C04 UHB doub 361 n y C04 C05 UHB sing 362 n y C04 N11 UHB sing 363 n n C05 C06 UHB doub 364 n y C05 C08 UHB sing 365 n n C06 C07 UHB sing 366 n n C07 N09 UHB sing 367 n n C07 O10 UHB doub 368 n n C08 N09 UHB sing 369 n n N11 C12 UHB sing 370 n n C12 O13 UHB doub 371 n n C12 C14 UHB sing 372 n n C14 N15 UHB sing 373 n n N15 C16 UHB sing 374 n n N15 C20 UHB sing 375 n n C16 C17 UHB sing 376 n n C17 N18 UHB sing 377 n n N18 C19 UHB sing 378 n n N18 C21 UHB sing 379 n n C19 C20 UHB sing 380 n n C21 C22 UHB sing 381 n n C21 O27 UHB doub 382 n n C22 C23 UHB sing 383 n n C22 O26 UHB sing 384 n n C23 C24 UHB sing 385 n n C23 O28 UHB sing 386 n n C24 C25 UHB sing 387 n n C24 O29 UHB sing 388 n n C25 O26 UHB sing 389 n n C25 N30 UHB sing 390 n n N30 C32 UHB sing 391 n y N30 C33 UHB sing 392 n y C31 C32 UHB doub 393 n y C31 N34 UHB sing 394 n y C31 C38 UHB sing 395 n y C32 N37 UHB sing 396 n y C33 N34 UHB doub 397 n y N35 C36 UHB sing 398 n y N35 C38 UHB doub 399 n y C36 N37 UHB doub 400 n y C38 N39 UHB sing 401 n n C01 H01 UHB sing 402 n n C02 H02 UHB sing 403 n n C03 H03 UHB sing 404 n n C08 H081 UHB sing 405 n n C08 H082 UHB sing 406 n n N09 HN09 UHB sing 407 n n C14 H14 UHB sing 408 n n C14 H14A UHB sing 409 n n C16 H16 UHB sing 410 n n C16 H16A UHB sing 411 n n C17 H17 UHB sing 412 n n C17 H17A UHB sing 413 n n C19 H19 UHB sing 414 n n C19 H19A UHB sing 415 n n C20 H20 UHB sing 416 n n C20 H20A UHB sing 417 n n C22 H22 UHB sing 418 n n C23 H23 UHB sing 419 n n C24 H24 UHB sing 420 n n C25 H25 UHB sing 421 n n O28 HO28 UHB sing 422 n n O29 HO29 UHB sing 423 n n C33 H33 UHB sing 424 n n C36 H36 UHB sing 425 n n N39 HN39 UHB sing 426 n n N39 HN3A UHB sing 427 n n N11 HN11 UHB sing 428 n n # _atom_sites.entry_id 5DSY _atom_sites.fract_transf_matrix[1][1] 0.01085 _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] 0.00834 _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] 0.008282 _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 E 2 UHB A 1 1001 1001 UHB UHB . F 2 UHB B 1 1001 1001 UHB UHB . G 2 UHB C 1 1001 1001 UHB UHB . H 2 UHB D 1 1001 1001 UHB UHB . I 3 HOH A 1 1101 23 HOH HOH . I 3 HOH A 2 1102 21 HOH HOH . I 3 HOH A 3 1103 8 HOH HOH . I 3 HOH A 4 1104 51 HOH HOH . I 3 HOH A 5 1105 33 HOH HOH . I 3 HOH A 6 1106 60 HOH HOH . I 3 HOH A 7 1107 9 HOH HOH . I 3 HOH A 8 1108 5 HOH HOH . I 3 HOH A 9 1109 55 HOH HOH . I 3 HOH A 10 1110 2 HOH HOH . I 3 HOH A 11 1111 4 HOH HOH . I 3 HOH A 12 1112 1 HOH HOH . I 3 HOH A 13 1113 6 HOH HOH . J 3 HOH B 1 1101 50 HOH HOH . J 3 HOH B 2 1102 3 HOH HOH . J 3 HOH B 3 1103 45 HOH HOH . J 3 HOH B 4 1104 47 HOH HOH . J 3 HOH B 5 1105 30 HOH HOH . J 3 HOH B 6 1106 29 HOH HOH . J 3 HOH B 7 1107 34 HOH HOH . J 3 HOH B 8 1108 46 HOH HOH . J 3 HOH B 9 1109 58 HOH HOH . J 3 HOH B 10 1110 24 HOH HOH . J 3 HOH B 11 1111 18 HOH HOH . J 3 HOH B 12 1112 49 HOH HOH . K 3 HOH C 1 1101 19 HOH HOH . K 3 HOH C 2 1102 25 HOH HOH . K 3 HOH C 3 1103 41 HOH HOH . K 3 HOH C 4 1104 44 HOH HOH . K 3 HOH C 5 1105 36 HOH HOH . K 3 HOH C 6 1106 39 HOH HOH . K 3 HOH C 7 1107 42 HOH HOH . K 3 HOH C 8 1108 43 HOH HOH . K 3 HOH C 9 1109 40 HOH HOH . K 3 HOH C 10 1110 32 HOH HOH . K 3 HOH C 11 1111 31 HOH HOH . K 3 HOH C 12 1112 26 HOH HOH . K 3 HOH C 13 1113 28 HOH HOH . K 3 HOH C 14 1114 38 HOH HOH . K 3 HOH C 15 1115 35 HOH HOH . K 3 HOH C 16 1116 37 HOH HOH . K 3 HOH C 17 1117 27 HOH HOH . L 3 HOH D 1 1101 54 HOH HOH . L 3 HOH D 2 1102 17 HOH HOH . L 3 HOH D 3 1103 14 HOH HOH . L 3 HOH D 4 1104 13 HOH HOH . L 3 HOH D 5 1105 20 HOH HOH . L 3 HOH D 6 1106 15 HOH HOH . L 3 HOH D 7 1107 16 HOH HOH . L 3 HOH D 8 1108 61 HOH HOH . L 3 HOH D 9 1109 53 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 C01 UHB . . . F 2 29.643 31.813 -21.022 1 34.07 ? C01 UHB 1001 B 1 HETATM 2 C C02 UHB . . . F 2 30.687 31.451 -20.188 1 37.76 ? C02 UHB 1001 B 1 HETATM 3 C C03 UHB . . . F 2 31.631 32.382 -19.804 1 36.34 ? C03 UHB 1001 B 1 HETATM 4 C C04 UHB . . . F 2 31.521 33.696 -20.247 1 35.25 ? C04 UHB 1001 B 1 HETATM 5 C C05 UHB . . . F 2 30.473 34.087 -21.105 1 33.1 ? C05 UHB 1001 B 1 HETATM 6 C C06 UHB . . . F 2 29.551 33.122 -21.477 1 30.46 ? C06 UHB 1001 B 1 HETATM 7 C C07 UHB . . . F 2 28.548 33.746 -22.374 1 38.09 ? C07 UHB 1001 B 1 HETATM 8 C C08 UHB . . . F 2 30.098 35.393 -21.75 1 36.53 ? C08 UHB 1001 B 1 HETATM 9 N N09 UHB . . . F 2 28.919 35.039 -22.516 1 36.49 ? N09 UHB 1001 B 1 HETATM 10 O O10 UHB . . . F 2 27.538 33.228 -22.866 1 38.54 ? O10 UHB 1001 B 1 HETATM 11 N N11 UHB . . . F 2 32.45 34.657 -19.757 1 41.29 ? N11 UHB 1001 B 1 HETATM 12 C C12 UHB . . . F 2 33.155 35.619 -20.388 1 37.82 ? C12 UHB 1001 B 1 HETATM 13 O O13 UHB . . . F 2 33.147 35.786 -21.603 1 42.8 ? O13 UHB 1001 B 1 HETATM 14 C C14 UHB . . . F 2 33.969 36.513 -19.466 1 34.32 ? C14 UHB 1001 B 1 HETATM 15 N N15 UHB . . . F 2 34.204 37.872 -19.961 1 38.03 ? N15 UHB 1001 B 1 HETATM 16 C C16 UHB . . . F 2 32.953 38.501 -20.414 1 37.38 ? C16 UHB 1001 B 1 HETATM 17 C C17 UHB . . . F 2 33.21 39.909 -20.903 1 37.55 ? C17 UHB 1001 B 1 HETATM 18 N N18 UHB . . . F 2 34.169 39.869 -22.006 1 46.17 ? N18 UHB 1001 B 1 HETATM 19 C C19 UHB . . . F 2 35.429 39.28 -21.553 1 41.88 ? C19 UHB 1001 B 1 HETATM 20 C C20 UHB . . . F 2 35.184 37.875 -21.057 1 41.24 ? C20 UHB 1001 B 1 HETATM 21 C C21 UHB . . . F 2 33.979 40.236 -23.286 1 44.26 ? C21 UHB 1001 B 1 HETATM 22 C C22 UHB . . . F 2 32.653 40.801 -23.762 1 45.07 ? C22 UHB 1001 B 1 HETATM 23 C C23 UHB . . . F 2 31.572 39.712 -23.857 1 44.76 ? C23 UHB 1001 B 1 HETATM 24 C C24 UHB . . . F 2 31.207 39.692 -25.344 1 45.23 ? C24 UHB 1001 B 1 HETATM 25 C C25 UHB . . . F 2 31.597 41.101 -25.765 1 45.2 ? C25 UHB 1001 B 1 HETATM 26 O O26 UHB . . . F 2 32.789 41.374 -25.07 1 44.39 ? O26 UHB 1001 B 1 HETATM 27 O O27 UHB . . . F 2 34.851 40.107 -24.115 1 48.96 ? O27 UHB 1001 B 1 HETATM 28 O O28 UHB . . . F 2 30.46 40.094 -23.062 1 41.75 ? O28 UHB 1001 B 1 HETATM 29 O O29 UHB . . . F 2 29.806 39.488 -25.493 1 42.84 ? O29 UHB 1001 B 1 HETATM 30 N N30 UHB . . . F 2 31.847 41.258 -27.191 1 44.78 ? N30 UHB 1001 B 1 HETATM 31 C C31 UHB . . . F 2 31.964 42.037 -29.244 1 44.54 ? C31 UHB 1001 B 1 HETATM 32 C C32 UHB . . . F 2 31.644 42.388 -27.944 1 44.31 ? C32 UHB 1001 B 1 HETATM 33 C C33 UHB . . . F 2 32.288 40.303 -28.068 1 47.45 ? C33 UHB 1001 B 1 HETATM 34 N N34 UHB . . . F 2 32.383 40.718 -29.308 1 46.21 ? N34 UHB 1001 B 1 HETATM 35 N N35 UHB . . . F 2 31.229 44.19 -29.856 1 48.71 ? N35 UHB 1001 B 1 HETATM 36 C C36 UHB . . . F 2 30.981 44.395 -28.557 1 50.44 ? C36 UHB 1001 B 1 HETATM 37 N N37 UHB . . . F 2 31.16 43.564 -27.528 1 49.48 ? N37 UHB 1001 B 1 HETATM 38 C C38 UHB . . . F 2 31.735 42.999 -30.24 1 45.09 ? C38 UHB 1001 B 1 HETATM 39 N N39 UHB . . . F 2 31.944 42.781 -31.535 1 47.09 ? N39 UHB 1001 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 39 #