data_1XOT # _model_server_result.job_id y-2GWdnWTwab8h5hyv5-eA _model_server_result.datetime_utc '2024-11-27 01:57:45' _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 1xot # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":101}' # _entry.id 1XOT # _exptl.entry_id 1XOT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 488.603 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-ONE _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 1XOT _cell.length_a 89.841 _cell.length_b 94.423 _cell.length_c 108.755 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XOT _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression B,F,G,H,J 1 1 A,C,D,E,I 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 ? 4 E N N ? 4 H 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 covale ? covale1 A C THR 63 B THR 193 1_555 A N CME 64 B CME 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale2 A C CME 64 B CME 194 1_555 A N ILE 65 B ILE 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale3 B C THR 63 A THR 193 1_555 B N CME 64 A CME 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.317 ? covale ? covale4 B C CME 64 A CME 194 1_555 B N ILE 65 A ILE 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? metalc ? metalc1 A NE2 HIS 108 B HIS 238 1_555 C ZN ZN . B ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc2 A NE2 HIS 144 B HIS 274 1_555 C ZN ZN . B ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc3 A OD2 ASP 145 B ASP 275 1_555 C ZN ZN . B ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc4 A OD1 ASP 145 B ASP 275 1_555 D MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc5 A OD2 ASP 262 B ASP 392 1_555 C ZN ZN . B ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc6 C ZN ZN . B ZN 1001 1_555 I O HOH . B HOH 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc7 C ZN ZN . B ZN 1001 1_555 I O HOH . B HOH 2008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc8 D MG MG . B MG 1002 1_555 I O HOH . B HOH 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc9 D MG MG . B MG 1002 1_555 I O HOH . B HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc10 D MG MG . B MG 1002 1_555 I O HOH . B HOH 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc11 D MG MG . B MG 1002 1_555 I O HOH . B HOH 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc12 D MG MG . B MG 1002 1_555 I O HOH . B HOH 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? metalc ? metalc13 B NE2 HIS 108 A HIS 238 1_555 F ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc14 B NE2 HIS 144 A HIS 274 1_555 F ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc15 B OD2 ASP 145 A ASP 275 1_555 F ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc16 B OD1 ASP 145 A ASP 275 1_555 G MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc17 B OD2 ASP 262 A ASP 392 1_555 F ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? metalc ? metalc18 F ZN ZN . A ZN 1001 1_555 J O HOH . A HOH 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc19 F ZN ZN . A ZN 1001 1_555 J O HOH . A HOH 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.765 ? metalc ? metalc20 G MG MG . A MG 1002 1_555 J O HOH . A HOH 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc21 G MG MG . A MG 1002 1_555 J O HOH . A HOH 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.885 ? metalc ? metalc22 G MG MG . A MG 1002 1_555 J O HOH . A