Displacing a Tightly Bound Water

The conserved SI water (Fig. 7.9) is one of the best defined, as judged by the low B-values (fhermal disorder parameters) observed with benzamide- or guanidine-type inhibitors. It was long regarded as simply part of the protein until Katz et al. 

Katz et al. [52] report binding constants for Ila APC-8696 of Ki=130nM for trypsin and Ki=320nM for thrombin. The compound is thus trypsin selective by 

It might have been expected that the chlorine would interact favorably with the alanine 190 side chain in thrombin and less well with the serine 190 -OH, giving selectivity for thrombin, but the inhibition constants reveal just the opposite. Trypsin is favored by AAG = 3 kcal moU, although the conserved water is indeed removed from both enzymes and the general binding mode is the same. 

The conserved water donates hydrogen bonds to the carbonyl oxygen of residue 227 and to the rc-electrons of Tyr228. Both of these interactions are lost when the water is displaced, but the energy change will be similar for both enzymes. 

The most important difference seems to be that in thrombin there is no fourth hydrogen bond partner for the amidino group, and this hydrogen bond is totally lost. Further, the chlorine is not quite large enough to fill the pocket left by the water, so a hole is generated, which as we have already seen, costs energy. 

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