data_1UDT # _model_server_result.job_id JSWyHiNtwOnTtrtefZS96g _model_server_result.datetime_utc '2024-11-28 17:26:09' _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 1udt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1000}' # _entry.id 1UDT # _exptl.entry_id 1UDT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 474.576 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE _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 1UDT _cell.length_a 60.122 _cell.length_b 155.632 _cell.length_c 89.896 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1UDT _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 4 _struct_asym.id D _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 E O HOH . A HOH 29 1_555 C MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc2 E O HOH . A HOH 72 1_555 C MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc3 E O HOH . A HOH 73 1_555 C MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc4 E O HOH . A HOH 76 1_555 C MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc5 E O HOH . A HOH 77 1_555 B ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc6 E O HOH . A HOH 77 1_555 C MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc7 E O HOH . A HOH 78 1_555 B ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc8 A NE2 HIS 81 A HIS 617 1_555 B ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc9 A NE2 HIS 117 A HIS 653 1_555 B ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc10 A OD2 ASP 118 A ASP 654 1_555 B ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc11 A OD1 ASP 118 A ASP 654 1_555 C MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc12 A OD1 ASP 228 A ASP 764 1_555 B ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? # _chem_comp.formula 'C22 H30 N6 O4 S' _chem_comp.formula_weight 474.576 _chem_comp.id VIA _chem_comp.mon_nstd_flag . _chem_comp.name 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms SILDENAFIL;VIAGRA # 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 C34 C33 VIA sing 376 n n C34 H341 VIA sing 377 n n C34 H342 VIA sing 378 n n C34 H343 VIA sing 379 n n C33 C32 VIA sing 380 n n C33 H331 VIA sing 381 n n C33 H332 VIA sing 382 n n C32 C30 VIA sing 383 n n C32 H321 VIA sing 384 n n C32 H322 VIA sing 385 n n C30 N29 VIA doub 386 n y C30 C25 VIA sing 387 n y N29 N28 VIA sing 388 n y N28 C31 VIA sing 389 n n N28 C24 VIA sing 390 n y C31 H311 VIA sing 391 n n C31 H312 VIA sing 392 n n C31 H313 VIA sing 393 n n C24 C23 VIA sing 394 n y C24 C25 VIA doub 395 n y C23 O27 VIA doub 396 n n C23 N22 VIA sing 397 n y N22 C21 VIA sing 398 n y N22 H22 VIA sing 399 n n C21 N26 VIA doub 400 n y C21 C9 VIA sing 401 n y N26 C25 VIA sing 402 n y C9 C8 VIA doub 403 n y C9 C4 VIA sing 404 n y C8 C7 VIA sing 405 n y C8 H8 VIA sing 406 n n C7 C6 VIA doub 407 n y C7 S10 VIA sing 408 n n C6 C5 VIA sing 409 n y C6 H6 VIA sing 410 n n C5 C4 VIA doub 411 n y C5 H5 VIA sing 412 n n C4 O3 VIA sing 413 n n O3 C2 VIA sing 414 n n C2 C1 VIA sing 415 n n C2 H21 VIA sing 416 n n C2 H22A VIA sing 417 n n C1 H11 VIA sing 418 n n C1 H12 VIA sing 419 n n C1 H13 VIA sing 420 n n S10 O11 VIA doub 421 n n S10 O12 VIA doub 422 n n S10 N14 VIA sing 423 n n N14 C19 VIA sing 424 n n N14 C15 VIA sing 425 n n C19 C18 VIA sing 426 n n C19 H191 VIA sing 427 n n C19 H192 VIA sing 428 n n C18 N17 VIA sing 429 n n C18 H181 VIA sing 430 n n C18 H182 VIA sing 431 n n N17 C20 VIA sing 432 n n N17 C16 VIA sing 433 n n C20 H201 VIA sing 434 n n C20 H202 VIA sing 435 n n C20 H203 VIA sing 436 n n C16 C15 VIA sing 437 n n C16 H161 VIA sing 438 n n C16 H162 VIA sing 439 n n C15 H151 VIA sing 440 n n C15 H152 VIA sing 441 n n # _atom_sites.entry_id 1UDT _atom_sites.fract_transf_matrix[1][1] 0.016633 _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] 0.006425 _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] 0.011124 _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 B 2 ZN A 1 1001 1001 ZN ZN2 . C 3 MG A 1 1002 1002 MG MG2 . D 4 VIA A 1 1000 1000 VIA VIA . E 5 HOH A 1 1 1 HOH WAT . E 5 HOH A 2 2 2 HOH WAT . E 5 HOH A 3 3 3 HOH WAT . E 5 HOH A 4 4 4 HOH WAT . E 5 HOH A 5 5 5 HOH WAT . E 5 HOH A 6 6 6 HOH WAT . E 5 HOH A 7 7 7 HOH WAT . E 5 HOH A 8 8 8 HOH WAT . E 5 HOH A 9 9 9 HOH WAT . E 5 HOH A 10 10 10 HOH WAT . E 5 HOH A 11 11 11 HOH WAT . E 5 HOH A 12 12 12 HOH WAT . E 5 HOH A 13 13 13 HOH WAT . E 5 HOH A 14 14 14 HOH WAT . E 5 HOH A 15 15 15 HOH WAT . E 5 HOH A 16 16 16 HOH WAT . E 5 HOH A 17 17 17 HOH WAT . E 5 HOH A 18 18 18 HOH WAT . E 5 HOH A 19 19 19 HOH WAT . E 5 HOH A 20 20 20 HOH WAT . E 5 HOH A 21 21 21 HOH WAT . E 5 HOH A 22 22 22 HOH WAT . E 5 HOH A 23 23 23 HOH WAT . E 5 HOH A 24 24 24 HOH WAT . E 5 HOH A 25 25 25 HOH WAT . E 5 HOH A 26 26 26 HOH WAT . E 5 HOH A 27 27 27 HOH WAT . E 5 HOH A 28 28 28 HOH WAT . E 5 HOH A 29 29 29 HOH WAT . E 5 HOH A 30 30 30 HOH WAT . E 5 HOH A 31 31 31 HOH WAT . E 5 HOH A 32 32 32 HOH WAT . E 5 HOH A 33 33 33 HOH WAT . E 5 HOH A 34 34 34 HOH WAT . E 5 HOH A 35 35 35 HOH WAT . E 5 HOH A 36 36 36 HOH WAT . E 5 HOH A 37 37 37 HOH WAT . E 5 HOH A 38 38 38 HOH WAT . E 5 HOH A 39 39 39 HOH WAT . E 5 HOH A 40 40 40 HOH WAT . E 5 HOH A 41 41 41 HOH WAT . E 5 HOH A 42 42 42 HOH WAT . E 5 HOH A 43 43 43 HOH WAT . E 5 HOH A 44 44 44 HOH WAT . E 5 HOH A 45 45 45 HOH WAT . E 5 HOH A 46 46 46 HOH WAT . E 5 HOH A 47 47 47 HOH WAT . E 5 HOH A 48 48 48 HOH WAT . E 5 HOH A 49 49 49 HOH WAT . E 5 HOH A 50 50 50 HOH WAT . E 5 HOH A 51 51 51 HOH WAT . E 5 HOH A 52 52 52 HOH WAT . E 5 HOH A 53 53 53 HOH WAT . E 5 HOH A 54 54 54 HOH WAT . E 5 HOH A 55 55 55 HOH WAT . E 5 HOH A 56 56 56 HOH WAT . E 5 HOH A 57 57 57 HOH WAT . E 5 HOH A 58 58 58 HOH WAT . E 5 HOH A 59 59 59 HOH WAT . E 5 HOH A 60 60 60 HOH WAT . E 5 HOH A 61 61 61 HOH WAT . E 5 HOH A 62 62 62 HOH WAT . E 5 HOH A 63 63 63 HOH WAT . E 5 HOH A 64 64 64 HOH WAT . E 5 HOH A 65 65 65 HOH WAT . E 5 HOH A 66 66 66 HOH WAT . E 5 HOH A 67 67 67 HOH WAT . E 5 HOH A 68 68 