data_M9X
# 
_chem_comp.id                                    M9X 
_chem_comp.name                                  "tert-butyl N-[1-[(2S)-3-cyclopropyl-1-[[(2S,3R)-4-(cyclopropylamino)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]amino]-1-oxidanylidene-propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C27 H39 N5 O7" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "tert-butyl (1-((S)-3-cyclopropyl-1-(((S)-4-(cyclopropylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate; MG-97 inhibitor (covalently bound to protein)" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-07-27 
_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                        545.628 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     M9X 
_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        8AIU 
_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_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_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 
M9X N1  N1  N 0 1 N N N N N N -8.145  1.100  18.421 4.907  0.997  -0.991 N1  M9X 1  
M9X N3  N2  N 0 1 N N N N N N -6.800  0.762  24.380 -1.760 0.010  0.992  N3  M9X 2  
M9X C4  C1  C 0 1 N N N N N N -8.518  1.579  14.381 6.518  -2.790 -0.462 C4  M9X 3  
M9X C5  C2  C 0 1 N N N N N N -8.770  0.723  17.279 5.268  -0.174 -0.430 C5  M9X 4  
M9X C6  C3  C 0 1 N N N N N N -8.771  1.656  19.545 3.558  1.253  -1.274 C6  M9X 5  
M9X C7  C4  C 0 1 N N N N N N -7.953  1.818  20.654 2.585  1.164  -0.255 C7  M9X 6  
M9X C8  C5  C 0 1 N N N N N N -9.897  2.714  21.816 0.907  1.750  -1.797 C8  M9X 7  
M9X C10 C6  C 0 1 N N N N N N -10.125 2.030  19.569 3.170  1.599  -2.540 C10 M9X 8  
M9X C13 C7  C 0 1 N N N N N N -8.194  3.657  23.921 -0.405 2.670  0.695  C13 M9X 9  
M9X C15 C8  C 0 1 N N N N N N -7.754  6.192  24.099 0.138  5.154  1.310  C15 M9X 10 
M9X C17 C9  C 0 1 N N S N N N -6.811  -0.449 25.184 -2.813 -0.925 0.588  C17 M9X 11 
M9X C20 C10 C 0 1 N N S N N N -6.112  -1.891 23.221 -3.474 -3.332 0.497  C20 M9X 12 
M9X C21 C11 C 0 1 N N N N N N -7.308  -2.828 23.132 -3.185 -4.753 1.034  C21 M9X 13 
M9X C22 C12 C 0 1 N N N N N N -6.995  -3.786 21.980 -3.593 -5.633 -0.168 C22 M9X 14 
M9X C24 C13 C 0 1 N N N N N N -7.094  -1.044 27.588 -4.512 0.862  0.853  C24 M9X 15 
M9X C26 C14 C 0 1 N N N N N N -10.013 -2.272 29.234 -6.061 2.638  -2.083 C26 M9X 16 
M9X C1  C15 C 0 1 N N N N N N -6.745  -0.187 14.424 6.054  -1.848 1.804  C1  M9X 17 
M9X C2  C16 C 0 1 N N N N N N -8.100  0.233  14.946 6.866  -1.670 0.520  C2  M9X 18 
M9X C3  C17 C 0 1 N N N N N N -9.159  -0.825 14.721 8.359  -1.726 0.849  C3  M9X 19 
M9X O1  O1  O 0 1 N N N N N N -7.848  0.303  16.401 6.550  -0.386 -0.079 O1  M9X 20 
M9X O2  O2  O 0 1 N N N N N N -9.961  0.774  17.094 4.435  -1.039 -0.241 O2  M9X 21 
M9X N2  N3  N 0 1 N N N N N N -8.570  2.391  21.779 1.292  1.412  -0.538 N2  M9X 22 
M9X C9  C18 C 0 1 N N N N N N -10.671 2.590  20.721 1.814  1.850  -2.795 C9  M9X 23 
M9X O3  O3  O 0 1 N N N N N N -6.774  1.477  20.716 2.915  0.861  0.880  O3  M9X 24 
M9X C11 C19 C 0 1 N N S N N N -7.762  2.513  23.006 0.288  1.317  0.525  C11 M9X 25 
M9X C12 C20 C 0 1 N N N N N N -7.852  1.166  23.684 -0.734 0.272  0.158  C12 M9X 26 
