data_1Y3Y # _model_server_result.job_id wB7miKpSSrFPIPZK9NQrYw _model_server_result.datetime_utc '2025-07-15 12:32:20' _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 1y3y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":2222}' # _entry.id 1Y3Y # _exptl.entry_id 1Y3Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 458.552 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (1R,3AS,4R,8AS,8BR)-4-(2-BENZO[1,3]DIOXOL-5-YL-1-CYCLOPROPYL-3-OXO-DECAHYDRO-PYRROLO[3,4-A]PYRROLIZIN-4-YL)-BENZAMIDINE _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 120 _cell.entry_id 1Y3Y _cell.length_a 54.852 _cell.length_b 54.852 _cell.length_c 109.166 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Y3Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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 _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 7 A CYS 22 1_555 A SG CYS 137 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 25 A CYS 42 1_555 A SG CYS 41 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 109 A CYS 128 1_555 A SG CYS 210 A CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf4 A SG CYS 116 A CYS 136 1_555 A SG CYS 183 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf5 A SG CYS 148 A CYS 168 1_555 A SG CYS 162 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf6 A SG CYS 173 A CYS 191 1_555 A SG CYS 197 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc1 A OE1 GLU 52 A GLU 70 1_555 B CA CA . A CA 3333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc2 A O ASN 54 A ASN 72 1_555 B CA CA . A CA 3333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc3 A O VAL 57 A VAL 75 1_555 B CA CA . A CA 3333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc4 A OE2 GLU 62 A GLU 80 1_555 B CA CA . A CA 3333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc5 B CA CA . A CA 3333 1_555 D O HOH . A HOH 9017 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc6 B CA CA . A CA 3333 1_555 D O HOH . A HOH 9020 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? # _chem_comp.formula 'C27 H30 N4 O3' _chem_comp.formula_weight 458.552 _chem_comp.id UIR _chem_comp.mon_nstd_flag . _chem_comp.name (1R,3AS,4R,8AS,8BR)-4-(2-BENZO[1,3]DIOXOL-5-YL-1-CYCLOPROPYL-3-OXO-DECAHYDRO-PYRROLO[3,4-A]PYRROLIZIN-4-YL)-BENZAMIDINE _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 N1 C3 UIR sing 358 n n N1 HN11 UIR sing 359 n n N1 HN12 UIR sing 360 n n C3 C4 UIR sing 361 n n C3 N2 UIR doub 362 n n C4 C9 UIR doub 363 n y C4 C5 UIR sing 364 n y C9 C8 UIR sing 365 n y C9 H9 UIR sing 366 n n C8 C7 UIR doub 367 n y C8 H8 UIR sing 368 n n C7 C10 UIR sing 369 n n C7 C6 UIR sing 370 n y C10 N11 UIR sing 371 n n C10 C22 UIR sing 372 n n C10 H10 UIR sing 373 n n N11 C12 UIR sing 374 n n N11 C15 UIR sing 375 n n C12 C13 UIR sing 376 n n C12 H121 UIR sing 377 n n C12 H122 UIR sing 378 n n C13 C14 UIR sing 379 n n C13 H131 UIR sing 380 n n C13 H132 UIR sing 381 n n C14 C15 UIR sing 382 n n C14 H141 UIR sing 383 n n C14 H142 UIR sing 384 n n C15 C16 UIR sing 385 n n C15 H15 UIR sing 386 n n C16 C17 UIR sing 387 n n C16 C22 UIR sing 388 n n C16 H16 UIR sing 389 n n C18 C17 UIR sing 390 n n C18 C42 UIR sing 391 n n C18 C41 UIR sing 392 n n C18 H18 UIR sing 393 n n C17 N19 UIR sing 394 n n C17 H17 UIR sing 395 n n C42 C41 UIR sing 396 n n C42 H421 