data_A1IUM
# 
_chem_comp.id                                    A1IUM 
_chem_comp.name                                  "(3~{S},3~{a}~{S},6~{a}~{R})-2-[(4-methoxy-1~{H}-indol-2-yl)carbonyl]-~{N}-[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]-3,3~{a},4,5,6,6~{a}-hexahydro-1~{H}-cyclopenta[c]pyrrole-3-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C33 H39 N5 O6" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-11-20 
_chem_comp.pdbx_modified_date                    2025-07-11 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        601.693 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1IUM 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        9HFY 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_chem_comp.pdbx_pcm                              Y 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
A1IUM C2  C1  C 0 1 N N N N N N 12.010 -3.384 2.843  2.365  3.742  -0.915 C2  A1IUM 1  
A1IUM C4  C2  C 0 1 N N N N N N 13.084 -1.827 1.503  2.301  6.012  -0.430 C4  A1IUM 2  
A1IUM C5  C3  C 0 1 N N N N N N 11.916 -2.371 0.714  2.191  5.289  0.930  C5  A1IUM 3  
A1IUM C6  C4  C 0 1 N N S N N N 11.056 -3.121 1.733  2.653  3.859  0.565  C6  A1IUM 4  
A1IUM C8  C5  C 0 1 N N N N N N 10.434 -4.401 1.215  1.850  2.820  1.351  C8  A1IUM 5  
A1IUM C12 C6  C 0 1 N N N N N N 7.569  -2.375 0.493  0.527  -0.108 1.059  C12 A1IUM 6  
A1IUM C17 C7  C 0 1 N N N N N N 4.755  -0.160 1.021  -2.019 -2.424 0.628  C17 A1IUM 7  
A1IUM C18 C8  C 0 1 N N R N N N 4.059  -1.387 0.503  -0.647 -3.120 0.500  C18 A1IUM 8  
A1IUM C21 C9  C 0 1 N N N N N N 3.487  -3.604 1.312  -0.947 -4.585 2.435  C21 A1IUM 9  
A1IUM C23 C10 C 0 1 N N S N N N 5.157  -2.349 0.130  0.147  -2.492 1.687  C23 A1IUM 10 
A1IUM O26 O1  O 0 1 N N N N N N 7.843  -0.660 2.809  -2.112 1.127  1.228  O26 A1IUM 11 
A1IUM C27 C11 C 0 1 Y N N N N N 6.804  1.402  2.569  -3.844 -0.135 0.314  C27 A1IUM 12 
A1IUM C30 C12 C 0 1 Y N N N N N 6.084  5.019  2.376  -7.049 0.852  -1.073 C30 A1IUM 13 
A1IUM C32 C13 C 0 1 N N N N N N 4.778  6.574  0.930  -8.459 2.676  -1.647 C32 A1IUM 14 
A1IUM C33 C14 C 0 1 Y N N N N N 6.716  5.927  3.202  -8.041 0.009  -1.533 C33 A1IUM 15 
A1IUM C34 C15 C 0 1 Y N N N N N 7.664  5.568  4.155  -7.868 -1.367 -1.494 C34 A1IUM 16 
A1IUM C35 C16 C 0 1 Y N N N N N 8.035  4.232  4.358  -6.707 -1.916 -0.996 C35 A1IUM 17 
A1IUM C36 C17 C 0 1 Y N N N N N 7.437  3.268  3.587  -5.690 -1.090 -0.525 C36 A1IUM 18 
A1IUM C38 C18 C 0 1 N N R N N N 8.823  -5.412 -0.519 3.837  1.337  1.654  C38 A1IUM 19 
A1IUM C40 C19 C 0 1 N N N N N N 9.775  -5.817 -1.643 4.399  -0.036 1.391  C40 A1IUM 20 
A1IUM O41 O2  O 0 1 N N N N N N 10.919 -6.219 -1.392 4.650  -0.776 2.319  O41 A1IUM 21 
