data_A1D9H
# 
_chem_comp.id                                    A1D9H 
_chem_comp.name                                  "tert-butyl N-[(2S)-1-[[(2S)-1-[[(2S)-1-azanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-3,3-dimethyl-1-oxidanylidene-butan-2-yl]carbamate" 
_chem_comp.type                                  peptide-like 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C27 H41 N5 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-06-27 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        515.645 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1D9H 
_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        9IK2 
_chem_comp.pdbx_subcomponent_list                "BOC TDD PHE 79I" 
_chem_comp.pdbx_processing_site                  PDBC 
_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 
A1D9H O1  O1  O 0 1 N N N N N N 19.720 37.597 -13.244 4.880  1.207  0.749  O1   BOC 1  
A1D9H C1  C15 C 0 1 N N N N N N 19.841 38.039 -12.124 4.639  0.419  -0.144 C    BOC 2  
A1D9H O2  O2  O 0 1 N N N N N N 19.671 39.320 -11.749 5.642  -0.264 -0.728 O2   BOC 3  
A1D9H C2  C22 C 0 1 N N N N N N 19.193 40.364 -12.681 6.985  -0.008 -0.240 CT   BOC 4  
A1D9H C4  C1  C 0 1 N N N N N N 17.821 39.967 -13.180 7.983  -0.869 -1.018 C1   BOC 5  
A1D9H C5  C2  C 0 1 N N N N N N 20.183 40.498 -13.819 7.326  1.470  -0.436 C2   BOC 6  
A1D9H C3  C26 C 0 1 N N N N N N 19.127 41.636 -11.866 7.062  -0.357 1.247  C3   BOC 7  
A1D9H N1  N1  N 0 1 N N N N N N 20.161 37.292 -11.054 3.368  0.225  -0.546 N    TDD 8  
A1D9H C6  C3  C 0 1 N N S N N N 20.378 35.862 -11.197 2.276  0.964  0.093  CA   TDD 9  
A1D9H C7  C4  C 0 1 N N N N N N 21.834 35.440 -10.829 2.124  2.331  -0.577 CB   TDD 10 
A1D9H C8  C5  C 0 1 N N N N N N 22.145 35.755 -9.363  1.658  2.142  -2.022 CG1  TDD 11 
A1D9H C10 C6  C 0 1 N N N N N N 22.830 36.195 -11.713 1.091  3.161  0.188  CG2  TDD 12 
A1D9H C9  C27 C 0 1 N N N N N N 22.014 33.937 -11.059 3.471  3.056  -0.566 CG3  TDD 13 
A1D9H C11 C16 C 0 1 N N N N N N 19.319 35.042 -10.458 0.992  0.188  -0.051 C    TDD 14 
A1D9H O5  O5  O 0 1 N N N N N N 19.107 35.228 -9.261  0.930  -0.744 -0.825 O    TDD 15 
A1D9H N2  N3  N 0 1 N N N N N N 18.641 34.146 -11.194 -0.088 0.530  0.679  N    PHE 16 
A1D9H C12 C17 C 0 1 N N S N N N 17.728 33.212 -10.560 -1.358 -0.174 0.483  CA   PHE 17 
A1D9H C20 C10 C 0 1 N N N N N N 18.473 32.136 -9.774  -2.497 0.720  0.902  C    PHE 18 
A1D9H O4  O4  O 0 1 N N N N N N 19.307 31.422 -10.325 -2.270 1.834  1.323  O    PHE 19 
A1D9H C13 C7  C 0 1 N N N N N N 16.800 32.563 -11.591 -1.371 -1.448 1.330  CB   PHE 20 
A1D9H C14 C18 C 0 1 Y N N N N N 15.850 31.585 -10.950 -0.309 -2.394 0.830  CG   PHE 21 
A1D9H C15 C8  C 0 1 Y N N N N N 16.114 30.225 -10.959 0.969  -2.336 1.353  CD1  PHE 22 
A1D9H C19 C21 C 0 1 Y N N N N N 14.704 32.029 -10.311 -0.616 -3.323 -0.147 CD2  PHE 23 
A1D9H C16 C19 C 0 1 Y N N N N N 15.243 29.331 -10.356 1.943  -3.204 0.894  CE1  PHE 24 
A1D9H C18 C20 C 0 1 Y N N N N N 13.838 31.134 -9.703  0.358  -4.191 -0.604 CE2  PHE 25 