UIR sing 397 n n C42 H422 UIR sing 398 n n C41 H411 UIR sing 399 n n C41 H412 UIR sing 400 n n N19 C20 UIR sing 401 n n N19 C23 UIR sing 402 n n C20 O21 UIR doub 403 n n C20 C22 UIR sing 404 n n C22 H22 UIR sing 405 n n C23 C24 UIR sing 406 n n C23 H231 UIR sing 407 n n C23 H232 UIR sing 408 n n C24 C25 UIR doub 409 n y C24 C32 UIR sing 410 n y C25 C26 UIR sing 411 n y C25 H25 UIR sing 412 n n C26 O27 UIR sing 413 n n C26 C30 UIR doub 414 n y O27 C28 UIR sing 415 n n C28 O29 UIR sing 416 n n C28 H281 UIR sing 417 n n C28 H282 UIR sing 418 n n O29 C30 UIR sing 419 n n C30 C31 UIR sing 420 n y C31 C32 UIR doub 421 n y C31 H31 UIR sing 422 n n C32 H32 UIR sing 423 n n C6 C5 UIR doub 424 n y C6 H6 UIR sing 425 n n C5 H5 UIR sing 426 n n N2 HN2 UIR sing 427 n n # _atom_sites.entry_id 1Y3Y _atom_sites.fract_transf_matrix[1][1] 0.018231 _atom_sites.fract_transf_matrix[1][2] 0.010526 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021051 _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] 0.00916 _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 CA A 1 3333 3333 CA CA . C 3 UIR A 1 2222 2222 UIR UIR . D 4 HOH A 1 9001 9001 HOH HOH . D 4 HOH A 2 9002 9002 HOH HOH . D 4 HOH A 3 9003 9003 HOH HOH . D 4 HOH A 4 9004 9004 HOH HOH . D 4 HOH A 5 9005 9005 HOH HOH . D 4 HOH A 6 9006 9006 HOH HOH . D 4 HOH A 7 9007 9007 HOH HOH . D 4 HOH A 8 9008 9008 HOH HOH . D 4 HOH A 9 9009 9009 HOH HOH . D 4 HOH A 10 9010 9010 HOH HOH . D 4 HOH A 11 9011 9011 HOH HOH . D 4 HOH A 12 9012 9012 HOH HOH . D 4 HOH A 13 9013 9013 HOH HOH . D 4 HOH A 14 9014 9014 HOH HOH . D 4 HOH A 15 9015 9015 HOH HOH . D 4 HOH A 16 9016 9016 HOH HOH . D 4 HOH A 17 9017 9017 HOH HOH . D 4 HOH A 18 9018 9018 HOH HOH . D 4 HOH A 19 9019 9019 HOH HOH . D 4 HOH A 20 9020 9020 HOH HOH . D 4 HOH A 21 9021 9021 HOH HOH . D 4 HOH A 22 9022 9022 HOH HOH . D 4 HOH A 23 9023 9023 HOH HOH . D 4 HOH A 24 9024 9024 HOH HOH . D 4 HOH A 25 9025 9025 HOH HOH . D 4 HOH A 26 9026 9026 HOH HOH . D 4 HOH A 27 9027 9027 HOH HOH . D 4 HOH A 28 9028 9028 HOH HOH . D 4 HOH A 29 9029 9029 HOH HOH . D 4 HOH A 30 9030 9030 HOH HOH . D 4 HOH A 31 9031 9031 HOH HOH . D 4 HOH A 32 9032 9032 HOH HOH . D 4 HOH A 33 9033 9033 HOH HOH . D 4 HOH A 34 9034 9034 HOH HOH . D 4 HOH A 35 9035 9035 HOH HOH . D 4 HOH A 36 9036 9036 HOH HOH . D 4 HOH A 37 9037 9037 HOH HOH . D 4 HOH A 38 9038 9038 HOH HOH . D 4 HOH A 39 9039 9039 HOH HOH . D 4 HOH A 40 9040 9040 HOH HOH . D 4 HOH A 41 9041 9041 HOH HOH . D 4 HOH A 42 9042 9042 HOH HOH . D 4 HOH A 43 9043 9043 HOH HOH . D 4 HOH A 44 9044 9044 HOH HOH . D 4 HOH A 45 9045 9045 HOH HOH . D 4 HOH A 46 9046 9046 HOH HOH . D 4 HOH A 47 9047 9047 HOH HOH . D 4 HOH A 48 9048 9048 HOH HOH . D 4 HOH A 49 9049 9049 HOH HOH . D 4 HOH A 50 9050 9050 HOH HOH . D 4 HOH A 51 9051 9051 HOH HOH . D 4 HOH A 52 9052 9052 HOH HOH . D 4 HOH A 53 9053 9053 HOH HOH . D 4 HOH A 54 9054 9054 HOH HOH . D 4 HOH A 55 9055 9055 HOH HOH . D 4 HOH A 56 9056 9056 HOH HOH . D 4 HOH A 57 9057 9057 HOH HOH . D 4 HOH A 58 9058 9058 HOH HOH . D 4 HOH A 59 9059 9059 HOH HOH . D 4 HOH A 60 9060 9060 HOH HOH . D 4 HOH A 61 9061 9061 HOH HOH . D 4 HOH A 62 9063 9063 HOH HOH . D 4 HOH A 63 9064 9064 HOH HOH . D 4 HOH A 64 9065 9065 HOH HOH . D 4 HOH A 65 9066 9066 HOH HOH . D 4 HOH A 66 9067 9067 HOH HOH . D 4 HOH A 67 9068 9068 