. Author manuscript; available in PMC: 2010 Aug 17.

Published in final edited form as: J Chem Inf Model. 2008 Jul 4;48(7):1464–1472. doi: 10.1021/ci800085c

Table 2.

Amino acid residues in papain and corresponding residues in cathepsin L and the interactions they make with CLIK-148 and the 3 inhibitors in the acyl hydrazine series: 1, 2, and 5.

Residue in papain	Corresponding Residue in cathepsin L	Types of binding interactions^a for compounds 1, 2, 5 and CLIK-148
Gln19	Gln19	H-bonding^b (CLIK-148, 1)
Cys25	Cys25	Covalent bond (CLIK-148, 1, 2, 5) H-bonding (1, 5)
Gly66	Gly68	H-bonding (CLIK-148, 1, 2, 5)
Asp158	Asp162	H-bonding (CLIK-148, 1, 5)
His159	His163	H-bonding (2, 5)
Trp177	Trp189	Hydrophobic/aromatic (CLIK-148, 1, 5) H-bonding (1)
Ser205	Ala214	Hydrophobic (CLIK-148, 1, 5)

Interactions were observed between the ligand and papain for the highest ranking poses obtained from ExtraPrecision Glide docking. Each compound was docked to papain without a covalent attachment to the Cys25 sulfur. A structural water was present in the catalytic site, near Asp158.

hydrogen bonding.