M9X C14 C21 C 0 1 N N N N N N -8.072  4.999  23.256 0.610  3.704  1.189  C14 M9X 27 
M9X C16 C22 C 0 1 N N N N N N -6.742  5.682  23.134 0.376  4.320  2.570  C16 M9X 28 
M9X O4  O4  O 0 1 N N N N N N -8.860  0.474  23.537 -0.634 -0.333 -0.888 O4  M9X 29 
M9X C18 C23 C 0 1 N N R N N N -6.672  0.011  26.637 -4.128 -0.536 1.265  C18 M9X 30 
M9X C19 C24 C 0 1 N N N N N N -5.781  -1.450 24.648 -2.423 -2.344 1.007  C19 M9X 31 
M9X N4  N4  N 0 1 N N N N N N -5.546  -3.661 21.827 -3.443 -4.775 -1.349 N4  M9X 32 
M9X C23 C25 C 0 1 N N N N N N -5.018  -2.643 22.490 -3.382 -3.475 -1.006 C23 M9X 33 
M9X O5  O5  O 0 1 N N N N N N -3.846  -2.374 22.525 -3.267 -2.555 -1.788 O5  M9X 34 
M9X O6  O6  O 0 1 N N N N N N -7.562  1.105  26.824 -3.966 -0.586 2.684  O6  M9X 35 
M9X N5  N5  N 0 1 N N N N N N -8.174  -0.721 28.315 -4.817 1.125  -0.433 N5  M9X 36 
M9X C25 C26 C 0 1 N N N N N N -8.734  -1.517 29.422 -5.190 2.484  -0.835 C25 M9X 37 
M9X O7  O7  O 0 1 N N N N N N -6.502  -2.117 27.641 -4.546 1.750  1.678  O7  M9X 38 
M9X C27 C27 C 0 1 N N N N N N -10.014 -0.998 29.992 -4.583 3.030  -2.129 C27 M9X 39 
M9X H1  H1  H 0 1 N N N N N N -7.154  0.971  18.465 5.581  1.665  -1.195 H1  M9X 40 
M9X H2  H2  H 0 1 N N N N N N -5.965  1.312  24.351 -1.801 0.441  1.860  H2  M9X 41 
M9X H3  H3  H 0 1 N N N N N N -9.506  1.854  14.780 5.455  -2.751 -0.697 H3  M9X 42 
M9X H4  H4  H 0 1 N N N N N N -7.781  2.343  14.669 7.097  -2.664 -1.377 H4  M9X 43 
M9X H5  H5  H 0 1 N N N N N N -8.571  1.516  13.284 6.755  -3.755 -0.013 H5  M9X 44 
M9X H6  H6  H 0 1 N N N N N N -10.332 3.074  22.737 -0.135 1.945  -2.002 H6  M9X 45 
M9X H7  H7  H 0 1 N N N N N N -10.742 1.883  18.695 3.899  1.677  -3.332 H7  M9X 46 
M9X H8  H8  H 0 1 N N N N N N -9.243  3.500  24.211 -0.814 2.992  -0.262 H8  M9X 47 
M9X H9  H9  H 0 1 N N N N N N -7.560  3.649  24.820 -1.211 2.577  1.423  H9  M9X 48 
M9X H10 H10 H 0 1 N N N N N N -7.591  6.072  25.180 0.860  5.939  1.083  H10 M9X 49 
M9X H11 H11 H 0 1 N N N N N N -8.261  7.150  23.908 -0.894 5.372  1.038  H11 M9X 50 
M9X H12 H12 H 0 1 N N N N N N -7.801  -0.917 25.084 -2.937 -0.887 -0.495 H12 M9X 51 
M9X H13 H13 H 0 1 N N N N N N -6.348  -0.988 22.638 -4.473 -3.010 0.789  H13 M9X 52 
M9X H14 H14 H 0 1 N N N N N N -8.226  -2.260 22.921 -2.127 -4.875 1.266  H14 M9X 53 
M9X H15 H15 H 0 1 N N N N N N -7.430  -3.385 24.073 -3.802 -4.974 1.906  H15 M9X 54 
M9X H16 H16 H 0 1 N N N N N N -7.517  -3.481 21.061 -2.933 -6.498 -0.244 H16 M9X 55 
M9X H17 H17 H 0 1 N N N N N N -7.277  -4.818 22.237 -4.628 -5.958 -0.064 H17 M9X 56 
M9X H18 H18 H 0 1 N N N N N N -10.482 -2.320 28.240 -6.357 1.728  -2.605 H18 M9X 57 
M9X H19 H19 H 0 1 N N N N N N -10.171 -3.225 29.761 -6.796 3.443  -2.088 H19 M9X 58 
M9X H20 H20 H 0 1 N N N N N N -6.473  -1.163 14.852 6.291  -2.812 2.254  H20 M9X 59 
M9X H21 H21 H 0 1 N N N N N N -6.783  -0.265 13.327 6.301  -1.050 2.504  H21 M9X 60 
M9X H22 H22 H 0 1 N N N N N N -5.993  0.562  14.713 4.990  -1.808 1.570  H22 M9X 61 
M9X H23 H23 H 0 1 N N N N N N -8.818  -1.782 15.144 8.938  -1.600 -0.065 H23 M9X 62 
M9X H24 H24 H 0 1 N N N N N N -10.094 -0.519 15.214 8.607  -0.928 1.549  H24 M9X 63 
M9X H25 H25 H 0 1 N N N N N N -9.335  -0.943 13.642 8.596  -2.690 1.299  H25 M9X 64 
