9CKW

X-ray diffraction structure of papain co-crystallized with E-64D

9CKW の概要

• エントリーDOI: 10.2210/pdb9ckw/pdb
• 関連するPDBエントリー: 9CKT
• 分子名称: 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)
• 機能のキーワード: protease, complex, inhibitor-bound, hydrolase
• 由来する生物種: Carica papaya (papaya)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 23828.79

構造登録者

Vlahakis, N.W.,Rodriguez, J.A. (登録日: 2024-07-10, 公開日: 2025-06-04, 最終更新日: 2025-11-05)

主引用文献

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., 21:1783-1793, 2025

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: 40346252
DOI: 10.1038/s41589-025-01907-2

実験手法

X-RAY DIFFRACTION (1.4 Å)