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Plexxikon is an American drug-discovery company based in Berkeley, California, that was co-founded in 2001 by Joseph Schlessinger of Yale University with Sung-Hou Kim of the University of California, Berkeley.

It uses a proprietary structural biology-based platform called Scaffold-Based Drug Discovery to build a pipeline of products in multiple therapeutic areas. This discovery process integrates multiple state-of-the-art technologies, including structural screening as one key component that it hopes will give a significant competitive advantage over other approaches. To date, the company has discovered several clinical and preclinical stage compounds. One of the most advanced drugs under development is an inhibitor of an activated (mutated) form of the B-Raf kinase. A V600E mutant of the B-Raf kinase is found in approximately 70% of malignant melanomas, a large percentage of colorectal and thyroid cancers and many other tumor types. PLX4032 selectively inhibits this form of the kinase, and is currently in clinical trials. Plexxikon has entered into a partnership with Roche Pharmaceuticals to develop PLX4032 as a targeted anti-cancer therapeutic, which has shown particular promise for treating melanoma. Plexxikon is also collaborating with Wyeth Pharmaceuticals on several products (centered on PPAR inhibitors) for use in type II diabetes and other metabolic disorders. The most advanced of these agents is PLX204, which is currently in Phase 2 clinical trials for type II diabetes.

In April 2011, Plexxikon was acquired by the Japanese pharmaceutical company Daiichi Sankyo for $805 million and an additional $130 m in potential milestone payments.