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 ? #