Compound or Compound-Specific Databases

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PubChem
is a freely available database of chemical structures of small organic molecules and information on their biological activities. It contains structure, nomenclature and calculated physico-chemical data and is linked with NIH PubMed/Entrez information. 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. PubChem has >19 million unique chemical structures.

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HMDB
The Human MetabolomeDatabase (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education