Hmdb loader
You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2021-09-14 15:20:01 UTC
HMDB IDHMDB0000325
Secondary Accession Numbers
  • HMDB00325
Metabolite Identification
Common Name3-Hydroxysuberic acid
Description3-Hydroxysuberic acid, also known as 3-hydroxysuberate or 3-hydroxyoctanedioate, 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. 3-Hydroxysuberic acid exists in all living organisms, ranging from bacteria to humans. 3-Hydroxysuberic acid has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make 3-hydroxysuberic acid a potential biomarker for the consumption of these foods. 3-Hydroxysuberic acid is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on 3-Hydroxysuberic acid.
Structure
Data?1582752124
Synonyms
ValueSource
3-HydroxysuberateGenerator
3-HydroxyoctanedioateHMDB
3-Hydroxyoctanedioic acidHMDB
3-Hydroxy-suberateHMDB
Chemical FormulaC8H14O5
Average Molecular Weight190.1938
Monoisotopic Molecular Weight190.084123558
IUPAC Name3-hydroxyoctanedioic acid
Traditional Name3-hydroxysuberic acid
CAS Registry Number73141-47-6
SMILES
OC(CCCCC(O)=O)CC(O)=O
InChI Identifier
InChI=1S/C8H14O5/c9-6(5-8(12)13)3-1-2-4-7(10)11/h6,9H,1-5H2,(H,10,11)(H,12,13)
InChI KeyARJZZFJXSNJKGR-UHFFFAOYSA-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
  • Beta-hydroxy acid
  • Hydroxy fatty acid
  • Dicarboxylic acid or derivatives
  • Fatty acyl
  • Fatty acid
  • Secondary alcohol
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Alcohol
  • Carbonyl group
  • Organic oxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
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 Solubility19.5 g/LALOGPS
logP-0.17ALOGPS
logP0.15ChemAxon
logS-0.99ALOGPS
pKa (Strongest Acidic)3.94ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area94.83 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity43.46 m³·mol⁻¹ChemAxon
Polarizability19.14 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]+143.73931661259
DarkChem[M-H]-139.03531661259
AllCCS[M+H]+142.90732859911
AllCCS[M-H]-140.77132859911
DeepCCS[M+H]+136.77230932474
DeepCCS[M-H]-132.93930932474
DeepCCS[M-2H]-170.20730932474
DeepCCS[M+Na]+145.69330932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-Hydroxysuberic acidOC(CCCCC(O)=O)CC(O)=O2840.9Standard polar33892256
3-Hydroxysuberic acidOC(CCCCC(O)=O)CC(O)=O1396.3Standard non polar33892256
3-Hydroxysuberic acidOC(CCCCC(O)=O)CC(O)=O1712.0Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3-Hydroxysuberic acid,1TMS,isomer #1C[Si](C)(C)OC(CCCCC(=O)O)CC(=O)O1737.3Semi standard non polar33892256
3-Hydroxysuberic acid,1TMS,isomer #2C[Si](C)(C)OC(=O)CCCCC(O)CC(=O)O1756.1Semi standard non polar33892256
3-Hydroxysuberic acid,1TMS,isomer #3C[Si](C)(C)OC(=O)CC(O)CCCCC(=O)O1750.7Semi standard non polar33892256
3-Hydroxysuberic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)CCCCC(CC(=O)O)O[Si](C)(C)C1822.1Semi standard non polar33892256
3-Hydroxysuberic acid,2TMS,isomer #2C[Si](C)(C)OC(=O)CC(CCCCC(=O)O)O[Si](C)(C)C1800.3Semi standard non polar33892256
3-Hydroxysuberic acid,2TMS,isomer #3C[Si](C)(C)OC(=O)CCCCC(O)CC(=O)O[Si](C)(C)C1826.6Semi standard non polar33892256
3-Hydroxysuberic acid,3TMS,isomer #1C[Si](C)(C)OC(=O)CCCCC(CC(=O)O[Si](C)(C)C)O[Si](C)(C)C1875.8Semi standard non polar33892256
3-Hydroxysuberic acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(CCCCC(=O)O)CC(=O)O2005.3Semi standard non polar33892256
3-Hydroxysuberic acid,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)CCCCC(O)CC(=O)O2022.1Semi standard non polar33892256
3-Hydroxysuberic acid,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)CC(O)CCCCC(=O)O2018.4Semi standard non polar33892256
3-Hydroxysuberic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CCCCC(CC(=O)O)O[Si](C)(C)C(C)(C)C2315.5Semi standard non polar33892256
3-Hydroxysuberic acid,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)CC(CCCCC(=O)O)O[Si](C)(C)C(C)(C)C2281.5Semi standard non polar33892256
3-Hydroxysuberic acid,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)CCCCC(O)CC(=O)O[Si](C)(C)C(C)(C)C2281.6Semi standard non polar33892256
