Last updated
PubChem logo.svg
DescriptionChemicals and their bioassays
Data types
Organisms Humans and other animals
Research center NCBI
Primary citation PMID   15879180
Download URL FTP
Web service URL PUG-View [1]
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 1,000 bonds. More than 80 database vendors contribute to the growing PubChem database. [2]



PubChem was released in 2004 as a component of the Molecular Libraries Program (MLP) of the NIH. As of November 2015, PubChem contains more than 150 million depositor-provided substance descriptions, 60 million unique chemical structures, and 225 million biological activity test results (from over 1 million assay experiments performed on more than 2 million small-molecules covering almost 10,000 unique protein target sequences that correspond to more than 5,000 genes). It also contains RNA interference (RNAi) screening assays that target over 15,000 genes. [3]

As of August 2018, PubChem contains 247.3 million substance descriptions, 96.5 million unique chemical structures, contributed by 629 data sources from 40 countries. It also contains 237 million bioactivity test results from 1.25 million biological assays, covering >10,000 target protein sequences. [4]

As of 2020, with data integration from over 100 new sources, PubChem contains more than 293 million depositor-provided substance descriptions, 111 million unique chemical structures, and 271 million bioactivity data points from 1.2 million biological assays experiments. [5]


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


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]

Database fields

Identification numbers
Identification number in current database[UID]
Substance identification number[SID]
Compound identification number[CID]
BioAssay identification number[BAID], [AID]

Any database field[ALL]
Deposition date[DDAT], [DEPDAT]
Depositor's external ID[SRID], [SRCID]
Source name[SRC], [SRCNAM], [SRCNAME]
Source release date[SRD], [SRDAT], [RLSDAT]
Medical Subject Heading (MeSH) term[MSHT], [MESHT]
MeSH tree node[MSHN], [MESHTN]
MeSH pharmacological actions[PHMA], [PHARMA]

Substance properties
Substance synonyms[SYNO]
International Chemical Identifier (InChI)[INCHI]
Molecular weight [MW], [MWT], [MOLWT]
Chemical elements [ELMT], [EL]
Non-Hydrogen atoms[HAC], [HACNT]
Isotope count[IAC], [IACNT]
Total formal charge [TFC], [CHG], [CHRG]
Chiral atom count[ACC], [ACCNT]
Defined chiral atom count[ACDC], [ACDCNT]
Undefined chiral atom count[ACUC], [ACUCNT]
Hydrogen bond acceptor count[HBAC], [HBACNT]
Hydrogen bond donor count[HBDC], [HBDCNT]
Tautomer count[TC], [TCNT], [TTMC]
Rotatable bond count[RBC], [RBCNT]
XLogP [11] [XLGP], [LOGP]

Compound properties
Compound synonyms[CSYN], [CSYNO]
Component count[CC], [CCNT]
Covalent unit (molecule) count[CUC], [CUCNT]
Total bioactivity count[TAC]

See also

Related Research Articles

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National Center for Biotechnology Information Database branch of the US National Library of Medicine

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A CAS Registry Number, also referred to as CAS RN or informally CAS Number, is a unique numerical identifier assigned by the Chemical Abstracts Service (CAS), US to every chemical substance described in the open scientific literature. It includes all substances described from 1957 through the present, plus some substances from as far back as the early 1800s. It includes organic and inorganic compounds, minerals, isotopes, alloys, mixtures, and nonstructurable materials. CAS RNs are generally serial numbers, so they do not contain any information about the structures themselves the way SMILES and InChI strings do.

Undecane (also known as hendecane) is a liquid alkane hydrocarbon with the chemical formula CH3(CH2)9CH3. It is used as a mild sex attractant for various types of moths and cockroaches, and an alert signal for a variety of ants. It has 159 isomers.

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Entrez Cross-database search engine for health sciences

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