data_1Y3W
#
_model_server_result.job_id            jxpNVXyYE6aQ9gJCuLt6NA 
_model_server_result.datetime_utc      '2025-08-12 16:18:57' 
_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          1y3w 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1994}' 
#
_entry.id    1Y3W 
#
_exptl.entry_id    1Y3W 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              446.541 
_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-YLMETHYL-1-ETHYL-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            1Y3W 
_cell.length_a            63.14 
_cell.length_b            69.28 
_cell.length_c            63.96 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1Y3W 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf2 A SG CYS 25 A CYS 42 1_555 A SG CYS 41 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf3 A SG CYS 109 A CYS 128 1_555 A SG CYS 210 A CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
disulf ? disulf4 A SG CYS 148 A CYS 168 1_555 A SG CYS 162 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? 
disulf ? disulf5 A SG CYS 173 A CYS 191 1_555 A SG CYS 197 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
metalc ? metalc1 A OE1 GLU 52 A GLU 70 1_555 B CA CA . A CA 3394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? 
metalc ? metalc2 A O ASN 54 A ASN 72 1_555 B CA CA . A CA 3394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? 
metalc ? metalc3 A O VAL 57 A VAL 75 1_555 B CA CA . A CA 3394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? 
metalc ? metalc4 A OE2 GLU 62 A GLU 80 1_555 B CA CA . A CA 3394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? 
metalc ? metalc5 B CA CA . A CA 3394 1_555 D O HOH . A HOH 3460 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? 
metalc ? metalc6 B CA CA . A CA 3394 1_555 D O HOH . A HOH 3501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? 
#
_chem_comp.formula           'C26 H30 N4 O3' 
_chem_comp.formula_weight    446.541 
_chem_comp.id                UIP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (1R,3AS,4R,8AS,8BR)-4-(2-BENZO[1,3]DIOXOL-5-YLMETHYL-1-ETHYL-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 UIP doub 358 n n 
N1 HN1 UIP sing 359 n n 
C3 N2 UIP sing 360 n n 
C3 C4 UIP sing 361 n n 
N2 HN21 UIP sing 362 n n 
N2 HN22 UIP sing 363 n n 
C4 C9 UIP doub 364 n y 
C4 C5 UIP sing 365 n y 
C9 C8 UIP sing 366 n y 
C9 H9 UIP sing 367 n n 
C8 C7 UIP doub 368 n y 
C8 H8 UIP sing 369 n n 
C7 C6 UIP sing 370 n y 
C7 C10 UIP sing 371 n n 
C6 C5 UIP doub 372 n y 
C6 H6 UIP sing 373 n n 
C5 H5 UIP sing 374 n n 
C10 N11 UIP sing 375 n n 
C10 C22 UIP sing 376 n n 
C10 H10 UIP sing 377 n n 
N11 C12 UIP sing 378 n n 
N11 C15 UIP sing 379 n n 
C12 C13 UIP sing 380 n n 
C12 H121 UIP sing 381 n n 
C12 H122 UIP sing 382 n n 
C13 C14 UIP sing 383 n n 
C13 H131 UIP sing 384 n n 
C13 H132 UIP sing 385 n n 
C14 C15 UIP sing 386 n n 
C14 H141 UIP sing 387 n n 
C14 H142 UIP sing 388 n n 
C15 C16 UIP sing 389 n n 
C15 H15 UIP sing 390 n n 
C16 C17 UIP sing 391 n n 
C16 C22 UIP sing 392 n n 
C16 H16 UIP sing 393 n n 
C17 N19 UIP sing 394 n n 
C17 C18 UIP sing 395 n n 
C17 H17 UIP sing 396 n n 
N19 C20 UIP sing 397 n n 
N19 C23 UIP sing 398 n n 
C20 O21 UIP doub 399 n n 
C20 C22 UIP sing 400 n n 
C22 H22 UIP sing 401 n n 
C23 C24 UIP sing 402 n n 
C23 H231 UIP sing 403 n n 
C23 H232 UIP sing 404 n n 
C24 C32 UIP doub 405 n y 
C24 C25 UIP sing 406 n y 
C32 C31 UIP sing 407 n y 
C32 H32 UIP sing 408 n n 
C31 C30 UIP doub 409 n y 
C31 H31 UIP sing 410 n n 
C30 O29 UIP sing 411 n n 
C30 C26 UIP sing 412 n y 
O29 C28 UIP sing 413 n n 
C28 O27 UIP sing 414 n n 
C28 H281 UIP sing 415 n n 
C28 H282 UIP sing 416 n n 
O27 C26 UIP sing 417 n n 
C26 C25 UIP doub 418 n y 
C25 H25 UIP sing 419 n n 
C18 C42 UIP sing 420 n n 
C18 H181 UIP sing 421 n n 
C18 H182 UIP sing 422 n n 
C42 H421 UIP sing 423 n n 
C42 H422 UIP sing 424 n n 
C42 H423 UIP sing 425 n n 
#
_atom_sites.entry_id                     1Y3W 
_atom_sites.fract_transf_matrix[1][1]    0.015838 
_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]    0.014434 
_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]    0.015635 
_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 UIP A 1 1994 1994 UIP UIP . 
