PubChem
Encyclopedia
PubChem is a database
of chemical
molecule
s 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 substance descriptions and small molecules with fewer than 1000 atoms and 1000 bonds. The American Chemical Society
tried to get the U.S. Congress to restrict the operation of PubChem, because they claim it competes with their Chemical Abstracts Service
. More than 80 database vendors contribute to the growing PubChem database.
, 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 format
s 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]
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.
Database
A database is an organized collection of data for one or more purposes, usually in digital form. The data are typically organized to model relevant aspects of reality , in a way that supports processes requiring this information...
of chemical
Chemistry
Chemistry is the science of matter, especially its chemical reactions, but also its composition, structure and properties. Chemistry is concerned with atoms and their interactions with other atoms, and particularly with the properties of chemical bonds....
molecule
Molecule
A molecule is an electrically neutral group of at least two atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their electrical charge...
s and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information
National Center for Biotechnology Information
The National Center for Biotechnology Information is part of the United States National Library of Medicine , a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper...
(NCBI), a component of the National Library of Medicine, which is part of the United States National Institutes of Health
National Institutes of Health
The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...
(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 substance descriptions and small molecules with fewer than 1000 atoms and 1000 bonds. The American Chemical Society
American Chemical Society
The American Chemical Society is a scientific society based in the United States that supports scientific inquiry in the field of chemistry. Founded in 1876 at New York University, the ACS currently has more than 161,000 members at all degree-levels and in all fields of chemistry, chemical...
tried to get the U.S. Congress to restrict the operation of PubChem, because they claim it competes with their Chemical Abstracts Service
Chemical Abstracts Service
Chemical Abstracts is a periodical index that provides summaries and indexes of disclosures in recently published scientific documents. Approximately 8,000 journals, technical reports, dissertations, conference proceedings, and new books, in any of 50 languages, are monitored yearly, as are patent...
. More than 80 database vendors contribute to the growing PubChem database.
Databases
PubChem consists of three dynamically growing primary databases. As of 7 January 2011:- Compounds, 31 million entries, contains pure and characterized chemical compounds.
- Substances, 75 million entries, contains also mixtures, extractExtractAn extract is a substance made by extracting a part of a raw material, often by using a solvent such as ethanol or water. Extracts may be sold as tinctures or in powder form....
s, complexesComplex (chemistry)In chemistry, a coordination complex or metal complex, is an atom or ion , bonded to a surrounding array of molecules or anions, that are in turn known as ligands or complexing agents...
and uncharacterized substances. - BioAssay, bioactivity results from 1644 high-throughput screeningHigh-throughput screeningHigh-throughput screening is a method for scientific experimentation especially used in drug discovery and relevant to the fields of biology and chemistry. Using robotics, data processing and control software, liquid handling devices, and sensitive detectors, High-Throughput Screening allows a...
programs with several million values.
Searching
Searching the databases is possible for a broad range of properties including chemical structure, name fragments, chemical formulaChemical formula
A chemical formula or molecular formula is a way of expressing information about the atoms that constitute a particular chemical compound....
, molecular weight
Molecular mass
The molecular mass of a substance is the mass of one molecule of that substance, in unified atomic mass unit u...
, XLogP, and hydrogen bond
Hydrogen bond
A hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen or fluorine, that comes from another molecule or chemical group. The hydrogen must be covalently bonded to another electronegative atom to create the bond...
donor and acceptor count.
PubChem contains its own online molecule editor
Molecule editor
A molecule editor is a computer program for creating and modifying representations of chemical structures.Molecule editors can manipulate chemical structure representations in either two- or three-dimensions. Two-Dimensional editors generate output used as illustrations or for querying chemical...
with SMILES
Simplified molecular input line entry specification
The simplified molecular-input line-entry specification or SMILES is a specification in form of a line notation for describing the structure of chemical molecules using short ASCII strings...
/SMARTS and InChI
International Chemical Identifier
The IUPAC International Chemical Identifier is a textual identifier for chemical substances, designed to provide a standard and human-readable way to encode molecular information and to facilitate the search for such information in databases and on the web...
support that allows the import and export of all common chemical file format
Chemical file format
This article discusses some common molecular file formats, including usage and converting between them.-Distinguishing formats:Chemical information is usually provided as files or streams and many formats have been created, with varying degrees of documentation. The format can be found by three...
s 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
PubMed
PubMed is a free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez information retrieval system...
.
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
Lipinski's Rule of Five
Lipinski's Rule of Five is a rule of thumb to evaluate druglikeness or determine if a chemical compound with a certain pharmacological or biological activity has properties that would make it a likely orally active drug in humans. The rule was formulated by Christopher A...
