Structure-based drug design tries to mutually map pharmacological space populated by putative target proteins onto chemical space comprising possible small molecule drug candidates. Both spaces are connected where proteins and ligands recognize each other: in the binding pockets. Therefore it is highly relevant to study the properties of the space composed by binding cavities. Analysis of this space helps to predict possible biochemical functions of novel proteins independent from sequence- or fold homologies. It can be used to cluster proteins of a particular family with respect to selectivity determining features. Furthermore, it can be exploited in structure-based design to propose novel leads as a starting point for a design project.