MSD Ligand Chemistry
This is a database of the small molecules, ligands and monomers which may appear in molecules that are classified in the larger Protein Data Bank database. This resource forms a part of the Macromolecular Structure Database at the European Bioinformatics Institute. The database is searchable by atom energy types, molecular classification, via a JME structure editor, and other properties.
http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl

TOXNET
Chemical information (nomenclature, identification, structures), references to literature on biochemical, physiological, pharmacological, and toxicological effects of drugs and other chemicals, developmental and reproductive toxicology, and environmental teratology.
http://toxnet.nlm.nih.gov/

WebReactions
WebReactions is a unique reaction search system offering direct retrieval of reaction precedents through the internet. The system is easy to learn and use and is extremely fast in locating matches for reaction queries from the database.
http://www.webreactions.net/

ZINC - a Free Database for Virtual Screening
ZINC a free database of over 2.7 million commercially-available compounds for virtual screening in ready-to-dock, 3D format. ZINC contains multiple representations of molecules, since molecules that are not in the biologically relevant protonation state, tautomeric, stereo- or regio-isomeric form in the virtual library often fail to dock and score well.
http://blaster.docking.org/zinc/