PubChem

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PubChem

Content
Description	Chemicals and their bioassays
Data types captured	dhsh
Organisms	Humans and other animals
Contact
Research center	NCBI
Primary citation	PMID 15879180
Access
Website	https://pubchem.ncbi.nlm.nih.gov/
Download URL	FTP
Web service URL	PUG-View[1]
Miscellaneous
License	Public domain

PubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information (NCBI), a component of the National Library of Medicine, which is part of the United States National Institutes of Health (NIH). PubChem can be accessed for free through a web user interface. Millions of compound structures and descriptive datasets can be freely downloaded via FTP. PubChem contains multiple substance descriptions and small molecules with fewer than 100 atoms and 1000 bonds. More than 80 database vendors contribute to the growing PubChem database.^[2]

Databases[]

PubChem consists of three dynamically growing primary databases. As of 5 November 2020 (number of BioAssays is unchanged):

• Compounds, 111 million entries^[3] (up from 94 million entries in 2017^[4]), contains pure and characterized chemical compounds.^[5]
• Substances, 293 million entries^[3] (up from 236 in 2017^[6] and 163 million entries in Sept 2014^[7]), contains also mixtures, extracts, complexes and uncharacterized substances.
• BioAssay, bioactivity results from 1.25 million^[8] (up from 6000 in Sept 2014^[9]) high-throughput screening programs with several million values.

Searching[]

Searching the databases is possible for a broad range of properties including chemical structure, name fragments, chemical formula, molecular weight, XLogP, and hydrogen bond donor and acceptor count.

PubChem contains its own online molecule editor with SMILES/SMARTS and InChI support that allows the import and export of all common chemical file formats to search for structures and fragments.

Each hit provides information about synonyms, chemical properties, chemical structure including SMILES and InChI strings, bioactivity, and links to structurally related compounds and other NCBI databases like PubMed.

In the text search form the database fields can be searched by adding the field name in square brackets to the search term. A numeric range is represented by two numbers separated by a colon. The search terms and field names are case-insensitive. Parentheses and the logical operators AND, OR, and NOT can be used. AND is assumed if no operator is used.

Example (Lipinski's Rule of Five):

0:500[mw] 0:5[hbdc] 0:10[hbac] -5:5[logp]

History[]

This section needs expansion. You can help by . (July 2018)

PubChem was released in 2004.^[10]

Database fields[]

See also[]

• Chemical database
  • CAS Common Chemistry - run by the American Chemical Society
  • Comparative Toxicogenomics Database - run by North Carolina State University
  • ChEMBL - run by European Bioinformatics Institute
  • ChemSpider - run by UK's Royal Society of Chemistry
  • DrugBank - run by the University of Alberta
  • IUPAC - run by Swiss-based International Union of Pure and Applied Chemistry (IUPAC)
  • - run by India's National Chemical Laboratory
  • PubChem - run by the National Institute of Health, USA
  • BindingDB - run by the University of California, San Diego
  • SCRIPDB - run by the University of Toronto, Canada
  • National Center for Biotechnology Information (NCBI) - run by the National Institute of Health, USA
  • Entrez - run by the National Institute of Health, USA
  • GenBank - run by the National Institute of Health, USA

References[]

External links[]

Wikidata has the property: PubChem CID (P662) (see uses)

Scholia has a profile for PubChem (Q278487).

• Official website