We constructed a three-dimensional model of the amino-terminal extracellular domain of three major types of nicotinic acetylcholine receptor, (␣7)5, (␣4)2(2)3, and (␣1)21␥␦, on the basis of the recent x-ray structure determination of the molluscan acetylcholine-binding protein. Comparative analysis of the three models reveals that the agonist-binding pocket is much more conserved than the overall structure. Differences exist, however, in the side chains of several residues. In particular, a phenylalanine residue, present in 2 but not in ␣7, is proposed to contribute to the high affinity for agonists in receptors containing the 2 subunit. The semiautomatic docking of agonists in the ligand-binding pocket of (␣7)5 led to positions consistent with labeling and mutagenesis experiments. Accordingly, the quaternary ammonium head group of nicotine makes a -cation interaction with W148 (␣7 numbering), whereas the pyridine ring is close to both the cysteine pair 189 -190 and the complementary component of the binding site. The intrinsic affinities inferred from docking give a rank order epibatidine > nicotine > acetylcholine, in agreement with experimental values. Finally, our models offer a structural basis for potentiation by external Ca 2؉ .