A1D9H C17 C9  C 0 1 Y N N N N N 14.107 29.788 -9.731  1.638  -4.130 -0.086 CZ   PHE 26 
A1D9H C27 C25 C 0 1 N N N N N N 17.768 29.900 -7.326  -5.093 1.021  2.701  C16  79I 27 
A1D9H C25 C24 C 0 1 N N N N N N 22.803 32.962 -6.524  -6.952 -0.864 -2.205 C12  79I 28 
A1D9H C24 C13 C 0 1 N N N N N N 20.826 33.431 -5.386  -4.911 0.058  -1.589 C14  79I 29 
A1D9H C26 C14 C 0 1 N N N N N N 21.770 31.941 -6.968  -7.256 0.593  -1.791 C11  79I 30 
A1D9H C23 C23 C 0 1 N N S N N N 20.448 32.592 -6.592  -5.970 0.978  -1.023 C10  79I 31 
A1D9H C21 C11 C 0 1 N N S N N N 18.754 31.013 -7.628  -4.875 1.148  1.216  C8   79I 32 
A1D9H C22 C12 C 0 1 N N N N N N 19.284 31.635 -6.336  -6.148 0.732  0.476  C9   79I 33 
A1D9H N3  N2  N 0 1 N N N N N N 18.149 32.020 -8.483  -3.767 0.280  0.808  N7   79I 34 
A1D9H N4  N4  N 0 1 N N N N N N 22.147 33.579 -5.376  -5.489 -0.961 -2.250 N13  79I 35 
A1D9H N5  N5  N 0 1 N N N N N N 18.145 28.711 -7.009  -4.353 0.238  3.392  N17  79I 36 
A1D9H O3  O3  O 0 1 N N N N N N 20.030 33.918 -4.564  -3.715 0.217  -1.466 O15  79I 37 
A1D9H H4  H4  H 0 1 N N N N N N 17.886 39.000 -13.700 7.739  -1.923 -0.879 H11  BOC 38 
A1D9H H5  H3  H 0 1 N N N N N N 17.448 40.733 -13.876 7.928  -0.621 -2.078 H12  BOC 39 
A1D9H H6  H5  H 0 1 N N N N N N 17.132 39.880 -12.327 8.991  -0.678 -0.652 H13  BOC 40 
A1D9H H7  H8  H 0 1 N N N N N N 20.265 39.537 -14.348 7.272  1.719  -1.496 H21  BOC 41 
A1D9H H8  H6  H 0 1 N N N N N N 19.836 41.273 -14.518 6.616  2.083  0.118  H22  BOC 42 
A1D9H H9  H7  H 0 1 N N N N N N 21.167 40.781 -13.417 8.335  1.662  -0.070 H23  BOC 43 
A1D9H H1  H33 H 0 1 N N N N N N 18.776 42.462 -12.502 6.819  -1.411 1.387  H31  BOC 44 
A1D9H H2  H35 H 0 1 N N N N N N 20.128 41.874 -11.476 8.071  -0.165 1.614  H32  BOC 45 
A1D9H H3  H34 H 0 1 N N N N N N 18.430 41.498 -11.027 6.352  0.256  1.801  H33  BOC 46 
A1D9H H10 H1  H 0 1 N N N N N N 20.250 37.722 -10.155 3.175  -0.404 -1.259 H    TDD 47 
A1D9H H11 H9  H 0 1 N N N N N N 20.258 35.624 -12.264 2.501  1.100  1.151  HA   TDD 48 
A1D9H H12 H10 H 0 1 N N N N N N 23.176 35.448 -9.132  0.699  1.625  -2.030 HG11 TDD 49 
A1D9H H13 H12 H 0 1 N N N N N N 21.445 35.208 -8.714  1.550  3.116  -2.499 HG12 TDD 50 
A1D9H H14 H11 H 0 1 N N N N N N 22.037 36.836 -9.190  2.394  1.550  -2.566 HG13 TDD 51 
A1D9H H18 H14 H 0 1 N N N N N N 22.637 35.956 -12.769 0.881  4.078  -0.364 HG21 TDD 52 
A1D9H H19 H15 H 0 1 N N N N N N 22.713 37.277 -11.555 0.172  2.586  0.299  HG22 TDD 53 
A1D9H H20 H13 H 0 1 N N N N N N 23.855 35.895 -11.450 1.484  3.412  1.173  HG23 TDD 54 
A1D9H H15 H36 H 0 1 N N N N N N 23.042 33.646 -10.798 4.207  2.465  -1.110 HG31 TDD 55 
A1D9H H16 H38 H 0 1 N N N N N N 21.824 33.703 -12.117 3.363  4.030  -1.043 HG32 TDD 56 
A1D9H H17 H37 H 0 1 N N N N N N 21.304 33.382 -10.428 3.803  3.191  0.464  HG33 TDD 57 
A1D9H H21 H39 H 0 1 N N N N N N 18.766 34.122 -12.186 -0.024 1.242  1.335  H    PHE 58 
A1D9H H22 H25 H 0 1 N N N N N N 17.098 33.767 -9.849  -1.469 -0.435 -0.569 HA   PHE 59 
A1D9H H23 H16 H 0 1 N N N N N N 16.217 33.350 -12.091 -1.171 -1.194 2.371  HB2  PHE 60 