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 . 
#
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 UIP . . . C 3 -5.116 9.53 19.72 1 21.75 ? N1 UIP 1994 A 1 
HETATM 2 C C3 UIP . . . C 3 -3.802 9.308 19.666 1 23.14 ? C3 UIP 1994 A 1 
HETATM 3 N N2 UIP . . . C 3 -3.046 10.326 19.145 1 16.49 ? N2 UIP 1994 A 1 
HETATM 4 C C4 UIP . . . C 3 -3.217 8.087 20.119 1 18.1 ? C4 UIP 1994 A 1 
HETATM 5 C C9 UIP . . . C 3 -3.983 7.063 20.681 1 21.63 ? C9 UIP 1994 A 1 
HETATM 6 C C8 UIP . . . C 3 -3.371 5.871 21.098 1 22.24 ? C8 UIP 1994 A 1 
HETATM 7 C C7 UIP . . . C 3 -1.99 5.693 21.014 1 27.11 ? C7 UIP 1994 A 1 
HETATM 8 C C6 UIP . . . C 3 -1.215 6.727 20.449 1 30.31 ? C6 UIP 1994 A 1 
HETATM 9 C C5 UIP . . . C 3 -1.826 7.897 20.03 1 24.65 ? C5 UIP 1994 A 1 
HETATM 10 C C10 UIP . . . C 3 -1.297 4.466 21.528 1 28.97 ? C10 UIP 1994 A 1 
HETATM 11 N N11 UIP . . . C 3 -2.15 3.238 21.431 1 38.54 ? N11 UIP 1994 A 1 
HETATM 12 C C12 UIP . . . C 3 -2.334 2.721 20.038 1 41.04 ? C12 UIP 1994 A 1 
HETATM 13 C C13 UIP . . . C 3 -1.457 1.449 19.932 1 44.47 ? C13 UIP 1994 A 1 
HETATM 14 C C14 UIP . . . C 3 -0.498 1.518 21.094 1 46.78 ? C14 UIP 1994 A 1 
HETATM 15 C C15 UIP . . . C 3 -1.353 2.193 22.192 1 38.85 ? C15 UIP 1994 A 1 
HETATM 16 C C16 UIP . . . C 3 -0.377 2.947 23.142 1 26.47 ? C16 UIP 1994 A 1 
HETATM 17 C C17 UIP . . . C 3 -0.713 2.706 24.649 1 30.04 ? C17 UIP 1994 A 1 
HETATM 18 N N19 UIP . . . C 3 -1.693 3.727 24.945 1 33.62 ? N19 UIP 1994 A 1 
HETATM 19 C C20 UIP . . . C 3 -1.672 4.781 24.069 1 30.84 ? C20 UIP 1994 A 1 
HETATM 20 O O21 UIP . . . C 3 -2.555 5.686 24.029 1 30.53 ? O21 UIP 1994 A 1 
HETATM 21 C C22 UIP . . . C 3 -0.688 4.448 22.932 1 18.64 ? C22 UIP 1994 A 1 
HETATM 22 C C23 UIP . . . C 3 -2.635 3.86 26.1 1 45.77 ? C23 UIP 1994 A 1 
HETATM 23 C C24 UIP . . . C 3 -2.047 4.511 27.346 1 63.32 ? C24 UIP 1994 A 1 
HETATM 24 C C32 UIP . . . C 3 -1.17 3.783 28.216 1 74.81 ? C32 UIP 1994 A 1 
HETATM 25 C C31 UIP . . . C 3 -0.673 4.337 29.416 1 76.98 ? C31 UIP 1994 A 1 
HETATM 26 C C30 UIP . . . C 3 -1.083 5.65 29.7 1 80.11 ? C30 UIP 1994 A 1 
HETATM 27 O O29 UIP . . . C 3 -0.744 6.424 30.787 1 83.22 ? O29 UIP 1994 A 1 
HETATM 28 C C28 UIP . . . C 3 -1.444 7.697 30.594 1 76.82 ? C28 UIP 1994 A 1 
HETATM 29 O O27 UIP . . . C 3 -2.209 7.66 29.362 1 75.77 ? O27 UIP 1994 A 1 
HETATM 30 C C26 UIP . . . C 3 -1.943 6.381 28.858 1 72.39 ? C26 UIP 1994 A 1 
HETATM 31 C C25 UIP . . . C 3 -2.442 5.823 27.664 1 63.65 ? C25 UIP 1994 A 1 
HETATM 32 C C18 UIP . . . C 3 0.52 2.732 25.585 1 33.22 ? C18 UIP 1994 A 1 
HETATM 33 C C42 UIP . . . C 3 1.318 1.436 25.576 1 34.35 ? C42 UIP 1994 A 1 
#
_model_server_stats.io_time_ms              39 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           381 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           33 
#