Syntheses are described of p1-(adenosine-5')-p3-(glucose-6) triphosphate (Ap3 glucose), Ap4 glucose, and p1-(adenosine-5')-P3-(thymidine-5') triphosphate (Ap3T). The compounds were not substrates of any of the enzymes used in the present studies. Ap3 glucose and Ap4 glucose were inhibitors of yeast hexokinase (HK) and the rat isozymes HK I-III; in general, they had less affinity for the enzymes than the substrates ATP and glucose. Inhibition constants (Ki values) of Ap3T with rat mitochondrial thymidine kinase (M-TK) and rat cytoplasmic TK (C-TK) were determined for variable thymidine (TdR) with a constant saturating level of ATP and for variable ATP with constant saturating TdR. Ap3T was a potent and selective inhibitor of M-TK [KM (TdR)/Ki = 1.6, KM (ATP)/Ki = 38 with variable ATP; KM (TdR) Ki = 0.06, KM (ATP)/Ki = 1.4 with variable TdR] relative to C-TK [KM (TdR)/Ki = 0.006, KM (ATP)/Ki = 0.7 with variable ATP; KM (TdR)/Ki = 0.001, KM (ATP)/Ki = 0.12 with variable TdR]. Inhibition of M-TK and C-TK by Ap3T differed qualitatively and quantitatively from inhibition under the same conditions by the metabolic feedback inhibitor TdR 5'-triphosphate.