Structural chemogenomics databases allow the integration and exploration of heterogeneous genomic, structural, chemical, and pharmacological data in order to extract useful information that is applicable for the discovery of new protein targets and biologically active molecules. Integrated databases provide proteome-wide, target family-specific, or mechanism-specific information depending on the way that different types of protein-ligand interaction data can be explored. The use of common ontologies allows efficient protein and ligand data curation and mapping that enable the integration of bioactivity data mining, ligand and protein similarity assessment, and structural protein-ligand interaction analyses for the identification of new protein-drug combinations.