PubChem

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PubChem is a database of chemical molecules . The system is maintained by the National Center for Biotechnology Information (NCBI) which belongs to the United States National Institutes of Health (NIH). PubChem can be accessed for free through a web user interface. PubChem contains mostly small molecules with a molecular mass below 500. The American Chemical Society have tried to get the U.S. Congress to shut down PubChem, because they claim it competes with their Chemical Abstracts Service.[1]

Contents

Databases

PubChem consists of three primary databases:

  • Compounds, 5.2 million entries, contains pure and characterized chemical compounds.
  • Substances, 7.7 million entries, contains also mixtures, extracts, complexes and uncharacterized substances.
  • BioAssay, bioactivity results from 176 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 an 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]

General
• Any database field [ALL]
• Comment [CMT]
• 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]
• IUPAC name [UPAC], [IUPAC]
• 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 [XLGP], [LOGP]

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

See also

External links

Retrieved from "http://en.freepedia.org/PubChem.html"


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