Common Chemistry
This database contains the CAS Registry Number, chemical names (both formal and common), molecular formulas, and structures or sequences for 7800 chemicals of widespread general public interest. These substances are of global commercial use or importance and have been cited 1,000 or more times in the CAS databases.
http://www.commonchemistry.org

CrossFire Beilstein
The CrossFire Beilstein database is the world's largest compilation of chemical facts. As the cornerstone database to organic chemistry, the CrossFire Beilstein database is essential for generating new leads, planning synthetic routes (including starting materials and intermediates), determining bioactivity and physical properties and ascertaining the environmental fates of compounds. With the second update in 2006, the 10 millionth reactions in CrossFire Beilstein have been released. Passing this important milestone emphasizes the enduring and increasing value of the database as the essential first step in chemical discovery.
http://www.beilstein.com

eMolecules
eMolecules is the world's free open-access chemistry search engine. eMolecules' mission is to discover, curate and index all of the public chemical information in the world, and make it available to the public. eMolecules distinguishes itself by extremely fast searches, an appealing presentation of results, and high-quality chemical drawings.
http://www.emolecules.com

HDAC Inhibitors Database
A small database contains information about molecules or drugs that block HDACs. Histone deacetylase inhibitors are emerging as a new class of potential anticancer agents.
http://www.hdacis.com

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

Sigma Aldrich
Online version of the well-known Sigma-Aldrich chemical catalog. Includes CAS registry numbers and a variety of physical and chemical properties of chemicals manufactured by Sigma-Aldrich. Free registration is required to access additional features such as MSDS and NMR and IR spectra.
http://www.sigmaaldrich.com

SpresiWeb
SpresiWeb a new dimension of integrating scientific databases. The search can be carried out for molecules, reactions and references. SpresiWeb combines a large chemical database with lots of links to additional information sources. SpresiWeb contains over 5,0 million compounds, 3,7 million reactions, 600.000 references and 164.000 patents.
http://www.spresi.com

The PubChem Project
PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem includes substance information, compound structures, and bioactivity data in three primary databases, PCSubstance, PCCompound, and PCBioAssay, respectively. PCSubstance contains more than 10 million records. PCCompound contains more than 5 million unique structures. PCBioAssay contains more than 200 bioassays. Each bioassay contains a various number of data points.
http://pubchem.ncbi.nlm.nih.gov

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/