3D QSAR studies were performed on a library of 120 GAPDH inhibitors, including a series of coumarins, flavonoids, and nucleosides. The VolSurf method was successfully used to calculate surface descriptors for protein-ligand affinity and binding site of the enzyme. PCA/PLS analyses have permitted the evaluation of the structural features crucial for potency, selectivity, and favorable pharmacokinetic properties, and are important for the design of new ligands.