This chapter focuses on the key databases integral to small molecule structure-based drug design. It begins with Comprehensive Libraries, such as PubChem, ChEMBL, and ChEBI, which provide extensive collections of chemical compounds and their associated properties. These databases are invaluable for chemoinformatics research and serve as primary resources for discovering potential drug candidates. The section also highlights Molecular Crystal Structure Databases, including the Cambridge Structural Database (CSD) and the Crystallography Open Database (COD), which store detailed crystallographic data on small molecules and their solid-state structures. This information is crucial for understanding molecular interactions and optimizing drug formulations. Natural Product Databases, such as Coconut, are discussed as vital tools for exploring bioactive compounds derived from natural sources, which are often a rich source of novel therapeutic agents. Finally, the chapter examines Virtual Screening Molecular Libraries, including ZINC, Generated Databases (GDB), and DrugSpaceX. These resources support high-throughput screening by offering vast collections of small molecules for computational drug discovery, aiding in the identification of potential hits for further experimental validation. Collectively, these databases play a pivotal role in accelerating the drug discovery process by providing accessible, structured data for virtual screening, chemoinformatics, and molecular modeling.