Structures of Enterovirus 71 3C proteinase (strain E2004104-TW-CDC) and its complex with rupintrivir

The crystal structure of 3C proteinase (3C^pro) from Entero­virus 71 (EV71) was determined in space group C222₁ to 2.2 Å resolution. The fold was similar to that of 3C^pro from other picornaviruses, but the difference in the β-ribbon reported in a previous structure was not observed. This β-ribbon was folded over the substrate-binding cleft and constituted part of the essential binding sites for interaction with the substrate. The structure of its complex with rupintrivir (AG7088), a peptido­mimetic inhibitor, was also characterized in space group P2₁2₁2₁ to 1.96 Å resolution. The inhibitor was accommodated without any spatial hindrance despite the more constricted binding site; this was confirmed by functional assays, in which the inhibitor showed comparable potency towards EV71 3C^pro and human rhinovirus 3C^pro, which is the target that rupintrivir was designed against.