ChEBI Home

1. Introduction

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.

ChEBI encompasses an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified.

ChEBI uses nomenclature, symbolism and terminology endorsed by the following international scientific bodies:

• International Union of Pure and Applied Chemistry (IUPAC)
• Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB)

Molecules directly encoded by the genome (e.g. nucleic acids, proteins and peptides derived from proteins by cleavage) are not as a rule included in ChEBI.

All data in the database is non-proprietary or is derived from a non-proprietary source. It is thus freely accessible and available to anyone. In addition, each data item is fully traceable and explicitly referenced to the original source.

The text on this website is available under the Creative Commons License.

2. Entity of the month

28 January 2009, Cucurbit[7]uril In 1905, Behrend, Meyer and Rusche described the reaction between glycoluril and formaldehyde which yielded a cross-linked amorphous polymer. Treatment of this substance with hot concentrated sulfuric acid produced a crystalline precipitate [1]. Some 75 years after the Behrend et al. paper, the crystal structure of this compound (now known as cucurbit[6]uril or CB[6]) was solved by Freeman et al. The footnote to their paper [2] says: "The trivial name cucurbituril is proposed because of a general resemblance of 2 to a gourd or pumpkin (family Cucurbitaceae), and by devolution from the similarly named (and shaped) component of the early chemists' alembic." Now, the term cucurbituril refers to any macrocycle consisting of repeating cis-glycoluril residues linked by methylene groups, with the number of repeated units in the macrocycle denoted by the "n" in the cucurbit[n]uril (CB[n]) name. By virtue of their shape, cucurbiturils can form stable inclusion compounds and thus are now employed for molecular recognition, self-assembly, and nanotechnology [3]. In addition to that of CB[6], the structures of CB[5], CB[7], CB[8] and CB[10] have been determined. Unlike CB[6] or CB[8], which are sparingly soluble in water, CB[7] (CHEBI:51434) has a moderate solubility in water which prompted Jeon et al. to study its inclusion of drugs and explore its potential as a drug carrier [4]. CB[7] forms a stable 1:1 complex with the anticancer drug oxaliplatin in aqueous solution. The authors suggest that the encapsulation of the drug not only increases the stability of the drug, but also reduces the unwanted side effects of oxaliplatin.

1. Behrend, R., Meyer, E. and Rusche, F. (1905) Ueber Condensationsproducte aus Glycoluril und Formaldehyd. Liebigs Ann. Chem. 339, 1–37.
2. Freeman, W.A., Mock, W.L. and Shih, N.-Y. (1981) Cucurbituril. J. Am. Chem. Soc. 103, 7367–7368.
3. Lagona, J., Muchophadyay, P., Chakrabarti, S. and Isaacs, L. (2005) The cucurbit[n]uril family. Angew. Chem. Int. Ed. 44, 4844–4870.
4. Jeon, Y.J., Kim, S.-Y., Ko, Y.H., Sakamoto, S., Yamaguchi, K. and Kim, K. (2005) Novel molecular drug carrier: encapsulation of oxaliplatin in cucurbit[7]uril and its effects on stability and reactivity of the drug. Org. Biomol. Chem. 3, 2122–2125.

3. Sources

In order to create ChEBI, data from a number of sources were incorporated and subjected to merging procedures to eliminate redundancy. No data from external sources have been in any way altered but the data have been enriched by information from manual annotation.

Two of the main sources from which the data are drawn are:

• IntEnz – the Integrated relational Enzyme database of the EBI. IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions.

• KEGG COMPOUND – One part of the Kyoto Encyclopedia of Genes and Genomes LIGAND database, COMPOUND is a collection of biochemical compound structures.

• MSDchem – The 'Ligand Chemistry' service providing web access to the 'ligands and small molecule dictionary' of the MSD database developed by the MSD group at EBI.

Other data sources are listed in the User Manual

4. Data

ChEBI shows the following data fields:

• ChEBI Identifer – the unique identifer

• ChEBI Name – the name recommended for use in biological databases

• ChEBI ASCII Name – the ChEBI name with any special characters rendered in ASCII format

• Structure – graphical representation(s) of a molecular structure and associated molfile(s), IUPAC International Chemical Identifier (InChI) and SMILES strings

• Formula – Molecular formula

• Charge

• Mass

• ChEBI Ontology

  • Parents and children
  • An option of a tree view of the position of the entry within the ChEBI Ontology
  
  

• IUPAC Name – name(s) generated according to recommendations of IUPAC

• INN – International Nonproprietary Name, also known as generic name, assigned by the World Health Organization (WHO)

• Synonyms – other names together with an indication of their source

• Brand Name – a trade or proprietary name

• Database Links – manually curated cross-references to other non-proprietary databases

• Registry Number – CAS Registry Number, Beilstein Registry Number, Gmelin Registry Number (if available)

In addition, a separate page called 'Automatic Xrefs' contains automatically generated cross-references to a number of biological and chemical databases.

5. Publication

How to cite ChEBI.

Degtyarenko, K., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcántara, R., Darsow, M., Guedj, M. and Ashburner, M. (2008) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36, D344–D350.

6. Acknowledgements

ChEBI is funded by the European Commission under FELICS, contract number 021902 (RII3) within the Research Infrastructure Action of the FP6 "Structuring the European Research Area" Programme.

In addition we would like to acknowledge the following software support.