D546 Nucleic Acids Research, 2012, Vol. 40, Database issue Figure 4. Color scheme for the superposed binding sites. Pink and cyan colored sticks, respectively, show the binding site of query and hit. The red sticks show a ligand of the query site (i.e. user-speciﬁed on the submit form). Figure 5. Superposition of a query site to a hit. (A) Superposition of a BIR-binding site of 1R1H (pink and red) a TI1-binding site of 1QF1 (cyan and green). Orange shows the conserved catalytic residues for both sites. (B) Superposition of a putative site of 3K0B (pink) and a SAH-binding site of 2ORE (cyan and green). and the utility of assigning functions to proteins with unknown function. In drug discovery, it is important to design chemical leads that show high speciﬁcity only to their target proteins, thereby avoiding unexpected side effects. An ap- propriate approach is to retrieve a set of related binding sites from non-homologous proteins. Then one can analyze the variation of ligands bound to them. SearchK is useful for such a task because it reports similar binding sites not only between structures within a speciﬁc family, but also among whole PDB structures. Neprilysin is involved in the regulation of amyloid b-peptide levels (27) whose structure (PDB ID: 1R1H) was determined in a complex with an inhibitor (HET code: BIR). Using the inhibitor binding site as a query, we searched for simi- lar sites using SearchK and found eight similar sites: ﬁve sites are from proteins whose CATH code is identical to that of the query (i.e. 3.40.390.10), whereas three other sites are from proteins whose fold topology dif- fers from that of the query (i.e. 3.10.170.10). Figure 5A shows superposition of an example of an analogous pair: an inhibitor (HET code: BIR) binding site from neprilysin (PDB ID: 1R1H) to an inhibitor (HET code: TI1) binding site from thermolysin (PDB ID: 1QF1). Although the global folds of the two proteins differ, their binding sites and conformations of the bound inhibi- tors were mutually overlapped. Furthermore, the three inhibitor-interacting residues (Glu-143, His-231 and Arg-203 of thermolysin; Glu-584, His-711 and Arg-717 of neprilysin) were well superimposed, which is regarded as representing conserved catalytic residues (28). These results support the general application of our database