Probably the largest database for commercial compounds is eMolecules- "Google for Molecules". Draw chemical structures using drawing packages such as JME (embedded applet), ISIS/Draw, ChemDraw or ChemSketch, and then instantly search over 8.0 million unique chemical structures from more than 140 leading chemical suppliers. Search results include reference links to properties and spectra from sources such as DrugBank, National Cancer Institute, NIST WebBook, PubChem, EPA and more. There is a Safari extension for eMolecules here.
Zinc is a free database of commercially available compounds ideal for virtual screening. One really nice feature is the property defined sub-sets, such as lead-like (Teague, Davis, Leeson, Oprea, Angew Chem Int Ed Engl. 1999 Dec 16;38(24):3743-3748.), drug-like (Lipinski, J Pharmacol Toxicol Methods. 2000 Jul-Aug;44(1):235-49.) etc. These can all be downloaded and searched locally.
MMsINCdatabase a free web-oriented database of commercially-available compounds for virtual screening and chemoinformatic applications. MMsINC contains over 4 million non-redundant chemical compounds in 3D formats. MMsINC is provided by the Molecular Modeling Section in the Department of Pharmaceutical Sciences at the University of Padova, (Italy) in collaboration with the Software Support Services & Development Laboratory (S3D) at the Center for Advanced Studies, Research and Development (CRS4) in Sardinia.
The largest chemical database is PubChem is organized as three linked databases within the NCBI's Entrez information retrieval system. These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides a fast chemical structure similarity search tool. The database also contains a variety of calculated physicochemical properties for each molecule. Many compounds have links to primary literature and increasingly other databases are providing links to PubChem. There is a Safari extension for PubChem here.
ChemSpider is a free access service providing a structure centric community for chemists. Providing access to millions of chemical structures and integration to a multitude of other online services, ChemSpider is the richest single source of structure-based chemistry information an invaluable source of spectral information. It also hosts a property prediction service. If like me you regularly come across drugs mentioned on web pages that you are unfamiliar with then this Safari Extension for ChemSpider will be of interest.
Two other databases that might be of interest are ChEMBL which provides data on drug-like compounds and BindingDB, which contains quantitative drug-binding constant data.
The Chemical Structure Lookup Service allows you to search through 39 million indexed structures from 80 different databases. Very fast and again you can use a variety of formats (including SMILES), including an embedded java applet, to create the query.
The DrugBank (http://www.drugbank.ca) is a richly annotated database of drug and drug target information. It contains extensive data on the nomenclature, ontology, chemistry, structure, function, action, pharmacology, pharmacokinetics, metabolism and pharmaceutical properties of both small molecule and large molecule drugs. As the table below shows the amount of information available in DrugBank has increased considerably since the first version. For Safari users this information is instantly available using the DrugBank Safari extension.
Comparison between the coverage in DrugBank 1.0, 2.0 and DrugBank 3.0
| Category | 1.0 | 2.0 | 3.0 |
| No. of data fields | 88 | 108 | 148 |
| No. of search types | 8 | 12 | 16 |
| No. of drug-action pathways | 0 | 0 | 223 |
| No. of drugs with metabolizing enzyme data | 0 | 0 | 762 |
| No. of drug metabolites | 0 | 0 | 811 |
| No. of drugs with drug transporter data | 0 | 0 | 516 |
| No. of SNP-associated drug effects | 0 | 0 | 113 |
| No. of drugs with patent/pricing/manufacturer data | 0 | 0 | 1208 |
| No. of food–drug interactions | 0 | 714 | 1039 |
| No. of drug–drug interactions | 0 | 13242 | 13795 |
| No. of ADMET parameters (Caco-2, LogS) | 0 | 276 | 890 |
| No. of QSAR parameters per drug | 5 | 6 | 14 |
| No. of FDA-approved small molecule drugs | 841 | 1344 | 1424 |
