Hmdb loader
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:54:18 UTC
Update Date2021-10-01 18:49:51 UTC
HMDB IDHMDB0245856
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-Deoxyglucosone
Description3-Deoxyglucosone belongs to the class of organic compounds known as fatty alcohols. These are aliphatic alcohols consisting of a chain of a least six carbon atoms. Based on a literature review a significant number of articles have been published on 3-Deoxyglucosone. This compound has been identified in human blood as reported by (PMID: 31557052 ). 3-deoxyglucosone is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 3-Deoxyglucosone is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
Thumb
SynonymsNot Available
Chemical FormulaC6H10O5
Average Molecular Weight162.141
Monoisotopic Molecular Weight162.052823422
IUPAC Name4,5,6-trihydroxy-2-oxohexanal
Traditional Name3-deoxyglucosone
CAS Registry NumberNot Available
SMILES
OCC(O)C(O)CC(=O)C=O
InChI Identifier
InChI=1S/C6H10O5/c7-2-4(9)1-5(10)6(11)3-8/h2,5-6,8,10-11H,1,3H2
InChI KeyZGCHLOWZNKRZSN-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as fatty alcohols. These are aliphatic alcohols consisting of a chain of a least six carbon atoms.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty alcohols
Direct ParentFatty alcohols
Alternative Parents
Substituents
  • Fatty alcohol
  • Medium-chain aldehyde
  • Beta-hydroxy ketone
  • Alpha-ketoaldehyde
  • 1,2-diol
  • Ketone
  • Secondary alcohol
  • Polyol
  • Aldehyde
  • Alcohol
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic oxide
  • Organic oxygen compound
  • Organooxygen compound
  • Primary alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect
Disposition
ProcessNot Available
Role
Physical Properties
StateNot Available
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
logP-1.6ALOGPS
logP-1.6ChemAxon
logS0.26ALOGPS
pKa (Strongest Acidic)10.46ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area94.83 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity35.38 m³·mol⁻¹ChemAxon
Polarizability14.63 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+133.93830932474
DeepCCS[M-H]-130.23130932474
DeepCCS[M-2H]-167.8130932474
DeepCCS[M+Na]+143.05930932474
AllCCS[M+H]+137.332859911
AllCCS[M+H-H2O]+133.432859911
AllCCS[M+NH4]+141.032859911
AllCCS[M+Na]+142.032859911
AllCCS[M-H]-131.032859911
AllCCS[M+Na-2H]-132.832859911
AllCCS[M+HCOO]-134.832859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20229.1791 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.0 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid721.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid294.2 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid53.8 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid173.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid50.7 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid255.4 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid245.9 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)459.2 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid570.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid48.5 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid797.3 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid178.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid177.5 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate559.0 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA292.6 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water287.6 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-DeoxyglucosoneOCC(O)C(O)CC(=O)C=O2947.9Standard polar33892256
3-DeoxyglucosoneOCC(O)C(O)CC(=O)C=O1416.5Standard non polar33892256
3-DeoxyglucosoneOCC(O)C(O)CC(=O)C=O1542.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3-Deoxyglucosone,4TMS,isomer #1C[Si](C)(C)OCC(O[Si](C)(C)C)C(C=C(C=O)O[Si](C)(C)C)O[Si](C)(C)C1868.2Semi standard non polar33892256
3-Deoxyglucosone,4TMS,isomer #1C[Si](C)(C)OCC(O[Si](C)(C)C)C(C=C(C=O)O[Si](C)(C)C)O[Si](C)(C)C1766.7Standard non polar33892256
3-Deoxyglucosone,4TMS,isomer #1C[Si](C)(C)OCC(O[Si](C)(C)C)C(C=C(C=O)O[Si](C)(C)C)O[Si](C)(C)C1716.5Standard polar33892256
3-Deoxyglucosone,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC(O[Si](C)(C)C(C)(C)C)C(C=C(C=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2765.7Semi standard non polar33892256
3-Deoxyglucosone,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC(O[Si](C)(C)C(C)(C)C)C(C=C(C=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2477.6Standard non polar33892256
3-Deoxyglucosone,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC(O[Si](C)(C)C(C)(C)C)C(C=C(C=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2193.8Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (Non-derivatized) - 70eV, Positivesplash10-0nmi-9400000000-9d62ca57cbbe910b72e02021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TMS_1_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TMS_2_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TMS_2_5) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TMS_2_6) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TMS_3_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TMS_3_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TMS_3_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TMS_3_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TBDMS_1_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TBDMS_2_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TBDMS_2_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TBDMS_2_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxyglucosone GC-MS (TBDMS_2_5) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Deoxyglucosone 10V, Positive-QTOFsplash10-004i-4900000000-31f51d6502205058d1052021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Deoxyglucosone 20V, Positive-QTOFsplash10-00g0-9400000000-3f30de686f245cbbe28d2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Deoxyglucosone 40V, Positive-QTOFsplash10-052f-9000000000-20f6d2049d9f87b606922021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Deoxyglucosone 10V, Negative-QTOFsplash10-029x-2900000000-878cfb225e7b8a57ad652021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Deoxyglucosone 20V, Negative-QTOFsplash10-05fu-9100000000-d8c27511c192cd6b304f2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Deoxyglucosone 40V, Negative-QTOFsplash10-0006-9000000000-f9d8541250d8b6b5c5752021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID10784988
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link3-Deoxyglucosone
METLIN IDNot Available
PubChem Compound15120156
PDB IDNot Available
ChEBI IDNot Available
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. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Enzymes

General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the NADPH-dependent reduction of a variety of aromatic and aliphatic aldehydes to their corresponding alcohols. Catalyzes the reduction of mevaldate to mevalonic acid and of glyceraldehyde to glycerol. Has broad substrate specificity. In vitro substrates include succinic semialdehyde, 4-nitrobenzaldehyde, 1,2-naphthoquinone, methylglyoxal, and D-glucuronic acid. Plays a role in the activation of procarcinogens, such as polycyclic aromatic hydrocarbon trans-dihydrodiols, and in the metabolism of various xenobiotics and drugs, including the anthracyclines doxorubicin (DOX) and daunorubicin (DAUN).
Gene Name:
AKR1A1
Uniprot ID:
P14550
Molecular weight:
36572.71
General function:
Not Available
Specific function:
Catalyzes the NADPH-dependent reduction of a wide variety of carbonyl-containing compounds to their corresponding alcohols. Displays enzymatic activity towards endogenous metabolites such as aromatic and aliphatic aldehydes, ketones, monosaccharides and bile acids, with a preference for negatively charged substrates, such as glucuronate and succinic semialdehyde (By similarity). Plays an important role in ascorbic acid biosynthesis by catalyzing the reduction of D-glucuronic acid and D-glucurono-gamma-lactone (By similarity). Functions as a detoxifiying enzyme by reducing a range of toxic aldehydes. Reduces methylglyoxal and 3-deoxyglucosone, which are present at elevated levels under hyperglycemic conditions and are cytotoxic. Involved also in the detoxification of lipid-derived aldehydes like acrolein (By similarity). Plays a role in the activation of procarcinogens, such as polycyclic aromatic hydrocarbon trans-dihydrodiols, and in the metabolism of various xenobiotics and drugs (By similarity). Displays no reductase activity towards retinoids (PubMed:12732097).
Gene Name:
AKR1A1
Uniprot ID:
P50578
Molecular weight:
36581.71