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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2021-09-14 15:00:08 UTC
HMDB IDHMDB0000350
Secondary Accession Numbers
  • HMDB0002534
  • HMDB00350
  • HMDB02534
Metabolite Identification
Common Name3-Hydroxysebacic acid
Description3-Hydroxydecanedioic is a dicarboxylic acid that belongs to the class of compounds known hydroxy fatty acids. Hydroxy fatty acids are fatty acids that have hydroxyl functional groups attached to the principal chain. 3-Hydroxydecanedioic acid is found in most vertebrates. Urine from patients with ketoacidosis typically contains a number of aliphatic 3-hydroxy dicarboxylic acids, with the major compound being 3-hydroxydecanedioic acid (PMID: 7353273 ). The excretion of 3-hydroxydecanedioic acid is correlated with the excretion of hexanedioic acid, another metabolite frequently found in ketoacidosis (PMID: 5031780 ). It is thought that the 3-hydroxy dicarboxylic acids such as 3-hydroxydecanedioic acid are formed from fatty acids by a combination of omega-oxidation and incomplete beta-oxidation (PMID: 7353273 ). Marked elevation of urinary 3-hydroxydecanedioic acid has also been reported in a malnourished infant with glycogen storage disease (PMID: 8295400 ). Subsequent studies have shown that increased amounts of dicarboxylic acids, such as 3-hydroxydecanedioic acid, are typically excreted in human urine under conditions of medium-chain triglyceride (MCT) feeding, abnormal fatty acid oxidation (FAO) and fasting (PMID: 8596483 ).
Structure
Data?1582752125
Synonyms
ValueSource
3-HydroxysebacateGenerator
(R)-3-Hydroxydecanedioic acidHMDB
(R)-3-Hydroxysebacic acidHMDB
3-Hydroxydecanedioic acidHMDB
3-Hydroxy-decanedioic acidHMDB
3-Hydroxy-sebacic acidHMDB
3-Hydroxy-decanedioateHMDB
3-Hydroxy-sebacateHMDB
3-HydroxydecanedioateHMDB
3-Hydroxysebacic acidHMDB
Chemical FormulaC10H18O5
Average Molecular Weight218.249
Monoisotopic Molecular Weight218.11542368
IUPAC Name(3R)-3-hydroxydecanedioic acid
Traditional Name(3R)-3-hydroxydecanedioic acid
CAS Registry Number446881-43-2
SMILES
O[C@H](CCCCCCC(O)=O)CC(O)=O
InChI Identifier
InChI=1S/C10H18O5/c11-8(7-10(14)15)5-3-1-2-4-6-9(12)13/h8,11H,1-7H2,(H,12,13)(H,14,15)/t8-/m1/s1
InChI KeyOQYZCCKCJQWHIE-MRVPVSSYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassHydroxy acids and derivatives
Sub ClassMedium-chain hydroxy acids and derivatives
Direct ParentMedium-chain hydroxy acids and derivatives
Alternative Parents
Substituents
  • Medium-chain hydroxy acid
  • Medium-chain fatty acid
  • Hydroxy fatty acid
  • Beta-hydroxy acid
  • Fatty acyl
  • Fatty acid
  • Dicarboxylic acid or derivatives
  • Secondary alcohol
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Biological location

Source

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 Solubility3.38 g/LALOGPS
logP0.63ALOGPS
logP1.04ChemAxon
logS-1.8ALOGPS
pKa (Strongest Acidic)4.45ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area94.83 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity52.66 m³·mol⁻¹ChemAxon
Polarizability23.36 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
DeepCCS[M+H]+151.3730932474
DeepCCS[M-H]-147.6330932474
DeepCCS[M-2H]-185.44330932474
DeepCCS[M+Na]+161.10630932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-Hydroxysebacic acidO[C@H](CCCCCCC(O)=O)CC(O)=O3075.6Standard polar33892256
3-Hydroxysebacic acidO[C@H](CCCCCCC(O)=O)CC(O)=O1693.0Standard non polar33892256
3-Hydroxysebacic acidO[C@H](CCCCCCC(O)=O)CC(O)=O1932.8Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3-Hydroxysebacic acid,1TMS,isomer #1C[Si](C)(C)O[C@H](CCCCCCC(=O)O)CC(=O)O1906.2Semi standard non polar33892256
3-Hydroxysebacic acid,1TMS,isomer #2C[Si](C)(C)OC(=O)CCCCCC[C@@H](O)CC(=O)O1915.3Semi standard non polar33892256