M9X H26 H26 H 0 1 N N N N N N -11.699 2.920  20.736 1.494  2.123  -3.790 H26 M9X 65 
M9X H27 H27 H 0 1 N N N N N N -6.713  2.684  22.721 0.774  1.037  1.460  H27 M9X 66 
M9X H28 H28 H 0 1 N N N N N N -8.772  5.179  22.427 1.641  3.534  0.881  H28 M9X 67 
M9X H29 H29 H 0 1 N N N N N N -5.833  5.185  23.502 1.254  4.555  3.172  H29 M9X 68 
M9X H30 H30 H 0 1 N N N N N N -6.502  6.262  22.231 -0.501 3.989  3.127  H30 M9X 69 
M9X H31 H31 H 0 1 N N N N N N -5.631  0.307  26.833 -4.912 -1.231 0.965  H31 M9X 70 
M9X H32 H32 H 0 1 N N N N N N -5.770  -2.335 25.301 -1.452 -2.595 0.581  H32 M9X 71 
M9X H33 H33 H 0 1 N N N N N N -4.788  -0.977 24.654 -2.369 -2.399 2.094  H33 M9X 72 
M9X H34 H34 H 0 1 N N N N N N -5.002  -4.289 21.271 -3.396 -5.103 -2.261 H34 M9X 73 
M9X H35 H35 H 0 1 N N N N N N -7.500  1.415  27.720 -3.283 0.009  3.023  H35 M9X 74 
M9X H36 H36 H 0 1 N N N N N N -8.640  0.134  28.086 -4.790 0.415  -1.093 H36 M9X 75 
M9X H37 H37 H 0 1 N N N N N N -8.017  -1.943 30.139 -5.352 3.187  -0.018 H37 M9X 76 
M9X H38 H38 H 0 1 N N N N N N -10.484 -0.102 29.560 -3.907 2.378  -2.682 H38 M9X 77 
M9X H39 H39 H 0 1 N N N N N N -10.174 -1.007 31.080 -4.345 4.093  -2.164 H39 M9X 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 
M9X C4  C2  SING N N 1  
M9X C1  C2  SING N N 2  
M9X C3  C2  SING N N 3  
M9X C2  O1  SING N N 4  
M9X O1  C5  SING N N 5  
M9X O2  C5  DOUB N N 6  
M9X C5  N1  SING N N 7  
M9X N1  C6  SING N N 8  
M9X C6  C10 DOUB N N 9  
M9X C6  C7  SING N N 10 
M9X C10 C9  SING N N 11 
M9X C7  O3  DOUB N N 12 
M9X C7  N2  SING N N 13 
M9X C9  C8  DOUB N N 14 
M9X N2  C8  SING N N 15 
M9X N2  C11 SING N N 16 
M9X N4  C22 SING N N 17 
M9X N4  C23 SING N N 18 
M9X C22 C21 SING N N 19 
M9X C23 O5  DOUB N N 20 
M9X C23 C20 SING N N 21 
M9X C11 C12 SING N N 22 
M9X C11 C13 SING N N 23 
M9X C21 C20 SING N N 24 
M9X C16 C14 SING N N 25 
M9X C16 C15 SING N N 26 
M9X C20 C19 SING N N 27 
M9X C14 C13 SING N N 28 
M9X C14 C15 SING N N 29 
M9X O4  C12 DOUB N N 30 
M9X C12 N3  SING N N 31 
M9X N3  C17 SING N N 32 
M9X C19 C17 SING N N 33 
M9X C17 C18 SING N N 34 
M9X C18 O6  SING N N 35 
M9X C18 C24 SING N N 36 
M9X C24 O7  DOUB N N 37 
M9X C24 N5  SING N N 38 
M9X N5  C25 SING N N 39 
M9X C26 C25 SING N N 40 
M9X C26 C27 SING N N 41 
M9X C25 C27 SING N N 42 
M9X N1  H1  SING N N 43 
M9X N3  H2  SING N N 44 
M9X C4  H3  SING N N 45 
M9X C4  H4  SING N N 46 
M9X C4  H5  SING N N 47 
M9X C8  H6  SING N N 48 
M9X C10 H7  SING N N 49 
M9X C13 H8  SING N N 50 
M9X C13 H9  SING N N 51 
M9X C15 H10 SING N N 52 
M9X C15 H11 SING N N 53 
M9X C17 H12 SING N N 54 
M9X C20 H13 SING N N 55 
M9X C21 H14 SING N N 56 
M9X C21 H15 SING N N 57 
M9X C22 H16 SING N N 58 
M9X C22 H17 SING N N 59 
M9X C26 H18 SING N N 60 
M9X C26 H19 SING N N 61 
M9X C1  H20 SING N N 62 
M9X C1  H21 SING N N 63 
M9X C1  H22 SING N N 64 
M9X C3  H23 SING N N 65 
M9X C3  H24 SING N N 66 
M9X C3  H25 SING N N 67 
M9X C9  H26 SING N N 68 
M9X C11 H27 SING N N 69 
M9X C14 H28 SING N N 70 
M9X C16 H29 SING N N 71 
M9X C16 H30 SING N N 72 
M9X C18 H31 SING N N 73 
M9X C19 H32 SING N N 74 
M9X C19 H33 SING N N 75 
M9X N4  H34 SING N N 76 
M9X O6  H35 SING N N 77 
M9X N5  H36 SING N N 78 
