ChemExper : Find a supplier for your specialty chemical needs. Search by structure, name, molecular formula, and CAS Number. After finding you compound, get an offer from one or more suppliers. I can't vouch for how this works in practice, but it sounds like a good idea.
The EBI Search engine: also known as EB-eye, is a scalable text search engine that provides easy and uniform access to the biological data resources hosted at the EMBL-EBI.The data resources represented in the EBI Search engine include: nucleotide and protein sequences at both the genomic and proteomic levels, structures ranging from chemicals to macro-molecular complexes, gene-expression experiments, binary level molecular interactions as well as reaction maps and pathway models, functional classifications, biological ontologies, and comprehensive literature libraries covering the biomedical sciences and related intellectual property.
ChemSpider : is a free chemical structure database providing fast access to over 30 million structures, properties and associated information. By integrating and linking compounds from more than 470 data sources, ChemSpider enables researchers to discover the most comprehensive view of freely available chemical data from a single online search. It is owned by the Royal Society of Chemistry.
PubChem : The granddaddy of all free chemistry databases. Search over 8 million compounds by a variety of criteria. Although some PubChem records are linked into the primary literature through MeSH, most are not. But this doesn't seem to be PubChem's true calling. Instead, PubChem may well evolve into the world's largest online collection of molecular data sheets. Increasingly, the other databases in this list are cross-referencing their entries into PubChem. PubChem's entire database can be downloaded by FTP. CAS Registry are correct to see PubChem as the first real competition they've had in decades.
CHEBI :"A freely available dictionary of molecular entities focused on ‘small’ chemical compounds." CHEBI draws its information from two main sources: Integrated Relational Enzyme Database of the EBI and the Kyoto Encyclopedia of Genes and Genomes. Find out what proteins a molecule has been associated with and in what context. Provides cross-links to CAS registry numbers, Beilstein registry numbers, and Gmelin registry numbers.
BioCyc : A collection of about 3,500 compounds involved as enzyme substrates, products, inhibitors, and activators. On accepting a license agreement, the entire database can be freely downloaded in Chemical Markup Language format.
NMRShiftDB :Organic structures and their nuclear magnetic resonance (nmr) chemical shifts. NMRShiftDB contains chemical shift data for over 22,000 organic compounds and 19,000 spectra. Records can be searched by structure, chemical shift and nucleus. NMRShiftDB is truly open; it can be accessed programmatically and the source code for the software that runs the online database can be freely downloaded. Individual users can submit their own spectral shifts for peer review and subsequent inclusion.
Network Science Corporation : a non-profit organization, was founded to assist in science education by supporting the development of science and technology, by facilitating the timely exchange of information as a means of enhancing professional development, and by fostering public awareness of advances in the therapeutic management of diseases.
Chemconnector : The domain of Chemical Information contains to gain in importance as scientists expand in their dexterity and understanding of how to more fully utilize both public domain and commercial tools in their work. The development of the internet has certainly been catalytic in providing new approaches to the dissemination of chemical information but has also enabled improved methods for networking and the distribution of data, knowledge and understanding.
Wiley Online Library : hosts the world's broadest and deepest multidisciplinary collection of online resources covering life, health and physical sciences, social science, and the humanities. It delivers seamless integrated access to over 4 million articles from 1500 journals, over 14,000 online books, and hundreds of reference works, laboratory protocols and databases.
Topics in current chemistry : Critical reviews of the present and future trends in modern chemical research. Subjects : Chemistry -- Periodicals.
Compendium of Common Pesticide Names : "This Compendium is believed to be the only place where all of the ISO-approved standard names of chemical pesticides are listed. It also includes more than 300 approved names from national and international bodies for pesticides that do not have ISO names."
DrugBank : "a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains 6707 drug entries including 1436 FDA-approved small molecule drugs, 134 FDA-approved biotech (protein/peptide) drugs, 83 nutraceuticals and 5086 experimental drugs."
IUPAC-NIST Solubility Database : "Data compiled and evaluated by IUPAC (International Union of Pure and Applied Chemistry)"
ChemMine : "ChemMine is a compound mining database that facilitates drug and agrochemical discovery and chemical genomics screens."
Organic Syntheses : "Each procedure is written in considerably more detail as compared to typical experimental procedures in other journals, and each reaction and all characterization data has been carefully "checked" for reproducibility in the laboratory of a member of the Board of Editors."
BindingDB : "BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. BindingDB contains 781,982 binding data, for 6,448 protein targets and 342,414 small molecules."
KEGG: Kyoto Encyclopedia of Genes and Genomes : is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
AffinDB : "affinity data for protein-ligand complexes of the PDB. Its purpose is to provide direct and free access to the experimental affinity of a given complex structure. As of Thursday, October 13th, 2011, AffinDB contains 748 affinity values covering 474 different PDB complexes."
Heterocycles Web Edition : "This journal will list the new natural products with a heterocyclic ring system, collected from current chemical literature, whose structure has been established."
CrystalEye : "The aim of the CrystalEye project is to aggregate crystallography from web resources, and to provide methods to easily browse, search, and to keep up to date with the latest published information."
Common Chemistry : "a web resource that contains CAS Registry Numbers for approximately 7,900 chemicals of widespread general public interest. Common Chemistry is helpful to non-chemists who know either a name or CAS Registry Number® of a common chemical and want to pair both pieces of information."
PheroBase :"Currently, there are over 30000 entries, around 8000 molecules, and over 100000 static php pages that make it the world's largest database of behaviour modifying chemicals. In addition, mass spectral, NMR, synthesis data for more than 2500 compounds are included."
Side Effect Resource (SIDER) : "SIDER contains information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information include side effect frequency, drug and side effect classifications as well as links to further information, for example drug–target relations."
ChemSynthesis : "ChemSynthesis is a freely accessible database of chemicals. This website contains substances with their synthesis references and physical properties such as melting point, boiling point and density. There are currently more than 40,000 compounds and more than 45,000 synthesis references in the database."
Human Metabolome Database : "The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. ... The database (version 2.5) contains over 7900 metabolite entries including both water-soluble and lipid soluble metabolites as well as metabolites that would be regarded as either abundant (> 1 uM) or relatively rare (< 1 nM)."
ChemWiki : "a collaborative approach toward chemistry education where an Open Access textbook environment is constantly being written and re-written partly by students and partly by faculty members resulting in a free Chemistry textbook to supplement conventional paper-based books."
LookChem : "There are 6,000,000 chemicals with CAS number which is an identity for one chemical. And about 10 million CAS numbers are on the top of first page on Google.com."
LipidBank : "The official database of Japanese Conference on the Biochemistry of Lipids"
Crystallography Open Database : "Open-access collection of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymers"