The activity of dihydroorotate dehydrogenase (DHO-dehase) has been reported to decrease both in vitro and in vivo in hepatocellular carcinomas. DHO-dehase, the fourth enzyme of the de novo pyrimidine biosynthetic pathway, is a mitochondrial enzyme which is both a potential rate-limiting reaction in the de novo pyrimidine biosynthetic pathway and a potential therapeutic target for tumor inhibitors. This paper reports results on a series of pyrimidine analogs of dihydroorotate (DHO) and orotic acid (OA) as inhibitors of DHO-dehase. The enzyme test results established that the intact amide and imide groups of the pyrimidine ring and the 6-carboxylic acid are required for significant enzyme inhibition. The testing of several functional groups similar in characteristics to that of the carboxylic acid, such as sulfonamide, tetrazole and phosphate, indicated that the carboxylic acid group is preferred by the enzyme. Using various 5-substituted OA and DHO derivatives, it was shown that there is a steric limitation of a methyl group at this position. The compound D,L-5-trans-methyl DHO (7) (Ki of 45 microM) was both an inhibitor and a weak substrate for the enzyme, demonstrating that mechanism-based enzyme inhibitors should be effective. The testing results further suggest that a negatively charged enzyme substituent may be present near the 5-position of the pyrimidine ring and that there may be an enzyme-substrate metal coordination site near the N-1 and carboxylic acid positions of the pyrimidine ring. The combined testing results were then used to define both conformational and steric substrate enzyme binding requirements from which a model was proposed for the binding of DHO and OA to the DHO-dehase active site.