Recent advances in the application of kinetic isotope effects to enzyme-catalyzed reactions have provided reliable information for enzymatic transition state structures, A method is presented for quantifying the similarity of substrates and inhibitors with their enzyme-stabilized transition states. On the basis of transition-state stabilization theory for enzymatic reactions, molecules most similar to the transition state structure bind with greatest affinity, Molecular similarity measures are applied to compare substrates, competitive inhibitors, and transition state inhibitors with the transition state structures stabilized by the enzymes AMP deaminase, adenosine deaminase, and AMP nucleosidase. (R)- and (S)-Coformycin 5’-phosphate are inhibitors for AMP deaminase, with the R-species superior to its enantiomer.