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Replacement of water from the uncomplexed binding pocket is assumed to be entropically favorable.
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The binding pocket is indicated as an exclusion surface.
The positively charged binding pocket is not big enough for ANP binding.
Moreover, a new binding pocket is also explored.
Docked ligand conformation, is presented with sticks and the binding pocket is shown as surface.
The negatively charged binding pocket is not big enough for ATP (Fig. 2B).
Specifically, the inhibitor binding pocket is located between the central β-sheet and the αHD of HadA.
The volume of the binding pocket is 495 Å.
Four binding pockets are marked as A, B, C, and D. Another binding pocket is marked as LBD.
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.
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