Article ID: 167 - Last Modified: May 4, 2011
I did a redocking calculation using Glide with a relatively large ligand. One part of it fits perfectly compared to the reference, the other part does not. Why did Glide fail to predict a fully correct binding mode?
If the ligand is larger than the binding pocket, it could be that a part of it is pointing out of the cavity. The orientation of the part outside the binding site might therefore be caused by crystal packing effects in the X-ray structure. Hence the conformation could be completely different in a solvated protein environment and Glide possibly did not predict a wrong binding mode. To see whether crystal packing might be responsible, display the PDB structure in the Workspace and choose Workspace → Crystal Mates. Crystallographically related copies of the protein are displayed, and you can examine the ligand's interaction with these copies.
Keywords: Glide, binding mode, ligand size
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