One hundred and five nucleobase analogues were screened as inhibitors of dihydrouracil dehydrogenase (DHUDase, EC 1.3.1.2) from mouse liver. 5-Benzyloxybenzyluracil, 1-deazauracil (2,6-pyridinediol), 3-deazauracil (2,4-pyridinediol), 5-benzyluracil, 5-nitrobarbituric acid and 5,6-dioxyuracil (alloxan) were identified as potent inhibitors of this activity, with apparent Ki values of 0.2, 0.5, 2.1, 3.4, 3.8 and 6.6 microM respectively. Both 5-benzyloxybenzyluracil and 1-deazauracil were also potent inhibitors of DHUDase from human livers. These findings along with an extensive review of literature allowed the formulation of a structure-activity relationship. The binding to DHUDase required intact C2 and C4 oxo groups. Replacement of N1 or N3 by an endocyclic carbon enhanced binding. In contrast, replacement of C5 or C6 by an endocyclic nitrogen abolished binding. Addition of a charged group to C5 and/or C6, and of a hydrophobic group to C5 but not C6 improved the binding.