A1D9H H24 H17 H 0 1 N N N N N N 17.411 32.031 -12.335 -2.348 -1.925 1.253  HB3  PHE 61 
A1D9H H25 H18 H 0 1 N N N N N N 17.008 29.857 -11.441 1.207  -1.613 2.119  HD1  PHE 62 
A1D9H H29 H28 H 0 1 N N N N N N 14.483 33.086 -10.286 -1.616 -3.371 -0.552 HD2  PHE 63 
A1D9H H26 H26 H 0 1 N N N N N N 15.457 28.273 -10.377 2.942  -3.159 1.302  HE1  PHE 64 
A1D9H H28 H27 H 0 1 N N N N N N 12.950 31.496 -9.206  0.118  -4.917 -1.367 HE2  PHE 65 
A1D9H H27 H19 H 0 1 N N N N N N 13.428 29.090 -9.263  2.398  -4.807 -0.444 HZ   PHE 66 
A1D9H H40 H32 H 0 1 N N N N N N 16.711 30.113 -7.379  -5.873 1.591  3.183  H1   79I 67 
A1D9H H36 H30 H 0 1 N N N N N N 23.001 33.700 -7.315  -7.354 -1.557 -1.466 H2   79I 68 
A1D9H H37 H31 H 0 1 N N N N N N 23.745 32.476 -6.232  -7.376 -1.073 -3.187 H3   79I 69 
A1D9H H38 H23 H 0 1 N N N N N N 21.829 31.767 -8.053  -7.392 1.227  -2.667 H4   79I 70 
A1D9H H39 H24 H 0 1 N N N N N N 21.905 30.988 -6.436  -8.129 0.640  -1.139 H5   79I 71 
A1D9H H34 H29 H 0 1 N N N N N N 20.157 33.272 -7.406  -5.711 2.020  -1.212 H7   79I 72 
A1D9H H31 H20 H 0 1 N N N N N N 19.609 30.569 -8.159  -4.634 2.182  0.971  H17  79I 73 
A1D9H H32 H21 H 0 1 N N N N N N 18.469 32.191 -5.850  -6.990 1.318  0.844  H18  79I 74 
A1D9H H33 H22 H 0 1 N N N N N N 19.627 30.830 -5.670  -6.339 -0.327 0.650  H19  79I 75 
A1D9H H30 H2  H 0 1 N N N N N N 17.471 32.644 -8.094  -3.948 -0.612 0.472  H33  79I 76 
A1D9H H35 H40 H 0 1 N N N N N N 22.641 34.064 -4.655  -5.001 -1.668 -2.699 H34  79I 77 
A1D9H H41 H41 H 0 1 N N N N N N 17.368 28.103 -6.843  -4.493 0.156  4.348  H35  79I 78 
# 
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 
A1D9H O1  C1  DOUB N N 1  
A1D9H C1  O2  SING N N 2  
A1D9H O2  C2  SING N N 3  
A1D9H C2  C3  SING N N 4  
A1D9H C2  C4  SING N N 5  
A1D9H C2  C5  SING N N 6  
A1D9H C1  N1  SING N N 7  
A1D9H N1  C6  SING N N 8  
A1D9H C6  C7  SING N N 9  
A1D9H C7  C8  SING N N 10 
A1D9H C7  C9  SING N N 11 
A1D9H C7  C10 SING N N 12 
A1D9H C6  C11 SING N N 13 
A1D9H C11 N2  SING N N 14 
A1D9H N2  C12 SING N N 15 
A1D9H C12 C13 SING N N 16 
A1D9H C13 C14 SING N N 17 
A1D9H C14 C15 DOUB Y N 18 
A1D9H C15 C16 SING Y N 19 
A1D9H C16 C17 DOUB Y N 20 
A1D9H C17 C18 SING Y N 21 
A1D9H C18 C19 DOUB Y N 22 
A1D9H C12 C20 SING N N 23 
A1D9H C20 N3  SING N N 24 
A1D9H N3  C21 SING N N 25 
A1D9H C21 C22 SING N N 26 
A1D9H C22 C23 SING N N 27 
A1D9H C23 C24 SING N N 28 
A1D9H C24 N4  SING N N 29 
A1D9H N4  C25 SING N N 30 
A1D9H C25 C26 SING N N 31 
A1D9H C24 O3  DOUB N N 32 
A1D9H C21 C27 SING N N 33 
A1D9H C27 N5  DOUB N N 34 
A1D9H C20 O4  DOUB N N 35 
A1D9H C11 O5  DOUB N N 36 
A1D9H C14 C19 SING Y N 37 
A1D9H C23 C26 SING N N 38 
A1D9H N1  H10 SING N N 39 
A1D9H N3  H30 SING N N 40 
A1D9H C4  H5  SING N N 41 
A1D9H C4  H4  SING N N 42 
A1D9H C4  H6  SING N N 43 
A1D9H C5  H8  SING N N 44 
A1D9H C5  H9  SING N N 45 
A1D9H C5  H7  SING N N 46 
A1D9H C6  H11 SING N N 47 
A1D9H C8  H12 SING N N 48 
A1D9H C8  H14 SING N N 49 
A1D9H C8  H13 SING N N 50 
A1D9H C10 H20 SING N N 51 
A1D9H C10 H18 SING N N 52 
A1D9H C10 H19 SING N N 53 
A1D9H C13 H23 SING N N 54 