):
0:500[mw] 0:5[hbdc] 0:10[hbac] -5:5[logp]
ACS's concerns
The American Chemical SocietyAmerican Chemical Society
The American Chemical Society is a scientific society based in the United States that supports scientific inquiry in the field of chemistry. Founded in 1876 at New York University, the ACS currently has more than 161,000 members at all degree-levels and in all fields of chemistry, chemical...
has raised concerns about the publicly supported PubChem database, since it appears to directly compete with their existing Chemical Abstracts Service
Chemical Abstracts Service
Chemical Abstracts is a periodical index that provides summaries and indexes of disclosures in recently published scientific documents. Approximately 8,000 journals, technical reports, dissertations, conference proceedings, and new books, in any of 50 languages, are monitored yearly, as are patent...
. 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.
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 International Chemical Identifier The IUPAC International Chemical Identifier is a textual identifier for chemical substances, designed to provide a standard and human-readable way to encode molecular information and to facilitate the search for such information in databases and on the web... (InChI) |
[INCHI] |
| • | Molecular weight Molecular mass The molecular mass of a substance is the mass of one molecule of that substance, in unified atomic mass unit u... |
[MW], [MWT], [MOLWT] |
| • | Chemical element Chemical element A chemical element is a pure chemical substance consisting of one type of atom distinguished by its atomic number, which is the number of protons in its nucleus. Familiar examples of elements include carbon, oxygen, aluminum, iron, copper, gold, mercury, and lead.As of November 2011, 118 elements... s |
[ELMT], [EL] |
| • | Non-Hydrogen atoms | [HAC], [HACNT] |
| • | Isotope Isotope Isotopes are variants of atoms of a particular chemical element, which have differing numbers of neutrons. Atoms of a particular element by definition must contain the same number of protons but may have a distinct number of neutrons which differs from atom to atom, without changing the designation... count |
[IAC], [IACNT] |
| • | Total formal charge Formal charge In chemistry, a formal charge is the charge assigned to an atom in a molecule, assuming that electrons in a chemical bond are shared equally between atoms, regardless of relative electronegativity.... |
[TFC], [CHG], [CHRG] |
| • | Chiral Chirality (chemistry) A chiral molecule is a type of molecule that lacks an internal plane of symmetry and thus has a non-superimposable mirror image. The feature that is most often the cause of chirality in molecules is the presence of an asymmetric carbon atom.... atom count |
[ACC], [ACCNT] |
| • | Defined chiral atom count | [ACDC], [ACDCNT] |
| • | Undefined chiral atom count | [ACUC], [ACUCNT] |
| • | Hydrogen bond Hydrogen bond A hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen or fluorine, that comes from another molecule or chemical group. The hydrogen must be covalently bonded to another electronegative atom to create the bond... acceptor count |
[HBAC], [HBACNT] |
| • | Hydrogen bond donor count | [HBDC], [HBDCNT] |
| • | Tautomer Tautomer Tautomers are isomers of organic compounds that readily interconvert by a chemical reaction called tautomerization. This reaction commonly results in the formal migration of a hydrogen atom or proton, accompanied by a switch of a single bond and adjacent double bond... 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
- Chemical databaseChemical databaseA chemical database is a database specifically designed to store chemical information. This information is about chemical and crystal structures, spectra, reactions and syntheses, and thermophysical data.- Chemical structures :...
- Comparative Toxicogenomics DatabaseComparative Toxicogenomics DatabaseThe Comparative Toxicogenomics Database is a public website and research tool that curates scientific data describing relationships between chemicals, genes, and human diseases....
- ChEMBLChEMBLChEMBL or ChEMBLdb is a manually curated chemical database of bioactive molecules with drug-like properties.It is maintained by the European Bioinformatics Institute , based on the Wellcome Trust Genome Campus, Hinxton, UK. The database, originally known as StARlite, was developed by a...
- ChemSpiderChemSpiderChemsSpider is a free chemical database, owned by the Royal Society of Chemistry.-Database:The database contains more than 26 million unique molecules from over 400 data sources including those listed below.* A-L: EPA DSSTox, U.S...
- eMoleculesEMoleculeseMolecules is a search engine for chemical molecules. The system was first launched in November 2005.-Database:* The database contains more than 7.0M unique molecules from commercial suppliers, like Acros, ASINEX, ChemBridge, ChemDiv, Comgenex, Enamine Ltd, Fluka, InterBioScreen, Key Organics, Life...
- DrugBankDrugBankThe DrugBank database available at the University of Alberta is a bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information...
- MoltableMoltableMoltable is a drug research initiative based in India, aimed at discovering new drugs to target cancer, AIDS, malaria and other potentially devastating infectious diseases, through chemoinformatics research....
- BindingDBBindingDBBindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of proteins considered to be candidate drug-targets with ligands that are small, drug-like molecules. As of March, 2011, BindingDB contains about 650,000 binding data, for 5,700...
- Comparative Toxicogenomics Database
- National Center for Biotechnology InformationNational Center for Biotechnology InformationThe National Center for Biotechnology Information is part of the United States National Library of Medicine , a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper...
(NCBI) - EntrezEntrezThe Entrez Global Query Cross-Database Search System is a powerful federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information website...
- PubMedPubMedPubMed is a free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez information retrieval system...
- GenBankGenBankThe GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information as part of the International Nucleotide Sequence...