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. Author manuscript; available in PMC: 2010 Sep 1.
Published in final edited form as: J Comput Aided Mol Des. 2009 Jun 25;23(9):621–632. doi: 10.1007/s10822-009-9270-7

Figure 2.

Figure 2

Structural elements of the x-ray crystal structure of liganded β secretase (BACE-1, PDB code 2va7) as modified by computational titration. All residues with ionizable functional groups within 6 Å of the ligand were included in the titratable pool. Water molecules within 4 Å of atoms in both the ligand and protein were selected for optimization. a) The amide group of Asn37 is flipped 180° – improving its contact with backbone atoms of Arg128. b) Flipping the amide of Gln12 improves its interaction with Lys9. c) Protonating the ligand’s amine improves its interactions with both Asp32 and Asp228.