The biosynthesis of l-threonine and l-isoleucine in bacteria and in fungi requires the action of 2 amino acid kinases: aspartate kinase and homoserine kinase. Although these kinases bind similar substrates and catalyze analogous phosphotransfer chemistry, they do not show high amino acid sequence homology. We show that despite this difference, both kinases form a ternary complex consisting of enzyme- adenosine triphosphate- amino acid to accomplish phosphoryl transfer. With this similarity in mind, we set out to identify molecules that could lead to inhibitors with activity against both kinases in the pathway. We synthesized a series of aspartic acid-adenosine bisubstrate compounds separated by a variable length alkyl linker that we hypothesized could bind to these kinases. These bisubstrate compounds only inhibited the bacterial aspartate kinase. These results reveal unexpected differences in small molecule interactions among these functionally similar enzymes.