A1IUM O1  O3  O 0 1 N N N N N N 11.847 -4.128 3.788  2.317  2.699  -1.533 O1  A1IUM 22 
A1IUM N3  N1  N 0 1 N N N N N N 13.120 -2.673 2.690  2.163  4.961  -1.445 N3  A1IUM 23 
A1IUM C9  C20 C 0 1 N N S N N N 9.334  -4.125 0.202  2.420  1.426  1.084  C9  A1IUM 24 
A1IUM N11 N2  N 0 1 N N N N N N 8.141  -3.551 0.818  1.571  0.420  1.728  N11 A1IUM 25 
A1IUM O13 O4  O 0 1 N N N N N N 8.078  -1.561 -0.279 0.343  0.182  -0.105 O13 A1IUM 26 
A1IUM C14 C21 C 0 1 N N S N N N 6.263  -2.074 1.148  -0.413 -1.057 1.757  C14 A1IUM 27 
A1IUM N16 N3  N 0 1 N N N N N N 6.029  -0.670 1.543  -1.717 -1.054 1.080  N16 A1IUM 28 
A1IUM C20 C22 C 0 1 N N N N N N 3.225  -2.116 1.530  -0.789 -4.602 0.903  C20 A1IUM 29 
A1IUM C22 C23 C 0 1 N N N N N N 4.507  -3.706 0.214  -0.331 -3.266 2.928  C22 A1IUM 30 
A1IUM C25 C24 C 0 1 N N N N N N 6.875  -0.048 2.305  -2.507 0.023  0.902  C25 A1IUM 31 
A1IUM C28 C25 C 0 1 Y N N N N N 6.061  2.430  1.955  -4.680 0.880  -0.027 C28 A1IUM 32 
A1IUM C29 C26 C 0 1 Y N N N N N 6.469  3.604  2.561  -5.858 0.308  -0.562 C29 A1IUM 33 
A1IUM O31 O5  O 0 1 N N N N N N 5.142  5.232  1.404  -7.222 2.198  -1.114 O31 A1IUM 34 
A1IUM N37 N4  N 0 1 Y N N N N N 7.588  1.940  3.517  -4.451 -1.342 0.014  N37 A1IUM 35 
A1IUM O39 O6  O 0 1 N N N N N N 7.577  -5.068 -1.162 3.800  1.575  3.063  O39 A1IUM 36 
A1IUM N42 N5  N 0 1 N N N N N N 9.299  -5.788 -2.908 4.623  -0.442 0.126  N42 A1IUM 37 
A1IUM C43 C27 C 0 1 N N N N N N 10.057 -6.130 -4.098 5.169  -1.777 -0.130 C43 A1IUM 38 
A1IUM C44 C28 C 0 1 Y N N N N N 10.844 -4.938 -4.641 5.323  -1.982 -1.615 C44 A1IUM 39 
A1IUM C45 C29 C 0 1 Y N N N N N 11.664 -5.177 -5.756 4.280  -2.514 -2.351 C45 A1IUM 40 
A1IUM C46 C30 C 0 1 Y N N N N N 12.428 -4.128 -6.301 4.422  -2.702 -3.713 C46 A1IUM 41 
A1IUM C47 C31 C 0 1 Y N N N N N 12.329 -2.850 -5.764 5.605  -2.357 -4.339 C47 A1IUM 42 
A1IUM C48 C32 C 0 1 Y N N N N N 11.542 -2.605 -4.644 6.647  -1.824 -3.603 C48 A1IUM 43 
A1IUM C49 C33 C 0 1 Y N N N N N 10.793 -3.654 -4.084 6.504  -1.632 -2.242 C49 A1IUM 44 
A1IUM H1  H1  H 0 1 N N N N N N 14.019 -1.914 0.930  1.498  6.742  -0.532 H1  A1IUM 45 
A1IUM H2  H2  H 0 1 N N N N N N 12.917 -0.774 1.776  3.270  6.502  -0.524 H2  A1IUM 46 
A1IUM H3  H3  H 0 1 N N N N N N 11.344 -1.550 0.257  2.859  5.738  1.665  H3  A1IUM 47 
A1IUM H4  H4  H 0 1 N N N N N N 12.267 -3.056 -0.072 1.162  5.287  1.289  H4  A1IUM 48 
A1IUM H5  H5  H 0 1 N N N N N N 10.258 -2.451 2.087  3.720  3.742  0.757  H5  A1IUM 49 
A1IUM H6  H6  H 0 1 N N N N N N 10.006 -4.957 2.062  1.914  3.042  2.417  H6  A1IUM 50 
A1IUM H7  H7  H 0 1 N N N N N N 11.216 -5.008 0.735  0.807  2.853  1.036  H7  A1IUM 51 