HOH 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc23 G MG MG . A MG 1002 1_555 J O HOH . A HOH 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc24 G MG MG . A MG 1002 1_555 J O HOH . A HOH 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? # _chem_comp.formula 'C23 H32 N6 O4 S' _chem_comp.formula_weight 488.603 _chem_comp.id VDN _chem_comp.mon_nstd_flag . _chem_comp.name 2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-ONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VARDENAFIL, LEVITRA' # 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 C1 C2 VDN sing 397 n n C1 H11 VDN sing 398 n n C1 H12 VDN sing 399 n n C1 H13 VDN sing 400 n n C2 O3 VDN sing 401 n n C2 H21 VDN sing 402 n n C2 H22 VDN sing 403 n n O3 C4 VDN sing 404 n n C4 C5 VDN doub 405 n y C4 C9 VDN sing 406 n y C5 C6 VDN sing 407 n y C5 H5 VDN sing 408 n n C6 C7 VDN doub 409 n y C6 H6 VDN sing 410 n n C7 C8 VDN sing 411 n y C7 S10 VDN sing 412 n n C8 C9 VDN doub 413 n y C8 H8 VDN sing 414 n n C9 C21 VDN sing 415 n y S10 O11 VDN doub 416 n n S10 O12 VDN doub 417 n n S10 N14 VDN sing 418 n n C13 C20 VDN sing 419 n n C13 H131 VDN sing 420 n n C13 H132 VDN sing 421 n n C13 H133 VDN sing 422 n n N14 C15 VDN sing 423 n n N14 C19 VDN sing 424 n n C15 C16 VDN sing 425 n n C15 H151 VDN sing 426 n n C15 H152 VDN sing 427 n n C16 N17 VDN sing 428 n n C16 H161 VDN sing 429 n n C16 H162 VDN sing 430 n n N17 C18 VDN sing 431 n n N17 C20 VDN sing 432 n n C18 C19 VDN sing 433 n n C18 H181 VDN sing 434 n n C18 H182 VDN sing 435 n n C19 H191 VDN sing 436 n n C19 H192 VDN sing 437 n n C20 H201 VDN sing 438 n n C20 H202 VDN sing 439 n n C21 N22 VDN doub 440 n y C21 N26 VDN sing 441 n y N22 C23 VDN sing 442 n y C23 C24 VDN sing 443 n y C23 O27 VDN doub 444 n n C24 N25 VDN sing 445 n y C24 C28 VDN doub 446 n y N25 N26 VDN sing 447 n y N25 C30 VDN sing 448 n y N26 H26 VDN sing 449 n n C28 N29 VDN sing 450 n y C28 C31 VDN sing 451 n n N29 C30 VDN doub 452 n y C30 C32 VDN sing 453 n n C31 H311 VDN sing 454 n n C31 H312 VDN sing 455 n n C31 H313 VDN sing 456 n n C32 C33 VDN sing 457 n n C32 H321 VDN sing 458 n n C32 H322 VDN sing 459 n n C33 C34 VDN sing 460 n n C33 H331 VDN sing 461 n n C33 H332 VDN sing 462 n n C34 H341 VDN sing 463 n n C34 H342 VDN sing 464 n n C34 H343 VDN sing 465 n n # _atom_sites.entry_id 1XOT _atom_sites.fract_transf_matrix[1][1] 0.011131 _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] 0.010591 _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] 0.009195 _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 2 ZN B 1 1001 1001 ZN ZN . D 3 MG B 1 1002 1002 MG MG . E 4 VDN B 1 102 2 VDN LIG . F 2 ZN A 1 1001 1001 ZN ZN . G 3 MG A 1 1002 1002 MG MG . H 4 VDN A 1 101 1 VDN LIG . I 5 HOH B 1 2 2 HOH HOH . I 5 HOH B 2 3 3 HOH HOH . I 5 HOH B 3 4 4 HOH HOH . I 5 HOH B 4 6 6 HOH HOH . I 5 HOH B 5 7 7 HOH HOH . I 5 HOH B 6 10 10 HOH HOH . I 5 HOH B 7 15 15 HOH HOH . I 5 HOH B 8 18 18 HOH HOH . I 5 HOH B 9 19 19 HOH HOH . I 5 HOH B 10 21 21 HOH HOH . I 5 HOH B 11 23 23 HOH HOH . I 5 HOH B 12 24 24 HOH HOH . I 5 HOH B 13 29 29 HOH HOH . I 5 HOH B 14 30 30 HOH HOH . I 5 HOH B 15 31 31 HOH HOH . I 5 HOH B 16 32 32 HOH HOH . I 5 HOH B 17 33 33 HOH HOH . I 5 HOH B 18 34 34 HOH HOH . I 5 HOH B 19 35 35 HOH HOH . I 5 HOH B 20 2003 1003 HOH HOH . I 5 HOH B 21 2004 1004 HOH HOH . I 5 HOH B 22 2005 1005 HOH HOH . I 5 HOH B 23 2006 1006 