HOH HOH . D 4 HOH A 68 9069 9069 HOH HOH . D 4 HOH A 69 9070 9070 HOH HOH . D 4 HOH A 70 9071 9071 HOH HOH . D 4 HOH A 71 9072 9072 HOH HOH . D 4 HOH A 72 9073 9073 HOH HOH . D 4 HOH A 73 9074 9074 HOH HOH . D 4 HOH A 74 9075 9075 HOH HOH . D 4 HOH A 75 9076 9076 HOH HOH . D 4 HOH A 76 9077 9077 HOH HOH . D 4 HOH A 77 9078 9078 HOH HOH . D 4 HOH A 78 9079 9079 HOH HOH . D 4 HOH A 79 9080 9080 HOH HOH . D 4 HOH A 80 9081 9081 HOH HOH . D 4 HOH A 81 9082 9082 HOH HOH . D 4 HOH A 82 9085 9085 HOH HOH . D 4 HOH A 83 9086 9086 HOH HOH . D 4 HOH A 84 9087 9087 HOH HOH . D 4 HOH A 85 9088 9088 HOH HOH . D 4 HOH A 86 9089 9089 HOH HOH . D 4 HOH A 87 9090 9090 HOH HOH . D 4 HOH A 88 9091 9091 HOH HOH . D 4 HOH A 89 9092 9092 HOH HOH . D 4 HOH A 90 9093 9093 HOH HOH . D 4 HOH A 91 9094 9094 HOH HOH . D 4 HOH A 92 9095 9095 HOH HOH . D 4 HOH A 93 9096 9096 HOH HOH . D 4 HOH A 94 9097 9097 HOH HOH . D 4 HOH A 95 9098 9098 HOH HOH . D 4 HOH A 96 9099 9099 HOH HOH . D 4 HOH A 97 9100 9100 HOH HOH . D 4 HOH A 98 9101 9101 HOH HOH . D 4 HOH A 99 9102 9102 HOH HOH . D 4 HOH A 100 9103 9103 HOH HOH . D 4 HOH A 101 9104 9104 HOH HOH . D 4 HOH A 102 9105 9105 HOH HOH . D 4 HOH A 103 9106 9106 HOH HOH . D 4 HOH A 104 9107 9107 HOH HOH . D 4 HOH A 105 9108 9108 HOH HOH . D 4 HOH A 106 9109 9109 HOH HOH . D 4 HOH A 107 9110 9110 HOH HOH . D 4 HOH A 108 9114 9114 HOH HOH . D 4 HOH A 109 9116 9116 HOH HOH . D 4 HOH A 110 9117 9117 HOH HOH . D 4 HOH A 111 9121 9121 HOH HOH . D 4 HOH A 112 9149 9149 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 N N1 UIR . . . C 3 46.782 18.521 54.803 1 20.44 ? N1 UIR 2222 A 1 HETATM 2 C C3 UIR . . . C 3 45.917 18.389 53.816 1 19.11 ? C3 UIR 2222 A 1 HETATM 3 C C4 UIR . . . C 3 45.414 19.445 53.008 1 33.68 ? C4 UIR 2222 A 1 HETATM 4 C C9 UIR . . . C 3 45.8 20.775 53.163 1 38.07 ? C9 UIR 2222 A 1 HETATM 5 C C8 UIR . . . C 3 45.267 21.753 52.308 1 37.66 ? C8 UIR 2222 A 1 HETATM 6 C C7 UIR . . . C 3 44.36 21.399 51.307 1 42.82 ? C7 UIR 2222 A 1 HETATM 7 C C10 UIR . . . C 3 43.765 22.444 50.399 1 46.16 ? C10 UIR 2222 A 1 HETATM 8 N N11 UIR . . . C 3 44.735 23.584 50.197 1 53.67 ? N11 UIR 2222 A 1 HETATM 9 C C12 UIR . . . C 3 45.827 23.235 49.234 1 47.3 ? C12 UIR 2222 A 1 HETATM 10 C C13 UIR . . . C 3 45.304 23.612 47.834 1 35.34 ? C13 UIR 2222 A 1 HETATM 11 C C14 UIR . . . C 3 43.987 24.306 48.008 1 39.58 ? C14 UIR 2222 A 1 HETATM 12 C C15 UIR . . . C 3 43.867 24.62 49.51 1 51.01 ? C15 UIR 2222 A 1 HETATM 13 C C16 UIR . . . C 3 42.391 24.343 49.937 1 50.58 ? C16 UIR 2222 A 1 HETATM 14 C C17 UIR . . . C 3 41.825 25.468 50.864 1 57.69 ? C17 UIR 2222 A 1 HETATM 15 N N19 UIR . . . C 3 42.356 25.129 52.174 1 61.16 ? N19 UIR 2222 A 1 HETATM 16 C C20 UIR . . . C 3 42.681 23.797 52.279 1 55.27 ? C20 UIR 2222 A 1 HETATM 17 O O21 UIR . . . C 3 43.149 23.269 53.322 1 29.73 ? O21 UIR 2222 A 1 HETATM 18 C C22 UIR . . . C 3 42.479 23.134 50.9 1 41.04 ? C22 UIR 2222 A 1 HETATM 19 C C23 UIR . . . C 3 41.867 25.87 53.393 1 66.34 ? C23 UIR 2222 A 1 HETATM 20 C C6 UIR . . . C 3 43.976 20.056 51.152 1 40.07 ? C6 UIR 2222 A 1 HETATM 21 C C5 UIR . . . C 3 44.507 19.09 51.983 1 37.33 ? C5 UIR 2222 A 1 HETATM 22 N N2 UIR . . . C 3 45.485 17.124 53.591 1 19.92 ? N2 UIR 2222 A 1 # _model_server_stats.io_time_ms 72 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 22 #