9CKW
X-ray diffraction structure of papain co-crystallized with E-64D
Summary for 9CKW
| Entry DOI | 10.2210/pdb9ckw/pdb |
| Related | 9CKT |
| Descriptor | Papain, METHANOL, ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate, ... (4 entities in total) |
| Functional Keywords | protease, complex, inhibitor-bound, hydrolase |
| Biological source | Carica papaya (papaya) |
| Total number of polymer chains | 1 |
| Total formula weight | 23828.79 |
| Authors | Vlahakis, N.W.,Rodriguez, J.A. (deposition date: 2024-07-10, release date: 2025-06-04, Last modification date: 2025-06-11) |
| Primary citation | Liu, M.,Zang, X.,Vlahakis, N.W.,Rodriguez, J.A.,Ohashi, M.,Tang, Y. Enzymatic combinatorial synthesis of E-64 and related cysteine protease inhibitors. Nat.Chem.Biol., 2025 Cited by PubMed Abstract: E-64 is an irreversible cysteine protease inhibitor prominently used in chemical biology and drug discovery. Here we uncover a nonribosomal peptide synthetase-independent biosynthetic pathway for E-64, which is widely conserved in fungi. The pathway starts with epoxidation of fumaric acid to the warhead (2S,3S)-trans-epoxysuccinic acid with an Fe(II)/α-ketoglutarate-dependent oxygenase, followed by successive condensation with an L-amino acid by an adenosine triphosphate grasp enzyme and with an amine by the fungal example of amide bond synthetase. Both amide bond-forming enzymes display notable biocatalytic potential, including scalability, stereoselectivity toward the warhead and broader substrate scopes in forming the amide bonds. Biocatalytic cascade with these amide bond-forming enzymes generated a library of cysteine protease inhibitors, leading to more potent cathepsin inhibitors. Additionally, one-pot reactions enabled the preparative synthesis of clinically relevant inhibitors. Our work highlights the importance of biosynthetic investigation for enzyme discovery and the potential of amide bond-forming enzymes in synthesizing small-molecule libraries. PubMed: 40346252DOI: 10.1038/s41589-025-01907-2 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.4 Å) |
Structure validation
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