data_1Y3V # _model_server_result.job_id vzaXUY4hZP2vVR6Ss2opZA _model_server_result.datetime_utc '2024-11-06 03:12:54' _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 1y3v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1994}' # _entry.id 1Y3V # _exptl.entry_id 1Y3V _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 90 _cell.entry_id 1Y3V _cell.length_a 63.17 _cell.length_b 69.17 _cell.length_c 63.97 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Y3V _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 ? _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf2 A SG CYS 25 A CYS 42 1_555 A SG CYS 41 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf3 A SG CYS 109 A CYS 128 1_555 A SG CYS 210 A CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? disulf ? disulf4 A SG CYS 116 A CYS 136 1_555 A SG CYS 183 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? disulf ? disulf5 A SG CYS 148 A CYS 168 1_555 A SG CYS 162 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf6 A SG CYS 173 A CYS 191 1_555 A SG CYS 197 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc1 A OE1 GLU 52 A GLU 70 1_555 B CA CA . A CA 3394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc2 A O ASN 54 A ASN 72 1_555 B CA CA . A CA 3394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc3 A O VAL 57 A VAL 75 1_555 B CA CA . A CA 3394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc4 A OE2 GLU 62 A GLU 80 1_555 B CA CA . A CA 3394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc5 B CA CA . A CA 3394 1_555 D O HOH . A HOH 3398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc6 B CA CA . A CA 3394 1_555 D O HOH . A HOH 3408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? # _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 1Y3V _atom_sites.fract_transf_matrix[1][1] 0.01583 _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] 0.014457 _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] 0.015632 _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 3394 3394 CA CA . C 3 UIR A 1 1994 1994 UIR UIR . D 4 HOH A 1 3395 1 HOH HOH . D 4 HOH A 2 3396 2 HOH HOH . D 4 HOH A 3 3397 3 HOH HOH . D 4 HOH A 4 3398 4 HOH HOH . D 4 HOH A 5 3399 5 HOH HOH . D 4 HOH A 6 3400 6 HOH HOH . D 4 HOH A 7 3401 7 HOH HOH . D 4 HOH A 8 3402 8 HOH HOH . D 4 HOH A 9 3403 9 HOH HOH . D 4 HOH A 10 3404 10 HOH HOH . D 4 HOH A 11 3405 11 HOH HOH . D 4 HOH A 12 3406 12 HOH HOH . D 4 HOH A 13 3407 13 HOH HOH . D 4 HOH A 14 3408 14 HOH HOH . D 4 HOH A 15 3409 15 HOH HOH . D 4 HOH A 16 3410 16 HOH HOH . D 4 HOH A 17 3411 17 HOH HOH . D 4 HOH A 18 3412 18 HOH HOH . D 4 HOH A 19 3413 19 HOH HOH . D 4 HOH A 20 3414 20 HOH HOH . D 4 HOH A 21 3415 21 HOH HOH . D 4 HOH A 22 3416 22 HOH HOH . D 4 HOH A 23 3417 23 HOH HOH . D 4 HOH A 24 3418 24 HOH HOH . D 4 HOH A 25 3419 25 HOH