Drugbank is a database of compounds that have a pharmaceutical effect. This would probably be a good starting point (it has info on around 4000 compounds)

ChEBI contains 'chemicals of biological interest'. It's a larger database but does have information about patents (in the XRefs, e.g. see oxytocin).

Importantly, you may want to keep in mind side effects. See SIDER: http://sideeffects.embl.de/ Although this database does not link drug to gene/protein, it could be where you go next for important information.

Another source could be the FDA orange book.

Update 2011-05-29:

• Check also DBPedia for drugs - here an example SPARQL query, which will return all drugs within DBPedia.
• ChEMBL has its own drugstore section and allows downloading this information via the web interface. This should also provide a pretty good start.

Kegg Drug might have something useful as well: http://www.kegg.jp/kegg/drug/

Approved oncology drug set http://dtp.nci.nih.gov/branches/dscb/oncology_drugset_explanation.html

Minor comment - depending on the question you want to answer, it could be worth paying attention to differences between drugs and co-drugs (the latter increase susceptibility of target organism to another drug and are not used on their own). From my experience certain databases treat co-drugs as regular drugs, which might lead to interesting mistakes.

where can i get database which shows patent on the same drug granted/rejected in one jurisdiction say US but rejected in anr say EU. pl mail me at charupatent@gmail.com