Notes on 3CLpro inhibitor (4MDS)

4MDS is a PDB structure showing the non-covalent binding of an inhibitor "N-[4-(acetylamino)phenyl]-2-(1H-benzotriazol-1-yl)-N-[(1R)-2-[(2-methylbutan-2-yl)amino]-1-(1-methyl-1H-pyrrol-2-yl)-2-oxoethyl]acetamide" to a 3-chymotrypsin-like protease (3CLpro) found in SARS and MERS coronaviruses, see: Turlington, Mark, Aspen Chun, Sakshi Tomar, Aimee Eggler, Valerie Grum-Tokars, Jon Jacobs, J. Scott Daniels et al. "Discovery of N-(benzo [1, 2, 3] triazol-1-yl)-N-(benzyl) acetamido) phenyl) carboxamides as severe acute respiratory syndrome coronavirus (SARS-CoV) 3CLpro inhibitors: identification of ML300 and noncovalent nanomolar inhibitors with an induced-fit binding." Bioorganic & medicinal chemistry letters 23, no. 22 (2013): 6172-6177.

The Specific Script shows the inhibitor, labeled 23H in 4MDS, in the active site.   For a good description of this system, see: Pillaiyar, Thanigaimalai, Manoj Manickam, Vigneshwaran Namasivayam, Yoshio Hayashi, and Sang-Hun Jung. "An overview of severe acute respiratory syndrome–coronavirus (SARS-CoV) 3CL protease inhibitors: peptidomimetics and small molecule chemotherapy." Journal of medicinal chemistry 59, no. 14 (2016): 6595-6628, and Figure 31 in that paper.