HOH . D 4 HOH A 26 3420 26 HOH HOH . D 4 HOH A 27 3421 27 HOH HOH . D 4 HOH A 28 3422 28 HOH HOH . D 4 HOH A 29 3423 29 HOH HOH . D 4 HOH A 30 3424 30 HOH HOH . D 4 HOH A 31 3425 31 HOH HOH . D 4 HOH A 32 3426 32 HOH HOH . D 4 HOH A 33 3427 33 HOH HOH . D 4 HOH A 34 3428 34 HOH HOH . D 4 HOH A 35 3429 35 HOH HOH . D 4 HOH A 36 3430 36 HOH HOH . D 4 HOH A 37 3431 37 HOH HOH . D 4 HOH A 38 3432 38 HOH HOH . D 4 HOH A 39 3433 39 HOH HOH . D 4 HOH A 40 3434 40 HOH HOH . D 4 HOH A 41 3435 41 HOH HOH . D 4 HOH A 42 3436 42 HOH HOH . D 4 HOH A 43 3437 43 HOH HOH . D 4 HOH A 44 3438 44 HOH HOH . D 4 HOH A 45 3439 45 HOH HOH . D 4 HOH A 46 3440 46 HOH HOH . D 4 HOH A 47 3441 47 HOH HOH . D 4 HOH A 48 3442 48 HOH HOH . D 4 HOH A 49 3443 49 HOH HOH . D 4 HOH A 50 3444 50 HOH HOH . D 4 HOH A 51 3445 51 HOH HOH . D 4 HOH A 52 3446 52 HOH HOH . D 4 HOH A 53 3447 53 HOH HOH . D 4 HOH A 54 3448 54 HOH HOH . D 4 HOH A 55 3449 55 HOH HOH . D 4 HOH A 56 3450 56 HOH HOH . D 4 HOH A 57 3451 57 HOH HOH . D 4 HOH A 58 3452 58 HOH HOH . D 4 HOH A 59 3453 59 HOH HOH . D 4 HOH A 60 3454 60 HOH HOH . D 4 HOH A 61 3455 61 HOH HOH . D 4 HOH A 62 3456 62 HOH HOH . D 4 HOH A 63 3457 63 HOH HOH . D 4 HOH A 64 3458 64 HOH HOH . D 4 HOH A 65 3459 65 HOH HOH . D 4 HOH A 66 3460 66 HOH HOH . D 4 HOH A 67 3461 67 HOH HOH . D 4 HOH A 68 3462 68 HOH HOH . D 4 HOH A 69 3463 69 HOH HOH . D 4 HOH A 70 3464 70 HOH HOH . D 4 HOH A 71 3465 71 HOH HOH . D 4 HOH A 72 3466 72 HOH HOH . D 4 HOH A 73 3467 73 HOH HOH . D 4 HOH A 74 3468 74 HOH HOH . D 4 HOH A 75 3469 75 HOH HOH . D 4 HOH A 76 3470 76 HOH HOH . D 4 HOH A 77 3471 77 HOH HOH . D 4 HOH A 78 3472 78 HOH HOH . D 4 HOH A 79 3473 79 HOH HOH . D 4 HOH A 80 3474 80 HOH HOH . D 4 HOH A 81 3475 81 HOH HOH . D 4 HOH A 82 3476 82 HOH HOH . D 4 HOH A 83 3477 83 HOH HOH . D 4 HOH A 84 3478 84 HOH HOH . D 4 HOH A 85 3479 85 HOH HOH . D 4 HOH A 86 3480 86 HOH HOH . D 4 HOH A 87 3481 87 HOH HOH . D 4 HOH A 88 3482 88 HOH HOH . D 4 HOH A 89 3483 89 HOH HOH . D 4 HOH A 90 3484 90 HOH HOH . D 4 HOH A 91 3485 91 HOH HOH . D 4 HOH A 92 3486 92 HOH HOH . D 4 HOH A 93 3487 93 HOH HOH . D 4 HOH A 94 3488 94 HOH HOH . D 4 HOH A 95 3489 95 HOH HOH . D 4 HOH A 96 3490 96 HOH HOH . D 4 HOH A 97 3491 97 HOH HOH . D 4 HOH A 98 3492 98 HOH HOH . D 4 HOH A 99 3493 99 HOH HOH . D 4 HOH A 100 3494 100 HOH HOH . D 4 HOH A 101 3495 101 HOH HOH . D 4 HOH A 102 3496 102 HOH HOH . D 4 HOH A 103 3497 103 HOH HOH . D 4 HOH A 104 3498 104 HOH HOH . D 4 HOH A 105 3499 105 HOH HOH . D 4 HOH A 106 3500 106 HOH HOH . D 4 HOH A 107 3501 107 HOH HOH . D 4 HOH A 108 3502 108 HOH HOH . D 4 HOH A 109 3503 109 HOH HOH . D 4 HOH A 110 3504 110 HOH HOH . D 4 HOH A 111 3505 111 HOH HOH . D 4 HOH A 112 3506 112 HOH HOH . D 4 HOH A 113 3507 113 HOH HOH . D 4 HOH A 114 3508 114 HOH HOH . D 4 HOH A 115 3509 115 