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Cyclic nucleotide-gated channels (CNGC) open in response to the binding of 3′,5′-cyclic nucleotides. Members of the CNGC family vary as much as 100-fold in their ability to respond to cAMP and cGMP. Molecular models of the nucleotide binding domains of the bovine retina and catfish and rat olfactory CNGCs were built from the crystal structure of cAMP bound to catabolite gene activator protein (CAP) with AMMP, a program for molecular mechanics and dynamics. The nucleotide conformation can be predicted from the number of strong and weak interactions between the purine ring and the binding site. The amino acids predicted to be important for determining the nucleotide affinity and specificity are residues 61, 83 (mediated through a water molecule), 119 and 127 (CAP sequence numbers) which interact with the purine ring. These residues also dictate the conformation of the ligand in the binding pocket cGMP is preferentially bound in the  syn  conformation in bovine retina, bovine olfactory and rat olfactory CNGCs due to Thr83, while either conformation can bind in catfish olfactory CNGC. cAMP is predicted to bind either in  syn  or  anti  conformation, depending on the interaction with residue 119: the  anti  conformation is preferentially bound in olfactory CNGCs.

Predicted ligand interactions for 3′,5′-cyclic nucleotide-gated channel binding sites: comparison of retina and olfactory binding site models