|Description||Chemicals and their bioassays|
|Organisms||Humans and other animals|
|Primary citation||PMID 15879180|
|Web service URL||PUG-View|
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.
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.
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]
This section needs expansion. You can help by adding to it. (July 2018)
PubChem was released in 2004.
The American Chemical Society has raised concerns about the publicly supported PubChem database, since it appears to directly compete with their existing Chemical Abstracts Service. They have a strong interest in the issue since the Chemical Abstracts Service generates a large percentage of the society's revenue. To advocate their position against the PubChem database, ACS has actively lobbied the US Congress.
|o||Identification number in current database||[UID]|
|o||Substance identification number||[SID]|
|o||Compound identification number||[CID]|
|o||BioAssay identification number||[BAID], [AID]|
|o||Any database field||[ALL]|
|o||Deposition date||[DDAT], [DEPDAT]|
|o||Depositor's external ID||[SRID], [SRCID]|
|o||Source name||[SRC], [SRCNAM], [SRCNAME]|
|o||Source release date||[SRD], [SRDAT], [RLSDAT]|
|o||Medical Subject Heading (MeSH) term||[MSHT], [MESHT]|
|o||MeSH tree node||[MSHN], [MESHTN]|
|o||MeSH pharmacological actions||[PHMA], [PHARMA]|
|o||IUPAC name||[UPAC], [IUPAC]|
|o||International Chemical Identifier (InChI)||[INCHI]|
|o||Molecular weight||[MW], [MWT], [MOLWT]|
|o||Chemical elements||[ELMT], [EL]|
|o||Non-Hydrogen atoms||[HAC], [HACNT]|
|o||Isotope count||[IAC], [IACNT]|
|o||Total formal charge||[TFC], [CHG], [CHRG]|
|o||Chiral atom count||[ACC], [ACCNT]|
|o||Defined chiral atom count||[ACDC], [ACDCNT]|
|o||Undefined chiral atom count||[ACUC], [ACUCNT]|
|o||Hydrogen bond acceptor count||[HBAC], [HBACNT]|
|o||Hydrogen bond donor count||[HBDC], [HBDCNT]|
|o||Tautomer count||[TC], [TCNT], [TTMC]|
|o||Rotatable bond count||[RBC], [RBCNT]|
|o||Compound synonyms||[CSYN], [CSYNO]|
|o||Component count||[CC], [CCNT]|
|o||Covalent unit (molecule) count||[CUC], [CUCNT]|
|o||Total bioactivity count||[TAC]|