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The potential at the binding pocket was reduced with acetylation of only Lys23, suggesting that acetylation specifically at this site could affect ADP binding affinity.
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Then, a binding pocket was generated.
A 10 Å sphere around the centre of the binding pocket was defined as binding pocket for the docking runs.
Furthermore, the physical binding environment of the binding pocket was evaluated using SiteMap [43, 44].
In addition, H334 residue that is structurally nearby the binding pocket was also examined.
First, the binding pocket was analyzed in the presence of the co-binding peptide using abacavir as the reference ligand.
The binding pocket was identified using Q-SiteFinder [46].
By using the built-in pocket finder, the binding pocket was identified.
The similarity in inhibition shown by cIDPR, 3 and 4 suggests that the ability of these analogues to enter the binding pocket is surprisingly not reduced by the pyrophosphate → 1,2,3-triazole substitution.
All the LCOs, except for p-FTAA-Ph, displayed considerably reduced Stokes shifts for Aβ1 42 fibrils compared to ethyl acetate, indicating that the Aβ1 42 binding pocket is substantially more nonpolar than ethyl acetate (ε=6.08).
Moreover, a new binding pocket is also explored.
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