68 HOH WAT . E 5 HOH A 69 69 69 HOH WAT . E 5 HOH A 70 70 70 HOH WAT . E 5 HOH A 71 71 71 HOH WAT . E 5 HOH A 72 72 72 HOH WAT . E 5 HOH A 73 73 73 HOH WAT . E 5 HOH A 74 74 74 HOH WAT . E 5 HOH A 75 75 75 HOH WAT . E 5 HOH A 76 76 76 HOH WAT . E 5 HOH A 77 77 77 HOH WAT . E 5 HOH A 78 78 78 HOH WAT . # 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 C34 VIA . . . D 4 -0.132 61.467 80.12 1 52.65 ? C34 VIA 1000 A 1 HETATM 2 C C33 VIA . . . D 4 -0.169 61.792 81.589 1 38.29 ? C33 VIA 1000 A 1 HETATM 3 C C32 VIA . . . D 4 -1.261 62.864 81.927 1 38.55 ? C32 VIA 1000 A 1 HETATM 4 C C30 VIA . . . D 4 -1.114 63.031 83.405 1 36.46 ? C30 VIA 1000 A 1 HETATM 5 N N29 VIA . . . D 4 -1.798 62.28 84.37 1 36.25 ? N29 VIA 1000 A 1 HETATM 6 N N28 VIA . . . D 4 -1.414 62.696 85.612 1 32.6 ? N28 VIA 1000 A 1 HETATM 7 C C31 VIA . . . D 4 -1.948 62.111 86.845 1 26.92 ? C31 VIA 1000 A 1 HETATM 8 C C24 VIA . . . D 4 -0.495 63.7 85.44 1 33.71 ? C24 VIA 1000 A 1 HETATM 9 C C23 VIA . . . D 4 0.26 64.519 86.346 1 30.27 ? C23 VIA 1000 A 1 HETATM 10 O O27 VIA . . . D 4 0.18 64.422 87.549 1 37.49 ? O27 VIA 1000 A 1 HETATM 11 N N22 VIA . . . D 4 1.125 65.474 85.816 1 33.4 ? N22 VIA 1000 A 1 HETATM 12 C C21 VIA . . . D 4 1.308 65.684 84.442 1 24.38 ? C21 VIA 1000 A 1 HETATM 13 N N26 VIA . . . D 4 0.597 64.907 83.52 1 27.33 ? N26 VIA 1000 A 1 HETATM 14 C C25 VIA . . . D 4 -0.293 63.928 84.046 1 31.4 ? C25 VIA 1000 A 1 HETATM 15 C C9 VIA . . . D 4 2.223 66.702 84.058 1 31.75 ? C9 VIA 1000 A 1 HETATM 16 C C8 VIA . . . D 4 1.731 67.655 83.084 1 33.1 ? C8 VIA 1000 A 1 HETATM 17 C C7 VIA . . . D 4 2.568 68.758 82.617 1 39.52 ? C7 VIA 1000 A 1 HETATM 18 C C6 VIA . . . D 4 3.952 68.86 83.18 1 40.25 ? C6 VIA 1000 A 1 HETATM 19 C C5 VIA . . . D 4 4.466 67.911 84.162 1 37.38 ? C5 VIA 1000 A 1 HETATM 20 C C4 VIA . . . D 4 3.609 66.806 84.633 1 32.41 ? C4 VIA 1000 A 1 HETATM 21 O O3 VIA . . . D 4 4.019 65.83 85.62 1 29.92 ? O3 VIA 1000 A 1 HETATM 22 C C2 VIA . . . D 4 5.304 65.803 86.273 1 29.07 ? C2 VIA 1000 A 1 HETATM 23 C C1 VIA . . . D 4 5.234 64.623 87.228 1 23.74 ? C1 VIA 1000 A 1 HETATM 24 S S10 VIA . . . D 4 2.023 69.831 81.561 1 45.77 ? S10 VIA 1000 A 1 HETATM 25 O O11 VIA . . . D 4 2.313 69.6 80.294 1 38.87 ? O11 VIA 1000 A 1 HETATM 26 O O12 VIA . . . D 4 0.712 69.861 81.611 1 41.13 ? O12 VIA 1000 A 1 HETATM 27 N N14 VIA . . . D 4 2.69 71.159 82.127 1 44.64 ? N14 VIA 1000 A 1 HETATM 28 C C19 VIA . . . D 4 1.724 72.087 82.963 1 35.86 ? C19 VIA 1000 A 1 HETATM 29 C C18 VIA . . . D 4 0.82 73.057 82.178 1 38.91 ? C18 VIA 1000 A 1 HETATM 30 N N17 VIA . . . D 4 1.426 73.686 80.956 1 49.12 ? N17 VIA 1000 A 1 HETATM 31 C C20 VIA . . . D 4 1.557 75.156 81.201 1 44.96 ? C20 VIA 1000 A 1 HETATM 32 C C16 VIA . . . D 4 2.752 73.145 80.416 1 44.41 ? C16 VIA 1000 A 1 HETATM 33 C C15 VIA . . . D 4 3.539 72.092 81.285 1 42.86 ? C15 VIA 1000 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 348 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 33 #