Question: Consider two ligands, A and B , binding to the same receptor at the same binding site. The ligands are of similar size and shape
Consider two ligands, A and B binding to the same receptor at the same binding site. The ligands are of similar size and shape and have similar hydrophobicities. Both of them are interacting in the same way with the binding pocket, ie the forces established with the receptor are very similar in type and strength. However, for ligand A the energy of the bioactive binding conformation is significantly larger than the conformation in solution, while for ligand B the binding conformation and the conformation in solution is essentially the same. For which of the ligands do you expect a higher binding affinity ie a lower free energy of binding
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