HOH HOH . I 5 HOH B 24 2007 1007 HOH HOH . I 5 HOH B 25 2008 1008 HOH HOH . J 5 HOH A 1 1 1 HOH HOH . J 5 HOH A 2 5 5 HOH HOH . J 5 HOH A 3 8 8 HOH HOH . J 5 HOH A 4 11 11 HOH HOH . J 5 HOH A 5 13 13 HOH HOH . J 5 HOH A 6 14 14 HOH HOH . J 5 HOH A 7 16 16 HOH HOH . J 5 HOH A 8 17 17 HOH HOH . J 5 HOH A 9 20 20 HOH HOH . J 5 HOH A 10 22 22 HOH HOH . J 5 HOH A 11 25 25 HOH HOH . J 5 HOH A 12 26 26 HOH HOH . J 5 HOH A 13 27 27 HOH HOH . J 5 HOH A 14 28 28 HOH HOH . J 5 HOH A 15 36 36 HOH HOH . J 5 HOH A 16 1003 1003 HOH HOH . J 5 HOH A 17 1004 1004 HOH HOH . J 5 HOH A 18 1005 1005 HOH HOH . J 5 HOH A 19 1006 1006 HOH HOH . J 5 HOH A 20 1007 1007 HOH HOH . J 5 HOH A 21 1008 1008 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 VDN . . . H 4 5.954 2.527 45.653 0.8 64.12 ? C1 VDN 101 A 1 HETATM 2 C C2 VDN . . . H 4 5.36 1.426 44.794 0.8 64.97 ? C2 VDN 101 A 1 HETATM 3 O O3 VDN . . . H 4 5.262 1.833 43.421 0.8 63.14 ? O3 VDN 101 A 1 HETATM 4 C C4 VDN . . . H 4 5.751 0.894 42.563 0.8 65.33 ? C4 VDN 101 A 1 HETATM 5 C C5 VDN . . . H 4 7.135 0.794 42.339 0.8 65.74 ? C5 VDN 101 A 1 HETATM 6 C C6 VDN . . . H 4 7.669 -0.187 41.474 0.8 67.09 ? C6 VDN 101 A 1 HETATM 7 C C7 VDN . . . H 4 6.816 -1.101 40.845 0.8 67.39 ? C7 VDN 101 A 1 HETATM 8 C C8 VDN . . . H 4 5.455 -0.982 41.072 0.8 66.46 ? C8 VDN 101 A 1 HETATM 9 C C9 VDN . . . H 4 4.913 0.004 41.901 0.8 65.38 ? C9 VDN 101 A 1 HETATM 10 S S10 VDN . . . H 4 7.283 -2.24 39.812 0.8 71.54 ? S10 VDN 101 A 1 HETATM 11 O O11 VDN . . . H 4 8.036 -3.298 40.475 0.8 67.73 ? O11 VDN 101 A 1 HETATM 12 O O12 VDN . . . H 4 6.097 -2.792 39.183 0.8 68.88 ? O12 VDN 101 A 1 HETATM 13 C C13 VDN . . . H 4 9.474 -0.119 34.222 0.8 68.82 ? C13 VDN 101 A 1 HETATM 14 N N14 VDN . . . H 4 8.059 -1.535 38.69 0.8 69.4 ? N14 VDN 101 A 1 HETATM 15 C C15 VDN . . . H 4 7.483 -0.263 38.208 0.8 68.76 ? C15 VDN 101 A 1 HETATM 16 C C16 VDN . . . H 4 7.827 -0.104 36.736 0.8 68.1 ? C16 VDN 101 A 1 HETATM 17 N N17 VDN . . . H 4 9.279 -0.196 36.665 0.8 68.06 ? N17 VDN 101 A 1 HETATM 18 C C18 VDN . . . H 4 9.886 -1.453 37.124 0.8 67.97 ? C18 VDN 101 A 1 HETATM 19 C C19 VDN . . . H 4 9.507 -1.707 38.586 0.8 68.55 ? C19 VDN 101 A 1 HETATM 20 C C20 VDN . . . H 4 9.914 0.502 35.54 0.8 68.33 ? C20 VDN 101 A 1 HETATM 21 C C21 VDN . . . H 4 3.442 -0.152 42.026 0.8 64.93 ? C21 VDN 101 A 1 HETATM 22 N N22 VDN . . . H 4 2.703 0.382 43.195 0.8 63.46 ? N22 VDN 101 A 1 HETATM 23 C C23 VDN . . . H 4 1.366 0.498 43.145 0.8 65.07 ? C23 VDN 101 A 1 HETATM 24 C C24 VDN . . . H 4 0.716 0.262 41.822 0.8 66.7 ? C24 VDN 101 A 1 HETATM 25 N N25 VDN . . . H 4 1.349 -0.099 40.719 0.8 65.4 ? N25 VDN 101 A 1 HETATM 26 N N26 VDN . . . H 4 2.736 -0.241 40.738 0.8 63.87 ? N26 VDN 101 A 1 HETATM 27 O O27 VDN . . . H 4 0.675 0.821 44.089 0.8 66.15 ? O27 VDN 101 A 1 HETATM 28 C C28 VDN . . . H 4 -0.65 0.343 41.473 0.8 66.05 ? C28 VDN 101 A 1 HETATM 29 N N29 VDN . . . H 4 -0.711 0.022 40.147 0.8 67.07 ? N29 VDN 101 A 1 HETATM 30 C C30 VDN . . . H 4 0.55 -0.247 39.677 0.8 65.62 ? C30 VDN 101 A 1 HETATM 31 C C31 VDN . . . H 4 -1.838 0.723 42.318 0.8 65.71 ? C31 VDN 101 A 1 HETATM 32 C C32 VDN . . . H 4 0.96 -0.689 38.306 0.8 65.82 ? C32 VDN 101 A 1 HETATM 33 C C33 VDN . . . H 4 0.899 0.442 37.314 0.8 66.27 ? C33 VDN 101 A 1 HETATM 34 C C34 VDN . . . H 4 1.017 -0.166 35.93 0.8 66.54 ? C34 VDN 101 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 34 #