Odorant-binding pocket

Kuang D, Yao Y, Wang M, Pattabiramann N, Kotra L, et al. 2003. Molecular similarities in the ligand binding pockets of an odorant receptor and the metabotropic glutamate receptors. J Biol Chem 278(43) 42551-42559. 

FIGURE 5.6 A transmembrane olfactory receptor. The sections shown as cylinders reside in the cell wall. These are the seven transmembrane hydrophobic domains. Loops on top (and the N-terminus) are outside the cell, those at the bottom (and the C-terminus) are inside the cell. For clarity, the cylinders are spread out but, in the cell, they are bundled into a ligand-binding pocket. The residues shown as black dots are especially diverse among known odorant receptors. This diversity enables the receptor family to interact with many different odor molecules. (From Buck, 1996.)... 

Structure-activity relationships have been largely employed for molecular design these correlations depend on the molecular representation and the activity landscape. The molecular representation depends only on the small molecule, whereas the activity landscape provides information on the ligand-receptor complex, for example, how permissive the binding pocket is. To exemplify the molecular similarity approach, a set of odorants (compared to benzaldehyde) will be presented. 

Figure 14.9 Schematic 2D representation of the OR seven TM segments. The 17 residues constituting proposed areas for odorant binding are marked with an asterisk. Area 1 is a conserved pocket, area 11 coincides with ligand-binding pockets in other GPCRs and area 111 is a variable pocket unique to ORs...

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