The information of the binding pocket of a receptor for its ligand is very important for drug design, particularly for conducting mutagenesis studies [14] . In the literatures, the binding pocket of a protein receptor to a ligand is usually defined by those residues that have at least one heavy atom (i.e., an atom other than hydrogen) with a distance #5 Å from a heavy atom of the ligand. Such a criterion was originally used to define the binding pocket of ATP in the Cdk5-Nck5a* complex [45] that has later proved quite useful in identifying functional domains and stimulating the relevant truncation experiments [46] . The similar approach has also been used to define the binding pockets of many other receptor-ligand interactions important for drug design [15, 17, 47, 48] . In this study, we also used the same criterion [45] to define the binding pockets of proteins 1k7l and 1k74 for the ligand GW409544. A close-up view for the protein-ligand interaction at the binding pocket thus defined is shown in Fig. 1 , where panel A is for the interaction between PPARa (1k71) and GW409544, while panel B for the interaction between PPARc (1k74) and GW409544.