Biomolecule Binding Database
The BindingDB is a public, web-accessible database of measured binding affinities for biomolecules, genetically or chemically modified biomolecules, and synthetic compounds.
http://www.bindingdb.org/bind/index.jsp

ChEBI
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on "small" chemical substances. ChEBI draws its information from two main sources: Integrated Relational Enzyme Database of the EBI and the Kyoto Encyclopedia of Genes and Genomes.
http://www.ebi.ac.uk/chebi/

ChemACX
ChemACX is a comprehensive online catalog containing current product information from 405 leading chemical supplier catalogs such as Sigma Aldrich, Fisher Scientific, Acros, Alfa Aesar, Lancaster, Novabiochem and TCI America. ChemACX provides rapid ordering information for over 352,300 unique chemical compounds, over 733,100 products, and is updated bi-annually.
http://chemacx.cambridgesoft.com/

Chemazone - Organic Chemicals for R&D
Are you looking for organic chemicals for research and development and cannot find them commercially available anywhere? The Chemazone website contains more than 2,000,000 readily available synthetic organic compounds.
http://www.chemazone.com

ChemBank
Chembank is a freely available collection of data about small molecules and resources for studying their properties, especially relating chemistry to biology, and a suite of informatics tools and databases aimed at promoting the development and use of chemical genetics by scientists worldwide. Chembank currently has a database of about 2000 compounds, with SMILES strings, chemical structures and biological activity. Soon other files will be downloadable.
http://chembank.broad.harvard.edu

ChemExper Chemical Directory
The ChemExper Chemical Directory displays information about chemicals (physical and chemical characteristics, structure, MSDS and more.) on the Internet in order to create a world-wide database. It is free to consult and easily accessible over the Internet on any computer using a web browser. The ChemExper Chemical Directory contains for now over 200,000 different chemicals, 10,000 MSDS and over 10,000 IR spectra.
http://www.chemexper.com

Chemical Structure Lookup Service
Look up whether a structure occurs in any of tens of different databases, both public and commercial. Currently loaded pointers to: over 39 million entries from more than 80 databases, representing more than 27 million unique chemical structures.
http://cactus.nci.nih.gov/lookup/

Chemicals for R&D
The R&D Chemicals is a free service that allows to find a chemical by its molecular formula, IUPAC name, smiles, common name, CAS number, catalog number, substructure or physical characteristics as well as chemical suppliers.
Examples of a textual query: Extrasynthese, Jrd Fluorochemicals, Frinton Laboratories.
http://www.rdchemicals.com

ChemIDplus
ChemIDplus provides access to structure and nomenclature information for the identification of chemical substances cited in NLM (National Library of Medicine) databases. The database contains over 380,000 chemical records, of which over 263,000 include chemical structures. ChemIDplus Lite is available for Name and RN searching without the need for plugins or applets.
http://chem.sis.nlm.nih.gov/chemidplus

Chemsink
ChemSink is a chemical reaction database. It is a place for anyone interested in chemical synthesis to come and discuss their successes and failures with specific chemical reactions. The chemsink database is free to download, alter, and use.
http://www.chemsink.com/

ChemSpider - Database of Chemical Structures
ChemSpider is a chemistry search engine. It has been built with the intention of aggregating and indexing chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge. ChemSpider is a value-added offering since many properties have been added to each of the chemical structures within the database - structure identifiers such as SMILES, InChI, IUPAC and Index Names as well as many physicochemical properties.
http://www.chemspider.com

ChemSub Online
ChemSub Online is a free web-based database which allows you to retreive information for over 237,000 chemical substances of which 138,000 include chemical structures.
http://chemsub.online.fr/

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

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