SitesBase: a database for structure-based protein-ligand binding site comparisons

Abstract

There are many components which govern the function of a protein within a cell. Here, we focus on the molecular recognition of small molecules and the prediction of common recognition by similarity between protein-ligand binding sites. SitesBase is an easily accessible database which is simple to use and holds information about structural similarities between known ligand binding sites found in the Protein Data Bank. These similarities are presented to the wider community enabling full analysis of molecular recognition and potentially protein structure-function relationships. SitesBase is accessible at http://www.bioinformatics.leeds.ac.uk/sb.

Figure 1

Collection of screen shots from SitesBase showing results of a search (A) with query 2npx (NADH peroxidase). This binding site has two SCOP classes attributed. The primary SCOP class is c.3.1.5 the NAD/FAD reductase family with an NAD/FAD binding domain fold. The SCOP and PDB codes are linked to the SCOP and PDBsum databases, respectively. Four of the listed hits are family relatives of the query (pink), ten are superfamily relatives (yellow) and ten are fold relatives (blue). There are also two high scoring hits which are yet to be classified in the SCOP database (purple). Note: in this illustration some high scoring hits have been removed in order to show more distantly related proteins. (B) Gives a multiple alignment of two selected hits with the same SCOP class (i.e. with different folds) as the query and clearly shows the sequence conserved GXGXXG dinucleotide binding motifs. (C) Illustrates these three protein sites (2npx, blue; 1guy, yellow; and 1ddo, green) superimposed in 3D.