3-Hydroxysebacic acid,1TMS,isomer #3C[Si](C)(C)OC(=O)C[C@H](O)CCCCCCC(=O)O1933.8Semi standard non polar33892256
3-Hydroxysebacic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)CCCCCC[C@H](CC(=O)O)O[Si](C)(C)C1964.6Semi standard non polar33892256
3-Hydroxysebacic acid,2TMS,isomer #2C[Si](C)(C)OC(=O)C[C@@H](CCCCCCC(=O)O)O[Si](C)(C)C1962.7Semi standard non polar33892256
3-Hydroxysebacic acid,2TMS,isomer #3C[Si](C)(C)OC(=O)CCCCCC[C@@H](O)CC(=O)O[Si](C)(C)C2012.8Semi standard non polar33892256
3-Hydroxysebacic acid,3TMS,isomer #1C[Si](C)(C)OC(=O)CCCCCC[C@H](CC(=O)O[Si](C)(C)C)O[Si](C)(C)C2071.0Semi standard non polar33892256
3-Hydroxysebacic acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)O[C@H](CCCCCCC(=O)O)CC(=O)O2161.2Semi standard non polar33892256
3-Hydroxysebacic acid,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)CCCCCC[C@@H](O)CC(=O)O2177.8Semi standard non polar33892256
3-Hydroxysebacic acid,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)C[C@H](O)CCCCCCC(=O)O2172.4Semi standard non polar33892256
3-Hydroxysebacic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CCCCCC[C@H](CC(=O)O)O[Si](C)(C)C(C)(C)C2473.2Semi standard non polar33892256
3-Hydroxysebacic acid,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)C[C@@H](CCCCCCC(=O)O)O[Si](C)(C)C(C)(C)C2441.4Semi standard non polar33892256
3-Hydroxysebacic acid,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)CCCCCC[C@@H](O)CC(=O)O[Si](C)(C)C(C)(C)C2479.4Semi standard non polar33892256
3-Hydroxysebacic acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CCCCCC[C@H](CC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2744.0Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysebacic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysebacic acid GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysebacic acid GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysebacic acid GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysebacic acid GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysebacic acid GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysebacic acid GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysebacic acid GC-MS (TMS_3_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysebacic acid GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysebacic acid GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysebacic acid GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysebacic acid GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysebacic acid GC-MS (TBDMS_2_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysebacic acid GC-MS (TBDMS_2_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysebacic acid GC-MS (TBDMS_3_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - 3-Hydroxysebacic acid Quattro_QQQ 10V, Positive-QTOF (Annotated)splash10-0159-0940000000-f4f483b1636137e439452020-02-05HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 3-Hydroxysebacic acid Quattro_QQQ 25V, Positive-QTOF (Annotated)splash10-014m-9400000000-d0cc01c70aafa53f34ab2020-02-05HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 3-Hydroxysebacic acid Quattro_QQQ 40V, Positive-QTOF (Annotated)splash10-00mo-9000000000-316ddd132092b08d73b42020-02-05HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxysebacic acid 10V, Negative-QTOFsplash10-014i-0290000000-c2d6bda5ce3b5556855b2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxysebacic acid 20V, Negative-QTOFsplash10-0a4i-2910000000-d9a15f8576b5fb9845032021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxysebacic acid 40V, Negative-QTOFsplash10-0a4i-9100000000-da86659557db0db21f6b2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxysebacic acid 10V, Positive-QTOFsplash10-0uxr-2970000000-01870c297f8d72ff6dc72021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxysebacic acid 20V, Positive-QTOFsplash10-0159-9200000000-b13018b3cea41f7ddcf12021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxysebacic acid 40V, Positive-QTOFsplash10-0aor-9000000000-6a2ece9abf2e1cb52c2c2021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Experimental 1D NMR1H NMR Spectrum (1D, 600 MHz, Methanol, experimental)2021-10-10Wishart LabView Spectrum
