The regulatory G-proteins of adenylyl cyclase (AC), G(i) and G(s), are not only activated by GTP and the stable GTP analogs, guanosine 5'-[gamma-thio]triphosphate (GTPgammaS) and guanosine 5'-[beta,gamma-imido]triphosphate (GppNHp), but also by hypoxanthine, xanthine, uracil and cytidine nucleotides. The latter nucleotides were previously used to analyze distinct active G-protein states. Surprisingly, recent studies have shown that inosine 5'-[gamma-thio]triphosphate and uridine 5'-[gamma-thio]triphosphate can also inhibit AC directly. Therefore, we systematically compared the interactions of nucleoside 5'-triphosphates (NTPs), nucleoside 5'-[gamma-thio]triphosphates (NTPgammaSs) and nucleoside 5'-[beta,gamma-imido]triphosphates (NppNHps) with G(i), G(s) and AC. NTPgammaSs exhibited up to 26,000-fold higher affinity for G-proteins than NTPs and NppNHps. NTPgammaSs were up to 150-fold more potent direct AC inhibitors than NTPs and NppNHps. G-proteins exhibited striking preference for guanine nucleotides compared to other purine and pyrimidine nucleotides, whereas base-selectivity of various ACs, particularly the purified catalytic subunits C1.C2, was rather poor. GTP, GTPgammaS and GppNHp exhibited much higher selectivity for G-proteins relative to AC than all other purine and pyrimidine nucleotides. We have energetically characterized the interactions of purine and pyrimidine nucleotides with AC in silico, constructing pharmacophore models that correlate well with experimental affinities and have elucidated specific amino acid residues with greatest influence on nucleotide binding. Collectively, both G-proteins and ACs bind purine and pyrimidine nucleotides, with G-proteins showing much higher base-selectivity than AC. Thus, direct inhibitory effects of nucleotides on AC should be understood and considered when probing distinct active G-protein states with non-guanine nucleotides.