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Porcine epidemic diarrhea virus (PEDV) is a coronavirus that infects pigs and can have mortality rates approaching 100% in piglets, causing serious economic impact. The 3C-like protease (3CL pro ) is essential for the coronaviral life cycle and is an appealing target for the development of therapeutics. We report the expression, purification, crystallization and 2.10 Å X-ray structure of 3CL pro  from PEDV. Analysis of the PEDV 3CL pro  structure and comparison to other coronaviral 3CL pro ’s from the same alpha-coronavirus phylogeny shows that the overall structures and active site architectures across 3CL pro ’s are conserved, with the exception of a loop that comprises the protease S 2  pocket. We found a known inhibitor of severe acute respiratory syndrome coronavirus (SARS-CoV) 3CL pro , ( R )- 16 , to have inhibitor activity against PEDV 3CL pro , despite that SARS-3CL pro  and PEDV 3CL pro  share only 45.4% sequence identity. Structural comparison reveals that the majority of residues involved in ( R )- 16  binding to SARS-3CL pro  are conserved in PEDV-3CL pro ; however, the sequence variation and positional difference in the loop forming the S 2  pocket may account for large observed difference in IC 50  values. This work advances our understanding of the subtle, but important, differences in coronaviral 3CL pro  architecture and contributes to the broader structural knowledge of coronaviral 3CL pro ’s.

X-Ray Structure and Inhibition of 3C-like Protease from Porcine Epidemic Diarrhea Virus