Variations in binding conformations of small molecules to proteins: A study using Protein Data Bank

Abstract

There are several databases incorporating vast data available on the protein structures and small molecules. They are useful in many fields of chemistry and biology for understanding the chemical and biological significance of the entries in the databases. Since the biochemical as well as pharmaceutical sciences are the interface for both chemistry and biology,

understanding the effect of chemicals on biological molecules is an important issue. While vast data is being generated on this front, these are not compiled or arranged in a proper way for user-friendly retrieval. The biological activity of a molecule is directly related to the way the molecule is bound to its target protein. There are many examples in the Protein Data Bank where small molecules are bound to proteins in different conformations. Some features of ligand conformational flexibility are presented in this paper.