We have previously shown that phosphatidic acid (PA) is a specific activator of some isoforms of type 4 cyclic nucleotide phosphodiesterases (PDE 4) and that accumulation of endogenous PA can, in this way, influence the cAMP signaling pathway in different cell types. Enzyme activation depends on direct binding of the effector to specific sites carried by the enzyme. To identify the binding domain, photoactivatable phosphatidic acid analogues 1-azidoPA (12) and 2-azidoPA (7 and 15), potentially suitable for covalent labeling of PDE4, have been synthesized. The ability of phospholipases A(2) and D to hydrolyze unnatural phospholipids has been considered in this paper. The effect of 1-azidoPA (12) and 2-azidoPA (7 and 15) on the activity of a recombinant PA-sensitive isoform PDE4D3 was evaluated. The three compounds were able to activate the enzyme with different efficiencies. A tritiated analogue of 15 was synthesized and used in PDE4D3 labeling experiments, which showed that this PA analogue was specifically and covalently linked to the enzyme after UV irradiation. Photoactivatable analogues thus appear as suitable tools for the characterization of PA binding sites.