Among the regulation mechanisms of cellular function, allosteric regulation is the most direct, rapid and
efficient. Due to the wider receptor selectivity and lower target-based toxicity, compared with orthosteric
ligands, allosteric modulators are expected to play a larger role in pharmaceutical research and
development. However, current difficulties, such as a low affinity and unknown structural features of
potential allosteric small-molecules, usually obstruct the discovery of allosteric modulators. In this study,
we compared known allosteric modulators with various compounds from different databases to unveil
the structural and qualitative characteristics of allosteric modulators. The results show that allosteric
modulators generally contain more hydrophobic scaffolds and have a higher structural rigidity, i.e., less
rotatable bonds and more rings. Based on this analysis, an empirical rule was defined to determine the
structural requirements for an allosteric modulator. It was found that a large proportion of allosteric
modulators (80%) can be successfully retrieved by this “allosteric-like” filter, which shows good discriminatory
power in identifying allosteric modulators. Therefore, the study provides deeper insight into the
chemical properties of allosteric modulators and has a good potential for the design or optimization of
allosteric compounds.