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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2009-02-24 15:43:08 UTC
Update Date2023-02-21 17:17:34 UTC
HMDB IDHMDB0011717
Secondary Accession Numbers
  • HMDB11717
Metabolite Identification
Common NameNonate
DescriptionNonic 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 ) 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 ).
Structure
Data?1676999854
Synonyms
ValueSource
NONic acidGenerator
(2R) - 2- PentylbutanedioateHMDB
(2R) - 2- Pentylbutanedioic acidHMDB
(2R) - 2- Pentylsuccinic acidHMDB
2- Pentylsuccinic acidHMDB
NONic acid EthanedisulfonateHMDB
(2S)-2-PentylbutanedioateGenerator, HMDB
Chemical FormulaC9H16O4
Average Molecular Weight188.2209
Monoisotopic Molecular Weight188.104859
IUPAC Name(2S)-2-pentylbutanedioic acid
Traditional Name(2S)-2-pentylbutanedioic acid
CAS Registry NumberNot Available
SMILES
CCCCC[C@@H](CC(O)=O)C(O)=O
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
InChI KeyFNZSVEHJZREFPF-ZETCQYMHSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentMedium-chain fatty acids
Alternative Parents
Substituents
  • Medium-chain fatty acid
  • Methyl-branched fatty acid
  • Branched fatty acid
  • Dicarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Process
Role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility3.86 g/LALOGPS
logP1.27ALOGPS
logP1.92ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)4.47ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity46.52 m³·mol⁻¹ChemAxon
Polarizability19.97 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+145.3931661259
DarkChem[M-H]-144.28531661259
DeepCCS[M+H]+143.64130932474
DeepCCS[M-H]-139.81430932474
DeepCCS[M-2H]-176.93230932474
DeepCCS[M+Na]+152.5230932474
AllCCS[M+H]+145.332859911
AllCCS[M+H-H2O]+141.532859911
AllCCS[M+NH4]+148.832859911
AllCCS[M+Na]+149.832859911
AllCCS[M-H]-143.332859911
AllCCS[M+Na-2H]-144.732859911
AllCCS[M+HCOO]-146.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
NonateCCCCC[C@@H](CC(O)=O)C(O)=O2472.5Standard polar33892256
NonateCCCCC[C@@H](CC(O)=O)C(O)=O1346.4Standard non polar33892256
NonateCCCCC[C@@H](CC(O)=O)C(O)=O1572.4Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Nonate,1TMS,isomer #1CCCCC[C@@H](CC(=O)O[Si](C)(C)C)C(=O)O1571.2Semi standard non polar33892256
Nonate,1TMS,isomer #2CCCCC[C@@H](CC(=O)O)C(=O)O[Si](C)(C)C1527.7Semi standard non polar33892256
Nonate,2TMS,isomer #1CCCCC[C@@H](CC(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C1643.1Semi standard non polar33892256
Nonate,1TBDMS,isomer #1CCCCC[C@@H](CC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O1805.7Semi standard non polar33892256
Nonate,1TBDMS,isomer #2CCCCC[C@@H](CC(=O)O)C(=O)O[Si](C)(C)C(C)(C)C1760.6Semi standard non polar33892256
Nonate,2TBDMS,isomer #1CCCCC[C@@H](CC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2105.7Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Nonate GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9500000000-38d1c2542c5109e116bf2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Nonate GC-MS (2 TMS) - 70eV, Positivesplash10-00rf-9051000000-67ad3f607bb0d0d8c5062017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Nonate GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 10V, Positive-QTOFsplash10-00di-0900000000-f9d5425ef98bcbccbe4f2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 20V, Positive-QTOFsplash10-00fu-5900000000-0096a6065c03ecab28fb2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 40V, Positive-QTOFsplash10-052e-9100000000-880e6119878c363e5c172017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 10V, Negative-QTOFsplash10-000l-0900000000-67d40c109b682dea3f482017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 20V, Negative-QTOFsplash10-00ko-1900000000-6c62d33822e53e2d220e2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 40V, Negative-QTOFsplash10-0a4l-9100000000-5d00db6240f4db0ae3012017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 10V, Positive-QTOFsplash10-007d-5900000000-80d0f819a79928c38c752021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 20V, Positive-QTOFsplash10-00lu-9400000000-2ceb2add929c737793ff2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 40V, Positive-QTOFsplash10-05g0-9000000000-004722dc9eff5a2d96802021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 10V, Negative-QTOFsplash10-014i-0900000000-cba41d731216dc0d13542021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 20V, Negative-QTOFsplash10-0006-4900000000-98ea4b0f0f9da5458c1e2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 40V, Negative-QTOFsplash10-0006-9100000000-0e1f126dd8b4b5da89d82021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-03FELIX labView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.5 (0.0-1.0) uMAdult (>18 years old)Both
Prostate Cancer
details
Associated Disorders and Diseases
Disease References
Prostate cancer
  1. 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. doi: 10.1038/nature07762. [PubMed:19212411 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB028402
KNApSAcK IDC00022257
Chemspider ID13183696
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound16058309
PDB IDNot Available
ChEBI ID88404
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot 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 ]
  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 ]
  3. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  4. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  5. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  6. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  7. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.