A1D9H C13 H24 SING N N 55 
A1D9H C15 H25 SING N N 56 
A1D9H C17 H27 SING N N 57 
A1D9H C21 H31 SING N N 58 
A1D9H C22 H32 SING N N 59 
A1D9H C22 H33 SING N N 60 
A1D9H C26 H38 SING N N 61 
A1D9H C26 H39 SING N N 62 
A1D9H C12 H22 SING N N 63 
A1D9H C16 H26 SING N N 64 
A1D9H C18 H28 SING N N 65 
A1D9H C19 H29 SING N N 66 
A1D9H C23 H34 SING N N 67 
A1D9H C25 H36 SING N N 68 
A1D9H C25 H37 SING N N 69 
A1D9H C27 H40 SING N N 70 
A1D9H C3  H1  SING N N 71 
A1D9H C3  H3  SING N N 72 
A1D9H C3  H2  SING N N 73 
A1D9H C9  H15 SING N N 74 
A1D9H C9  H17 SING N N 75 
A1D9H C9  H16 SING N N 76 
A1D9H N2  H21 SING N N 77 
A1D9H N4  H35 SING N N 78 
A1D9H N5  H41 SING N N 79 
# 
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 
A1D9H InChI            InChI                1.06  "InChI=1S/C27H41N5O5/c1-26(2,3)21(32-25(36)37-27(4,5)6)24(35)31-20(14-17-10-8-7-9-11-17)23(34)30-19(16-28)15-18-12-13-29-22(18)33/h7-11,16,18-21,28H,12-15H2,1-6H3,(H,29,33)(H,30,34)(H,31,35)(H,32,36)/b28-16+/t18-,19+,20+,21-/m1/s1" 
A1D9H InChIKey         InChI                1.06  YWXGXHNDBCVDDN-NFIWZKORSA-N                                                                                                                                                                                                             
A1D9H SMILES_CANONICAL CACTVS               3.385 "CC(C)(C)OC(=O)N[C@H](C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)C=N)C(C)(C)C"                                                                                                                                                 
A1D9H SMILES           CACTVS               3.385 "CC(C)(C)OC(=O)N[CH](C(=O)N[CH](Cc1ccccc1)C(=O)N[CH](C[CH]2CCNC2=O)C=N)C(C)(C)C"                                                                                                                                                        
A1D9H SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C/[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)(C)C)NC(=O)OC(C)(C)C"                                                                                                                                              
A1D9H SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)(C)C(C(=O)NC(Cc1ccccc1)C(=O)NC(CC2CCNC2=O)C=N)NC(=O)OC(C)(C)C"                                                                                                                                                                    
# 
_pdbx_chem_comp_identifier.comp_id           A1D9H 
_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        "~{tert}-butyl ~{N}-[(2~{S})-1-[[(2~{S})-1-[[(2~{S})-1-azanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-3,3-dimethyl-1-oxidanylidene-butan-2-yl]carbamate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1D9H "Create component" 2024-06-27 PDBC 
A1D9H "Initial release"  2024-07-31 RCSB 
A1D9H "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            A1D9H 
_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               C27 
_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      ? 
# 
