Alexander Bayden’s favorite structure is:

HIV-1 Protease Complexed with KNI-1689

3A2O

Source: Created from PDB described in Hidaka, Koushi, et al. “Small-sized human immunodeficiency virus type-1 protease inhibitors containing allophenylnorstatine to explore the S2′ pocket.” Journal of medicinal chemistry 52.23 (2009): 7604-7617.

Why?

This is the one of the highest resolution structures of HIV-1 protease. The reason I like it is because this protein is challenging in many ways. For decades we have been trying, but were unable to create a cure for HIV. HIV-1 protease is especially tricky. Its crystals of are notoriously hard to prepare because this protein eats up the cells that produce it in significant amounts. In addition to that, there are non-standard protonation states in the active site of HIV-1 protease. They change depending on the ligand bound and the pH of the environment.—Alexander Bayden

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