A1IUM H8  H8  H 0 1 N N N N N N 4.926  0.564  0.211  -2.523 -2.401 -0.338 H8  A1IUM 52 
A1IUM H9  H9  H 0 1 N N N N N N 4.167  0.315  1.820  -2.638 -2.937 1.364  H9  A1IUM 53 
A1IUM H10 H10 H 0 1 N N N N N N 3.450  -1.140 -0.379 -0.181 -2.982 -0.476 H10 A1IUM 54 
A1IUM H11 H11 H 0 1 N N N N N N 2.558  -4.113 1.015  -2.003 -4.626 2.702  H11 A1IUM 55 
A1IUM H12 H12 H 0 1 N N N N N N 3.876  -4.060 2.235  -0.419 -5.431 2.874  H12 A1IUM 56 
A1IUM H13 H13 H 0 1 N N N N N N 5.517  -2.152 -0.891 1.228  -2.533 1.550  H13 A1IUM 57 
A1IUM H14 H14 H 0 1 N N N N N N 4.005  6.491  0.152  -8.567 2.336  -2.676 H14 A1IUM 58 
A1IUM H15 H15 H 0 1 N N N N N N 4.390  7.167  1.771  -9.285 2.293  -1.048 H15 A1IUM 59 
A1IUM H16 H16 H 0 1 N N N N N N 5.667  7.069  0.512  -8.468 3.766  -1.622 H16 A1IUM 60 
A1IUM H17 H17 H 0 1 N N N N N N 6.461  6.972  3.103  -8.958 0.424  -1.926 H17 A1IUM 61 
A1IUM H18 H18 H 0 1 N N N N N N 8.126  6.339  4.754  -8.652 -2.015 -1.857 H18 A1IUM 62 
A1IUM H19 H19 H 0 1 N N N N N N 8.772  3.968  5.102  -6.585 -2.989 -0.970 H19 A1IUM 63 
A1IUM H20 H20 H 0 1 N N N N N N 8.702  -6.232 0.204  4.469  2.086  1.176  H20 A1IUM 64 
A1IUM H21 H21 H 0 1 N N N N N N 13.896 -2.713 3.320  1.956  5.125  -2.378 H21 A1IUM 65 
A1IUM H22 H22 H 0 1 N N N N N N 9.722  -3.434 -0.561 2.448  1.244  0.010  H22 A1IUM 66 
A1IUM H23 H23 H 0 1 N N N N N N 7.709  -4.079 1.549  1.761  0.134  2.635  H23 A1IUM 67 
A1IUM H24 H24 H 0 1 N N N N N N 6.125  -2.734 2.017  -0.535 -0.758 2.798  H24 A1IUM 68 
A1IUM H25 H25 H 0 1 N N N N N N 3.527  -1.820 2.546  -1.672 -5.038 0.437  H25 A1IUM 69 
A1IUM H26 H26 H 0 1 N N N N N N 2.158  -1.891 1.384  0.104  -5.159 0.621  H26 A1IUM 70 
A1IUM H27 H27 H 0 1 N N N N N N 4.019  -3.957 -0.740 -1.082 -2.684 3.463  H27 A1IUM 71 
A1IUM H28 H28 H 0 1 N N N N N N 5.255  -4.475 0.457  0.515  -3.475 3.584  H28 A1IUM 72 
A1IUM H29 H29 H 0 1 N N N N N N 5.325  2.323  1.172  -4.481 1.935  0.089  H29 A1IUM 73 
A1IUM H30 H30 H 0 1 N N N N N N 8.208  1.414  4.099  -4.064 -2.220 0.157  H30 A1IUM 74 
A1IUM H31 H31 H 0 1 N N N N N N 6.943  -4.806 -0.505 3.255  0.945  3.554  H31 A1IUM 75 
A1IUM H32 H32 H 0 1 N N N N N N 8.347  -5.508 -3.034 4.422  0.150  -0.616 H32 A1IUM 76 
A1IUM H33 H33 H 0 1 N N N N N N 9.360  -6.478 -4.875 6.142  -1.870 0.353  H33 A1IUM 77 
A1IUM H34 H34 H 0 1 N N N N N N 10.762 -6.937 -3.850 4.491  -2.530 0.273  H34 A1IUM 78 
A1IUM H35 H35 H 0 1 N N N N N N 11.708 -6.163 -6.194 3.356  -2.783 -1.861 H35 A1IUM 79 
A1IUM H36 H36 H 0 1 N N N N N N 13.089 -4.316 -7.134 3.608  -3.118 -4.288 H36 A1IUM 80 
A1IUM H37 H37 H 0 1 N N N N N N 12.871 -2.036 -6.223 5.715  -2.504 -5.403 H37 A1IUM 81 
