Nicotinic acid adenine dinucleotide phosphate (NAADP) mobilizes Ca2+ through a mechanism totally independent of cyclic ADP-ribose or inositol trisphosphate. The structural determinants important for its Ca2+ release activity were investigated using a series of analogs. It is shown that changing the 3-carboxyl group of the nicotinic acid (NA) moiety in NAADP to either an uncharged carbinol or from the 3-position to the 4-position of the pyridine ring totally eliminates the Ca2+ release activity. Conversion of the 3-carboxyl to other negatively charged groups, either 3-sulfonate, 3-acetate, or 3-quinoline carboxylate, retains the Ca2+ release activity, although their half-maximal effective concentrations (EC50) are 100-200-fold higher. Changing the 6-amino group of the adenine to a hydroxyl group results in more than a 1000-fold decrease in the Ca2+ release activity. Conversion of the 2'-phosphate to 2',3'-cyclic phosphate or 3'-phosphate likewise increases the EC50 by about 5- and 20-fold, respectively. Similar to NAADP, all of the active analogs can also desensitize the Ca2+ release mechanism at subthreshold concentrations, suggesting that this novel property is intrinsic to the release mechanism. The series of analogs used was produced by using ADP-ribosyl cyclase to catalyze the exchange of the nicotinamide group of various analogs of NADP with various analogs of NA. An important determinant in NA that is crucial to the base exchange reaction was shown to be the 2-position of the pyridine ring. Neither pyridine-2-carboxylate nor 2-methyl-NA support the exchange reaction. The negative charge and the position of the 3-carboxyl group are nonessential since both pyridine-3-carbinol and pyridine-4-carboxylate support the base exchange reaction. In addition to the information on the structure-activity relationships of NAADP and NA, this study also demonstrates the utility of the base exchange reaction as a general approach for synthesizing NAADP analogs.