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, CD3OD, experimental)2020-02-05Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
details
BloodDetected and Quantified0.65(0.32-1.2) uMInfant (0-1 year old)Not SpecifiedNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
UrineDetected and Quantified5.8 umol/mmol creatinineInfant (0-1 year old)BothNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
UrineDetected and Quantified0-0.6 umol/mmol creatinineInfant (0-1 year old)Male
Normal
details
UrineDetected and Quantified0.0-0.4 umol/mmol creatinineInfant (0-1 year old)Female
Normal
details
UrineDetected and Quantified7.7 (1.5-24.1) umol/mmol creatinineNewborn (0-30 days old)BothNormal details
UrineDetected and Quantified1.9 (0.1-7.0) umol/mmol creatinineChildren (1-13 years old)Both
Normal
details
UrineDetected and Quantified1.4 (1.0-1.7) umol/mmol creatinineChildren (1-13 years old)Both
Normal
details
UrineDetected and Quantified2.7 (1.3-4.0) umol/mmol creatinineAdolescent (13-18 years old)Both
Normal
details
UrineDetected and Quantified2.9(1.7-3.8) umol/mmol creatinineAdult (>18 years old)Both
Normal
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.95-33.5 uMInfant (0-1 year old)Female3-Hydroxydicarboxylic aciduria details
UrineDetected and Quantified10.628-308.767 umol/mmol creatinineChildren (1-13 years old)Not SpecifiedMedium Chain Acyl-CoA Dehydrogenase Deficiency details
Associated Disorders and Diseases
Disease References
Medium Chain Acyl-CoA Dehydrogenase Deficiency
  1. Duran M, De Klerk JB, Wadman SK, Bruinvis L, Ketting D: The differential diagnosis of dicarboxylic aciduria. J Inherit Metab Dis. 1984;7 Suppl 1:48-51. [PubMed:6434845 ]
Associated OMIM IDs
  • 201450 (Medium Chain Acyl-CoA Dehydrogenase Deficiency)
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB021973
KNApSAcK IDC00052146
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound124350389
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00000150
Good Scents IDNot Available
References
Synthesis ReferenceHill, Frank Friedrich. Manufacture of 3-hydroxydicarboxylic acids. Ger. Offen. (1986), 14 pp.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Boulat O, Gradwohl M, Matos V, Guignard JP, Bachmann C: Organic acids in the second morning urine in a healthy Swiss paediatric population. Clin Chem Lab Med. 2003 Dec;41(12):1642-58. [PubMed:14708889 ]
  2. Guneral F, Bachmann C: Age-related reference values for urinary organic acids in a healthy Turkish pediatric population. Clin Chem. 1994 Jun;40(6):862-6. [PubMed:8087979 ]
  3. Muth A, Jung J, Bilke S, Scharrer A, Mosandl A, Sewell AC, Bohles H: Simultaneous enantioselective analysis of chiral urinary metabolites in patients with Zellweger syndrome. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Jul 25;792(2):269-77. [PubMed:12860034 ]
  4. Bergoffen J, Kaplan P, Hale DE, Bennett MJ, Berry GT: Marked elevation of urinary 3-hydroxydecanedioic acid in a malnourished infant with glycogen storage disease, mimicking long-chain L-3-hydroxyacyl-CoA dehydrogenase deficiency. J Inherit Metab Dis. 1993;16(5):851-6. [PubMed:8295400 ]
  5. Greter J, Lindstedt S, Seeman H, Steen G: 3-hydroxydecanedioic acid and related homologues: urinary metabolites in ketoacidosis. Clin Chem. 1980 Feb;26(2):261-5. [PubMed:7353273 ]