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. Author manuscript; available in PMC: 2017 Apr 5.
Published in final edited form as: J Comput Chem. 2015 Dec 15;37(9):836–847. doi: 10.1002/jcc.24274

Figure 3.

Figure 3

The binding mode of the compound 135 from the in-house crystal structure (pdb code: 3UIC). The nitrogen atom at the 3 position of the benzimidazole ring forms key hydrogen bonds with the NADH nicotinamide ribose (truncated for clarity) and Tyr156. The 5 and 6 positions of the benzimidazole ring fall into a lipophilic cavity, formed by the Ile91, Ala92, Phe93, Ala94, Pro95, and Ala197 side chains. The para-chloride might form a weak halogen bond with the carbonyl backbone of Pro154, as discussed in the “Further Validation and Medicinal Chemistry Perspective” section. The meta-chloride is in a hydrophobic pocket formed by the Leu99 and Ile200 side chains.