Exploring the binding of peptidic West Nile virus NS2B-NS3 protease inhibitors by NMR

► P3 residues are not necessary for potent inhibition of WNV protease. ► Acetyl-KR-aldehyde has a IC50 of 170 nM against WNV protease. ► Acetyl-K-agmatine (without an aldehyde warhead) does not inhibit WNV protease. ► Small modifications of inhibitor structure can lead to major changes in the conformation of the WNV protease.