Soluble in 50% acetic acid, water, or DMSO.

E-64 is an effective ligand for affinity purification of cysteine proteases. When coupled to a thiolated affinity matrix, binding is no longer irreversible, but specificity is retained.

E-64 is an irreversible, potent, and highly selective cysteine protease inhibitor. E-64 does not react with the functional thiol group of non-protease enzymes, such as L-lactate dehydrogenase or creatine kinase. E-64 will not inhibit serine proteases (except trypsin) like other cysteine protease inhibitors, leupeptin and antipain. The trans-epoxysuccinyl group (active moiety) of E-64 irreversibly binds to an active thiol group in many cysteine proteases, such as papain, actinidase, and cathepsins B, H, and L to form a thioether linkage. E-64 is a very useful cysteine protease inhibitor for use in in vivo studies because it has a specific inhibition, it is permeable in cells and tissues and has low toxicity.