A1IUM H38 H38 H 0 1 N N N N N N 11.507 -1.617 -4.208 7.571  -1.554 -4.093 H38 A1IUM 82 
A1IUM H39 H39 H 0 1 N N N N N N 10.174 -3.469 -3.219 7.316  -1.211 -1.668 H39 A1IUM 83 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
A1IUM C46 C47 DOUB Y N 1  
A1IUM C46 C45 SING Y N 2  
A1IUM C47 C48 SING Y N 3  
A1IUM C45 C44 DOUB Y N 4  
A1IUM C48 C49 DOUB Y N 5  
A1IUM C44 C43 SING N N 6  
A1IUM C44 C49 SING Y N 7  
A1IUM C43 N42 SING N N 8  
A1IUM N42 C40 SING N N 9  
A1IUM C40 O41 DOUB N N 10 
A1IUM C40 C38 SING N N 11 
A1IUM O39 C38 SING N N 12 
A1IUM C38 C9  SING N N 13 
A1IUM O13 C12 DOUB N N 14 
A1IUM C23 C22 SING N N 15 
A1IUM C23 C18 SING N N 16 
A1IUM C23 C14 SING N N 17 
A1IUM C9  N11 SING N N 18 
A1IUM C9  C8  SING N N 19 
A1IUM C22 C21 SING N N 20 
A1IUM C12 N11 SING N N 21 
A1IUM C12 C14 SING N N 22 
A1IUM C18 C17 SING N N 23 
A1IUM C18 C20 SING N N 24 
A1IUM C5  C4  SING N N 25 
A1IUM C5  C6  SING N N 26 
A1IUM C32 O31 SING N N 27 
A1IUM C17 N16 SING N N 28 
A1IUM C14 N16 SING N N 29 
A1IUM C8  C6  SING N N 30 
A1IUM C21 C20 SING N N 31 
A1IUM O31 C30 SING N N 32 
A1IUM C4  N3  SING N N 33 
A1IUM N16 C25 SING N N 34 
A1IUM C6  C2  SING N N 35 
A1IUM C28 C29 SING Y N 36 
A1IUM C28 C27 DOUB Y N 37 
A1IUM C25 C27 SING N N 38 
A1IUM C25 O26 DOUB N N 39 
A1IUM C30 C29 DOUB Y N 40 
A1IUM C30 C33 SING Y N 41 
A1IUM C29 C36 SING Y N 42 
A1IUM C27 N37 SING Y N 43 
A1IUM N3  C2  SING N N 44 
A1IUM C2  O1  DOUB N N 45 
A1IUM C33 C34 DOUB Y N 46 
A1IUM N37 C36 SING Y N 47 
A1IUM C36 C35 DOUB Y N 48 
A1IUM C34 C35 SING Y N 49 
A1IUM C4  H1  SING N N 50 
A1IUM C4  H2  SING N N 51 
A1IUM C5  H3  SING N N 52 
A1IUM C5  H4  SING N N 53 
A1IUM C6  H5  SING N N 54 
A1IUM C8  H6  SING N N 55 
A1IUM C8  H7  SING N N 56 
A1IUM C17 H8  SING N N 57 
A1IUM C17 H9  SING N N 58 
A1IUM C18 H10 SING N N 59 
A1IUM C21 H11 SING N N 60 
A1IUM C21 H12 SING N N 61 
A1IUM C23 H13 SING N N 62 
A1IUM C32 H14 SING N N 63 
A1IUM C32 H15 SING N N 64 
A1IUM C32 H16 SING N N 65 
A1IUM C33 H17 SING N N 66 
A1IUM C34 H18 SING N N 67 
A1IUM C35 H19 SING N N 68 
A1IUM C38 H20 SING N N 69 
A1IUM N3  H21 SING N N 70 
A1IUM C9  H22 SING N N 71 
A1IUM N11 H23 SING N N 72 
A1IUM C14 H24 SING N N 73 
A1IUM C20 H25 SING N N 74 
A1IUM C20 H26 SING N N 75 
A1IUM C22 H27 SING N N 76 
A1IUM C22 H28 SING N N 77 
A1IUM C28 H29 SING N N 78 
A1IUM N37 H30 SING N N 79 
A1IUM O39 H31 SING N N 80 
A1IUM N42 H32 SING N N 81 
A1IUM C43 H33 SING N N 82 
A1IUM C43 H34 SING N N 83 
A1IUM C45 H35 SING N N 84 
A1IUM C46 H36 SING N N 85 
A1IUM C47 H37 SING N N 86 
A1IUM C48 H38 SING N N 87 
A1IUM C49 H39 SING N N 88 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
