A chemogenomic analysis of the transmembrane binding cavity of human G‐protein‐coupled receptors

The amino acid sequences of 369 human nonolfactory G‐protein‐coupled receptors (GPCRs) have been aligned at the seven transmembrane domain (TM) and used to extract the nature of 30 critical residues supposed—from the X‐ray structure of bovine rhodopsin bound to retinal—to line the TM binding cavity of ground‐state receptors. Interestingly, the clustering of human GPCRs from these 30 residues mirrors the recently described phylogenetic tree of full‐sequence human GPCRs (Fredriksson et al., Mol Pharmacol 2003;63:1256–1272 ) with few exceptions. A TM cavity could be found for all investigated GPCRs with physicochemical properties matching that of their cognate ligands. The current approach allows a very fast comparison of most human GPCRs from the focused perspective of the predicted TM cavity and permits to easily detect key residues that drive ligand selectivity or promiscuity. Proteins 2006. © 2005 Wiley‐Liss, Inc.