3-Hydroxysuberic acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CCCCC(CC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2534.1Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysuberic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9600000000-8161524f0f04ddabd28f2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysuberic acid GC-MS (3 TMS) - 70eV, Positivesplash10-00a9-9185000000-26b8219023a90b94803c2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysuberic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysuberic acid GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysuberic acid GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysuberic acid GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysuberic acid GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysuberic acid GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysuberic acid GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysuberic acid GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysuberic acid GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysuberic acid GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysuberic acid GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysuberic acid GC-MS (TBDMS_2_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysuberic acid GC-MS (TBDMS_2_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxysuberic 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-Hydroxysuberic acid Quattro_QQQ 10V, Positive-QTOF (Annotated)splash10-052r-0900000000-c8110c0a94d4b56b34cb2012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 3-Hydroxysuberic acid Quattro_QQQ 25V, Positive-QTOF (Annotated)splash10-053r-9300000000-4f9255a9b03fdc58054e2012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 3-Hydroxysuberic acid Quattro_QQQ 40V, Positive-QTOF (Annotated)splash10-00pi-9000000000-cc672b33ccef862ae95b2012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 3-Hydroxysuberic acid 6V, Positive-QTOFsplash10-004i-1900000000-a0b84d8dc173f05ecfd52021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 3-Hydroxysuberic acid 6V, Negative-QTOFsplash10-004i-1900000000-8cf7ff12fa71e34040a62021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxysuberic acid 10V, Positive-QTOFsplash10-05fr-0900000000-61e1c6b1517c58dc07952017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxysuberic acid 20V, Positive-QTOFsplash10-076r-1900000000-ad988528de191a2d13dc2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxysuberic acid 40V, Positive-QTOFsplash10-0bvu-9300000000-60e11695eca6da0261242017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxysuberic acid 10V, Negative-QTOFsplash10-0079-0900000000-991a42c3d23f65a313062017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxysuberic acid 20V, Negative-QTOFsplash10-00g1-0900000000-e1fb76486e14d8491dde2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxysuberic acid 40V, Negative-QTOFsplash10-0a6u-9500000000-9846767c99c61860ada32017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxysuberic acid 10V, Negative-QTOFsplash10-00g0-0900000000-a3fda362228faa530ae12021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxysuberic acid 20V, Negative-QTOFsplash10-004i-3900000000-c74f29ced60b12eaaa942021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxysuberic acid 40V, Negative-QTOFsplash10-0a4i-9100000000-14e61d30d5ca51ba50b72021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxysuberic acid 10V, Positive-QTOFsplash10-001r-5900000000-39bf66242dafebd878292021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxysuberic acid 20V, Positive-QTOFsplash10-05fr-9200000000-b4ff1b0586d3b7059d942021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxysuberic acid 40V, Positive-QTOFsplash10-0a4l-9000000000-6433a1c93128c79da3222021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Experimental 1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)2012-12-04Wishart LabView Spectrum
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 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)2012-12-05Wishart 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
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
UrineDetected and Quantified0.1 umol/mmol creatinineInfant (0-1 year old)BothNormal details
UrineDetected and Quantified2.7 umol/mmol creatinineChildren (1-13 years old)Both
Normal
details
UrineDetected and Quantified5.5 (2.0-28.1) umol/mmol creatinineNewborn (0-30 days old)BothNormal details
UrineDetected and Quantified2.0 (0.8-5.6) umol/mmol creatinineChildren (1-13 years old)Both
Normal
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB021951
KNApSAcK IDNot Available
Chemspider ID13498677
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5314
PubChem Compound22328017
PDB IDNot Available
ChEBI ID70766
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceChiruta, Chandramouli; Jachak, Santosh; Clive, Derrick L. J. A convenient general method for the synthesis of hydroxy diacids. Tetrahedron Letters (2007), 48(18), 3141-3143.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]
  2. Tserng KY, Jin SJ: Metabolic origin of urinary 3-hydroxy dicarboxylic acids. Biochemistry. 1991 Mar 5;30(9):2508-14. [PubMed:2001377 ]
  3. Verhaeghe BJ, Van Bocxlaer JF, De Leenheer AP: Gas chromatographic/mass spectrometric identification of 3-hydroxydicarboxylic acids in urine. Biol Mass Spectrom. 1992 Jan;21(1):27-32. [PubMed:1591279 ]