Figure 3.

Chemical space consisting of sc-PDB-derived ligands, defined by the first two factors derived from 70 descriptors. The figure illustrates that super ligands (shared by 3+ folds; in blue), especially those that are shared by 10+ folds (in red), concentrate in the relatively upper part of the space (the area of the circle is directly proportional to the number of folds that bind the ligand), which suggests that polar molecular surface area, H-bond donor counts, H-bond acceptor counts and partition coefficient are responsible for the strong protein-binding potential of the super ligands, which is supported by the different average values of the four kinds of parameters for ligands with different protein-binding potentials (Table 2).