Human Metabolome Database Version 3.5

Showing metabocard for Nonate (HMDB11717)

Record Information
Version 3.5
Creation Date 2009-02-24 08:43:08 -0700
Update Date 2013-05-29 13:46:54 -0600
Secondary Accession Numbers None
Metabolite Identification
Common Name Nonate
Description Nonic acid or the anion, nonate, is a derivative of succinic acid, which is a dicarboxylic acid. The anion, succinate, is a component of the citric acid cycle capable of donating electrons to the electron transfer chain. Succinate dehydrogenase (SDH) plays an important role in the mitochondria, being both part of the respiratory chain and the Krebs cycle. SDH with a covalently attached FAD prosthetic group, binds enzyme substrates (succinate and fumarate) and physiological regulators (oxaloacetate and ATP). Oxidizing succinate links SDH to the fast-cycling Krebs cycle portion where it participates in the breakdown of acetyl-CoA throughout the whole Krebs cycle. The succinate can readily be imported into the mitochondrial matrix by the n-butylmalonate- (or phenylsuccinate-) sensitive dicarboxylate carrier in exchange with inorganic phosphate or another organic acid, e. g. malate. (PMID 16143825 Link_out) Mutations in the four genes encoding the subunits of the mitochondrial respiratory chain succinate dehydrogenase are associated with a wide spectrum of clinical presentations (i.e.: Huntington's disease. (PMID 11803021 Link_out).
Structure Thumb
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
  1. (2R) - 2- pentylbutanedioate
  2. (2R) - 2- pentylbutanedioic acid
  3. (2R) - 2- pentylsuccinic acid
  4. 2- Pentylsuccinic acid
  5. Nonic acid
  6. Nonic acid ethanedisulfonate
Chemical Formula C9H16O4
Average Molecular Weight 188.2209
Monoisotopic Molecular Weight 188.104859
IUPAC Name (2S)-2-pentylbutanedioic acid
Traditional IUPAC Name (2S)-2-pentylbutanedioic acid
CAS Registry Number Not Available
InChI Identifier InChI=1S/C9H16O4/c1-2-3-4-5-7(9(12)13)6-8(10)11/h7H,2-6H2,1H3,(H,10,11)(H,12,13)/t7-/m0/s1
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Organic Acids and Derivatives
Class Carboxylic Acids and Derivatives
Sub Class Dicarboxylic Acids and Derivatives
Other Descriptors
  • Aliphatic Acyclic Compounds
  • Branched Fatty Acids
  • Carboxylic Acid
Direct Parent Dicarboxylic Acids and Derivatives
Status Detected and Quantified
  • Endogenous
Biofunction Not Available
Application Not Available
Cellular locations Not Available
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point Not Available Not Available
Boiling Point Not Available Not Available
Water Solubility Not Available Not Available
LogP Not Available Not Available
Predicted Properties
Property Value Source
Water Solubility 3.86 g/L ALOGPS
LogP 1.27 ALOGPS
LogP 1.92 ChemAxon
LogS -1.69 ALOGPS
pKa (strongest acidic) 4.47 ChemAxon
Hydrogen Acceptor Count 4 ChemAxon
Hydrogen Donor Count 2 ChemAxon
Polar Surface Area 74.6 A2 ChemAxon
Rotatable Bond Count 7 ChemAxon
Refractivity 46.52 ChemAxon
Polarizability 19.97 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge -2 ChemAxon
Not Available
Biological Properties
Cellular Locations Not Available
Biofluid Locations
  • Blood
Tissue Location Not Available
Pathways Not Available
Normal Concentrations
Not Available
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified 0.5 (0.0-1.0) uM Adult (>18 years old) Both Comment Prostate Cancer
Associated Disorders and Diseases
Disease References
Prostate cancer
  • Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. Pubmed: 19212411 Link_out
      Associated OMIM IDs
      DrugBank ID Not Available
      DrugBank Metabolite ID Not Available
      Phenol Explorer Compound ID Not Available
      Phenol Explorer Metabolite ID Not Available
      FoodDB ID FDB028402
      KNApSAcK ID Not Available
      Chemspider ID 13183696 Link_out
      KEGG Compound ID Not Available
      BioCyc ID 2-DH-3-DO-D-ARABINONATE Link_out
      BiGG ID Not Available
      Wikipedia Link Not Available
      NuGOwiki Link HMDB11717 Link_out
      Metagene Link HMDB11717 Link_out
      METLIN ID Not Available
      PubChem Compound 16058309 Link_out
      PDB ID Not Available
      ChEBI ID Not Available
      Synthesis Reference Not Available
      Material Safety Data Sheet (MSDS) Not Available
      General References
      1. Briere JJ, Favier J, El Ghouzzi V, Djouadi F, Benit P, Gimenez AP, Rustin P: Succinate dehydrogenase deficiency in human. Cell Mol Life Sci. 2005 Oct;62(19-20):2317-24. Pubmed: 16143825 Link_out
      2. Rustin P, Rotig A: Inborn errors of complex II--unusual human mitochondrial diseases. Biochim Biophys Acta. 2002 Jan 17;1553(1-2):117-22. Pubmed: 11803021 Link_out