Although the majority of effective therapeutics are small molecules, there is relatively little readily accessible public domain data mapping drugs to their molecular targets. When one considers clinical trial stage, or discovery stage data, the situation deteriorates further. However, this type of data is essential for Chemical Biology experiments, and is crucial for informed target selection in drug discovery. To address this issue, we have built a series of large scale databases, known as ChEMBL, that map small molecule structures to their target genes and also their functional effects. This data also captures a large ammount of human and model organism pharmacological data, systems often used in pre-clinical validation and safety pharmacology testing. A variety of applications of these databases in the area of target prioritisation, lead discovery, lead optimisation and drug repurposing will be described.