A1IUM InChI            InChI                1.06  "InChI=1S/C33H39N5O6/c1-44-27-12-6-11-24-23(27)16-26(36-24)33(43)38-18-21-9-5-10-22(21)28(38)31(41)37-25(15-20-13-14-34-30(20)40)29(39)32(42)35-17-19-7-3-2-4-8-19/h2-4,6-8,11-12,16,20-22,25,28-29,36,39H,5,9-10,13-15,17-18H2,1H3,(H,34,40)(H,35,42)(H,37,41)/t20-,21-,22-,25-,28-,29+/m0/s1" 
A1IUM InChIKey         InChI                1.06  SRQDXOQIFPGVGN-FQVIVOBNSA-N                                                                                                                                                                                                                                                                     
A1IUM SMILES_CANONICAL CACTVS               3.385 "COc1cccc2[nH]c(cc12)C(=O)N3C[C@@H]4CCC[C@@H]4[C@H]3C(=O)N[C@@H](C[C@@H]5CCNC5=O)[C@@H](O)C(=O)NCc6ccccc6"                                                                                                                                                                                      
A1IUM SMILES           CACTVS               3.385 "COc1cccc2[nH]c(cc12)C(=O)N3C[CH]4CCC[CH]4[CH]3C(=O)N[CH](C[CH]5CCNC5=O)[CH](O)C(=O)NCc6ccccc6"                                                                                                                                                                                                 
A1IUM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COc1cccc2c1cc([nH]2)C(=O)N3C[C@@H]4CCC[C@@H]4[C@H]3C(=O)N[C@@H](C[C@@H]5CCNC5=O)[C@H](C(=O)NCc6ccccc6)O"                                                                                                                                                                                       
A1IUM SMILES           "OpenEye OEToolkits" 2.0.7 "COc1cccc2c1cc([nH]2)C(=O)N3CC4CCCC4C3C(=O)NC(CC5CCNC5=O)C(C(=O)NCc6ccccc6)O"                                                                                                                                                                                                                   
# 
_pdbx_chem_comp_identifier.comp_id           A1IUM 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "(3~{S},3~{a}~{S},6~{a}~{R})-2-[(4-methoxy-1~{H}-indol-2-yl)carbonyl]-~{N}-[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]-3,3~{a},4,5,6,6~{a}-hexahydro-1~{H}-cyclopenta[c]pyrrole-3-carboxamide" 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            A1IUM 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C38 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1IUM "Create component" 2024-11-20 PDBE 
A1IUM "Modify PCM"       2024-11-27 PDBE 
A1IUM "Initial release"  2025-07-16 RCSB 
# 