HOH HOH . D 4 HOH A 116 3510 116 HOH HOH . D 4 HOH A 117 3511 117 HOH HOH . D 4 HOH A 118 3512 118 HOH HOH . D 4 HOH A 119 3513 119 HOH HOH . D 4 HOH A 120 3514 120 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 -5.005 9.576 19.765 1 22.81 ? N1 UIR 1994 A 1 HETATM 2 C C3 UIR . . . C 3 -3.703 9.306 19.677 1 18.34 ? C3 UIR 1994 A 1 HETATM 3 C C4 UIR . . . C 3 -3.117 8.072 20.115 1 22.69 ? C4 UIR 1994 A 1 HETATM 4 C C9 UIR . . . C 3 -3.892 7.054 20.706 1 26.06 ? C9 UIR 1994 A 1 HETATM 5 C C8 UIR . . . C 3 -3.292 5.855 21.151 1 24.02 ? C8 UIR 1994 A 1 HETATM 6 C C7 UIR . . . C 3 -1.909 5.649 21.004 1 18.33 ? C7 UIR 1994 A 1 HETATM 7 C C10 UIR . . . C 3 -1.191 4.445 21.574 1 25.9 ? C10 UIR 1994 A 1 HETATM 8 N N11 UIR . . . C 3 -2.176 3.305 21.564 1 34.97 ? N11 UIR 1994 A 1 HETATM 9 C C12 UIR . . . C 3 -2.446 2.826 20.166 1 37.53 ? C12 UIR 1994 A 1 HETATM 10 C C13 UIR . . . C 3 -1.511 1.62 19.957 1 39.11 ? C13 UIR 1994 A 1 HETATM 11 C C14 UIR . . . C 3 -0.734 1.372 21.234 1 42.77 ? C14 UIR 1994 A 1 HETATM 12 C C15 UIR . . . C 3 -1.418 2.227 22.314 1 36.69 ? C15 UIR 1994 A 1 HETATM 13 C C16 UIR . . . C 3 -0.309 2.928 23.168 1 25.08 ? C16 UIR 1994 A 1 HETATM 14 C C18 UIR . . . C 3 0.494 2.73 25.72 1 42.17 ? C18 UIR 1994 A 1 HETATM 15 C C17 UIR . . . C 3 -0.624 2.695 24.695 1 32.67 ? C17 UIR 1994 A 1 HETATM 16 C C42 UIR . . . C 3 0.286 1.804 26.926 1 36.15 ? C42 UIR 1994 A 1 HETATM 17 C C41 UIR . . . C 3 1.296 1.409 25.816 1 36.88 ? C41 UIR 1994 A 1 HETATM 18 N N19 UIR . . . C 3 -1.644 3.66 24.997 1 33.15 ? N19 UIR 1994 A 1 HETATM 19 C C20 UIR . . . C 3 -1.7 4.695 24.087 1 28.1 ? C20 UIR 1994 A 1 HETATM 20 O O21 UIR . . . C 3 -2.58 5.626 24.104 1 26.83 ? O21 UIR 1994 A 1 HETATM 21 C C22 UIR . . . C 3 -0.629 4.452 23.003 1 21.77 ? C22 UIR 1994 A 1 HETATM 22 C C23 UIR . . . C 3 -2.719 3.693 26.081 1 43.75 ? C23 UIR 1994 A 1 HETATM 23 C C24 UIR . . . C 3 -2.508 4.816 27.101 1 52.39 ? C24 UIR 1994 A 1 HETATM 24 C C25 UIR . . . C 3 -1.327 4.867 27.858 1 60.78 ? C25 UIR 1994 A 1 HETATM 25 C C26 UIR . . . C 3 -1.208 5.914 28.868 1 59.65 ? C26 UIR 1994 A 1 HETATM 26 O O27 UIR . . . C 3 -0.133 6.143 29.733 1 64.8 ? O27 UIR 1994 A 1 HETATM 27 C C28 UIR . . . C 3 -0.543 7.306 30.508 1 53.55 ? C28 UIR 1994 A 1 HETATM 28 O O29 UIR . . . C 3 -1.875 7.725 30.078 1 56.47 ? O29 UIR 1994 A 1 HETATM 29 C C30 UIR . . . C 3 -2.238 6.847 29.079 1 57.03 ? C30 UIR 1994 A 1 HETATM 30 C C31 UIR . . . C 3 -3.42 6.787 28.333 1 62.69 ? C31 UIR 1994 A 1 HETATM 31 C C32 UIR . . . C 3 -3.54 5.781 27.344 1 60.6 ? C32 UIR 1994 A 1 HETATM 32 C C6 UIR . . . C 3 -1.12 6.64 20.372 1 18.44 ? C6 UIR 1994 A 1 HETATM 33 C C5 UIR . . . C 3 -1.732 7.822 19.939 1 19.8 ? C5 UIR 1994 A 1 HETATM 34 N N2 UIR . . . C 3 -2.987 10.348 19.114 1 18.53 ? N2 UIR 1994 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 34 #