Table 2.

Active site parameters of convergently related Cys proteases

Clan	Enzyme	PDB	Complex	Reactive rotamer	ϕ, ψ angles	Catalytic motif	Oxyanion hole	Face of attack	χcat	αcat	χoxy	Reference
PA	SARS protease	3SND	Thioacetal	g−	(−56, 142)	C-H	N	re	−168	82	−41	(74)
CD	Caspase 8	1QTN	Thioacetal	g−	(−73, 159)	C-H	N	re	NA	NA	−2	(75)
CF	Pyrrolidone carboxylate peptidase	1IU8		g−	(−64, -52)	C-H-E	N	re	−169			(76)
CL	L,D-transpeptidase	1ZAT		g−	(−65, 164)	C-H	N	re	179			(77)
CM	HCV NS2 protease	2HD0		g−	(−66, 141)	C-H-E	N	re	153			(78)
PC	PH1704	1G2I		t	(60, −115)	C-E	N + 1	si	180			(79)
CA	Papain	1POP	Thioacetal	g+	(−56, −32)	C-H	N	si	−177	76	30	(80)
CE	Ulp1	1EUV	Thioacetal	g+	(−52, −46)	C-H-D	N	si	−169	82	36	(81)
CN	Equine encephalitis alphavirus nsP2	2HWK		g+	(−54, −26)	C-H	N	si	ND			(82)
CO	Diamino endopeptidase	2HBQ		g+	(−64, −47)	C-H-H	N	si	−160			(83)
CP	deSUMOylase DeSI-1	2WP7	Unmodeled	g+	(−59, −32)	C-H	N	si	179			(84)

Members of clan CD do not use the same general base for activation of the nucleophile and protonation of the leaving group. The structure 2HWK crystallized with the base in an inactive state and 2WP7 has a ligand covalently bound to the nucleophile that was not modeled.