| No. of biotech drugs | 113 | 123 | 132 |
| No. of nutraceutical drugs | 61 | 69 | 82 |
| No. of withdrawn drugs | 0 | 57 | 68 |
| No. of illicit drugs | 0 | 188 | 189 |
| No. of experimental drugs | 2894 | 3116 | 5210 |
| Total No. of experimental and FDA small molecule drugs | 3796 | 4774 | 6684 |
| Total No. of experimental and FDA drugs | 3909 | 4897 | 6816 |
| No. of names/brands/synonyms | 18304 | 28447 | 37171 |
| No. of approved-drug drug targets (unique) | 524 | 1565 | 1768 |
| No. of all drug targets (unique) | 2133 | 3037 | 4326 |
| No. of approved-drug enzymes/carriers (unique) | 0 | 0 | 164 |
| No. of all drug enzymes/carriers (unique) | 0 | 0 | 169 |
| No. of external database links | 12 | 18 | 31 |
A Natural product database http://bioinformatics.charite.de/supernatural/
ChemBioFinder is the latest version of the suite of databases provided by Cambridgesoft, there about 500,000 compounds indexed from a variety of databases including (The Merck Index, R&D Insight/Chemists, ChemINDEX Database, NCI, AIDS & Cancer, Traditional Chinese Medicines, Ashgate Drugs: Synonyms & Properties, Nanogen Index, ChemACX, Sigma Aldrich MSDS)
CoCoCo is a suite of molecular databases for high throughput virtual screening purposes. CoCoCo collects molecular structural information of commercial compounds from various chemical vendors by providing it in a ready-to-use format. The main characteristic of CoCoCo is to include structural information about conformational states of the compounds.
RxList (www.rxlist.com) provides electronic versions of the FDA’s drug-product data sheets
Who are the good suppliers?
Derek Lowe on his “In the Pipeline” blog has been compiling a list of chemical suppliers based on users feedback, the most up to date list can be found here. However I’ve included the “Good Suppliers” below, if a supplier is not listed here it might be worth heading over to the up to date list to check and see if any feedback is available, it might save you money and time!
Good Suppliers
- ABCR: good prices and hit rate on orders. Very professional.
- Activate: expensive, but what's there is there, and it's the right stuff.
- Adesis: not cheap, but very reliable and willing to work with customers to deliver similar compounds.
- Advanced Chem Tech: recommended for peptide/amino acid stuff.
- AK Scientific: several good reports on availability and purity.
- Alinda: have ordered one thing from them, which was fine.
- Anaspec: good reports on reliability
- Apollo: good stuff, but catalog needs to be a bit more in line with their real stock.
- Array: very pricey, but it's all there.
- Astatech: good experience reported
- Bionet: interesting catalog, doesn't back-order you.
- Chembridge: a big catalog, but it's all real. Occasional purity problem.
- Chem/Impex: good hit rate on availability. Some questions on their chiral purities.
- Combi-Blocks: good list of useful intermediates, delivers on them.
- Enamine: similar to ChemBridge in many ways. Big catalog. Not the fastest out there.
- Florida Center for Heterocyclics: occasional purity issues, but they do deliver.
- Frontier: great source for boronic acids and the like.
- Life Chemicals: have had good experiences with compound purity here.
- Lu: good source for custom peptides.
- Matrix: interesting catalog, which they will really ship to you.
- Maybridge: on the border of being one of the big guys. Very reliable.
- Midwest: good reports on reliability.
- Netchem: custom synthesis, but (for once!) with good turnaround and purity.
- Oakwood/Fluorochem: good prices and reliability.
- Peptide Protein Research: good for custom peptides.
- Pharmacore: good stock of intermediates.
- Rieke: reliable, only game in town for many odd reagents.
- Strem: well known for quality inorganics and organometallics.
- Synquest: used to be PCR. Good customer service.
- Synthonix: stuff is in stock, customer service is responsive.
- TCI: has always delivered, and quickly.
- Transworld: very reliable and responsive.
- Tyger: have never had a problem with them.
- Waterstone Chemicals: good experience on pricing and availability
Last Update 8 July 2011
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