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Kinetic Categories: Km, Kcat, IC50

KENDA (Kinetic ENzyme DAta)
KENDA is a new supplement to the BRENDA database providing an additional overview on functional kinetic data of enzymes.This additional resource is based on a text-mining resource extracting kinetic values and expressions (KM, Ki, kcat, Vmax etc.), combined with the organism and enzyme name from more than 2.2 million PubMed abstracts [1] retrieved from the FRENDA database [2] This approach is based on an automatic text interpretation supported by dictionaries, consisting of:
  • 6151 EC classes
  • 2000 kinetic terms, including units and different spellings
  • 206,818 ligand names, including synonyms from the Brenda Ligand database and ~130,000,000 ligand names, including synonyms from the PubChem database
  • 74,141 enzyme names (recommended names, systematic names, synonyms from BRENDA database)
  • 2,269,66 organism names, consisting of the organisms names in BRENDA and the synonyms of the NCBI Taxonomy [1]
  • 2000 (linguistic) terms for the interpretation of the sentence structure (e.g. negations, marker for spellings etc.)
This text mining approach, in the preliminary release resulted in:
  • ~13,000 kinetic values in total
  • ~13,000 kinetic values connected to an organism
  • ~13,500 kinetic values connected to a ligand
  • distribution of the results regarding the different kinetic categories:

Kinetic category
Relative occurrence [%]
KM
31
IC50
31
kcat
5.2
Ki
20
specific activity
6.4
Vmax
4.4
kcat/KM
0.8
Table: Relative occurences of the kinetic categories

Reference:
Reference of KENDA
  • [1] Chang A., Schomburg I., Placzek S., Jeske L., Ulbrich M., Xiao M., Sensen C.W., Schomburg D. (2015) BRENDA in 2015: exciting developments in its 25th year of existence. Nucleic Acids Res., 43, D439-46
  • [2] Sayers,E.W., Barrett,T., Benson,D.A., Bolton,E., Bryant,S.H., Canese,K., Chetvernin,V., Church,D.M., Dicuccio,M., Federhen,S., Feolo,M., Fingerman,I.M., Geer, LY, Helmberg,W., Kapustin,Y., Krasnov,S., Landsman,D., Lipman,D.J., Lu,Z., Madden,T.L., Madej,T., Maglott,R., Marchler-Bauer,A., Miller,V., Karsch-Mizrachi,I., Ostell,J., Panchenko,A., Phan,L., Pruitt,K.D., Schuler,G.D., Sequeira,E., Sherry,S.T., Shumway,M., Sirotkin,K., Slotta,D., Souvorov,A., Starchenko,G., Tatusova,T.A., Wagner,L., Wang,Y., Wilbur,W.J., Yaschenko,E., Ye,J. (2012) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 40, D13-D25
  • [3] Chang,A., Scheer,M., Grote,A., Schomburg,I. and Schomburg,D. (2009) BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res., 37, D588-D592.
Funding:
This work was supported by SLING: Serving Life-science Information for the Next Generation