M9X C25 H37 SING N N 79 
M9X C27 H38 SING N N 80 
M9X C27 H39 SING N N 81 
# 
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 
M9X InChI            InChI                1.06  "InChI=1S/C27H39N5O7/c1-27(2,3)39-26(38)31-18-5-4-12-32(25(18)37)20(13-15-6-7-15)23(35)30-19(14-16-10-11-28-22(16)34)21(33)24(36)29-17-8-9-17/h4-5,12,15-17,19-21,33H,6-11,13-14H2,1-3H3,(H,28,34)(H,29,36)(H,30,35)(H,31,38)/t16-,19-,20-,21+/m0/s1" 
M9X InChIKey         InChI                1.06  AQQKBKPJQNKDPI-LRGNLBRXSA-N                                                                                                                                                                                                                           
M9X SMILES_CANONICAL CACTVS               3.385 "CC(C)(C)OC(=O)NC1=CC=CN([C@@H](CC2CC2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@@H](O)C(=O)NC4CC4)C1=O"                                                                                                                                                        
M9X SMILES           CACTVS               3.385 "CC(C)(C)OC(=O)NC1=CC=CN([CH](CC2CC2)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)C(=O)NC4CC4)C1=O"                                                                                                                                                                
M9X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)(C)OC(=O)NC1=CC=CN(C1=O)[C@@H](CC2CC2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](C(=O)NC4CC4)O"                                                                                                                                                         
M9X SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)(C)OC(=O)NC1=CC=CN(C1=O)C(CC2CC2)C(=O)NC(CC3CCNC3=O)C(C(=O)NC4CC4)O"                                                                                                                                                                            
# 
_pdbx_chem_comp_identifier.comp_id           M9X 
_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}-[1-[(2~{S})-3-cyclopropyl-1-[[(2~{S},3~{R})-4-(cyclopropylamino)-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]amino]-1-oxidanylidene-propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate" 
# 
loop_
_pdbx_chem_comp_synonyms.ordinal 
_pdbx_chem_comp_synonyms.comp_id 
_pdbx_chem_comp_synonyms.name 
_pdbx_chem_comp_synonyms.provenance 
_pdbx_chem_comp_synonyms.type 
1 M9X "tert-butyl (1-((S)-3-cyclopropyl-1-(((S)-4-(cyclopropylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate" AUTHOR ? 
2 M9X "MG-97 inhibitor (covalently bound to protein)"                                                                                                                                   AUTHOR ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
M9X "Create component"  2022-07-27 PDBE 
M9X "Modify synonyms"   2022-08-14 PDBE 
M9X "Initial release"   2023-08-16 RCSB 
M9X "Modify descriptor" 2023-09-23 RCSB 
M9X "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            M9X 
_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               C18 
_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      ? 
# 
