Figure 2.

Chemical space consisting of ligands (derived from sc-PDB) and ordinary molecules (randomly selected from ACD-SC), defined by the first two factors derived from 70 descriptors. The figure illustrates that ligands (in red) occupy the relatively upper part of the space, while ordinary molecules (in blue) occupy the relatively lower part, which means that it is the second factor that discriminates ligands from ordinary molecules. From the loadings of the second factor, it can be deduced that polar molecular surface area, H-bond donor counts, H-bond acceptor counts and partition coefficient are likely responsible for the differences between ligands and ordinary molecules, which is supported by the different average values of the four kinds of parameters for ligands and ordinary molecules (Table 2).