Representative Crystal Structures of NS3 and NS5 with Small Molecule Inhibitors. Cartoon representations of the (A) NS2B-NS3 protease, (B,C) NS5 RNA-dependent RNA polymerase (RdRp), and (D,E) NS5 methyltransferase (MTase) crystal structures are shown with inhibitor-bound small molecule (green sticks). (A) Compound 8 is bound to the protease active site of the NS3 protein; (B) RK-0404678 is bound to the RNA binding site of the NS5 RdRp, close to the priming loop; (C) HeE1-2Tyr is bound to the RNA template tunnel, between the fingers subdomain and the priming loop; (D) Ribavirin 5′-triphosphate is bound to the GTP binding site of the NS5 MTase; (E) Sinefungin is bound to the SAM binding site of the NS5 MTase. All structure representations were made in PyMOL.