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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 06:56:22 UTC
Update Date2021-09-24 06:56:22 UTC
HMDB IDHMDB0304074
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-keto-3-deoxy-L-rhamnonate
Description2-keto-3-deoxy-l-rhamnonate, also known as kdr or 2-dehydro-3,6-dideoxy-L-mannonate, belongs to medium-chain keto acids and derivatives class of compounds. Those are keto acids with a 6 to 12 carbon atoms long side chain. 2-keto-3-deoxy-l-rhamnonate is soluble (in water) and a weakly acidic compound (based on its pKa). 2-keto-3-deoxy-l-rhamnonate can be found in a number of food items such as red beetroot, evergreen huckleberry, winter squash, and pepper (c. pubescens), which makes 2-keto-3-deoxy-l-rhamnonate a potential biomarker for the consumption of these food products.
Structure
Thumb
Synonyms
ValueSource
2-Dehydro-3-deoxy-L-rhamnonate anionChEBI
2-Dehydro-3-deoxy-L-rhamnonate(1-)ChEBI
2-Dehydro-3-deoxy-L-rhamnonic acid anionGenerator
2-Dehydro-3-deoxy-L-rhamnonic acid(1-)Generator
2-Dehydro-3-deoxy-L-rhamnonic acidGenerator
2-Keto-3-deoxy-L-rhamnonic acidGenerator
Chemical FormulaC6H9O5
Average Molecular Weight161.134
Monoisotopic Molecular Weight161.04554697
IUPAC Name(4R,5S)-4,5-dihydroxy-2-oxohexanoate
Traditional Name2-dehydro-3-deoxy-L-rhamnonate
CAS Registry NumberNot Available
SMILES
[H][C@@](C)(O)[C@]([H])(O)CC(=O)C([O-])=O
InChI Identifier
InChI=1S/C6H10O5/c1-3(7)4(8)2-5(9)6(10)11/h3-4,7-8H,2H2,1H3,(H,10,11)/p-1/t3-,4+/m0/s1
InChI KeyFRIWJYNKZPJVRL-IUYQGCFVSA-M
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain keto acids and derivatives. These are keto acids with a 6 to 12 carbon atoms long side chain.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassKeto acids and derivatives
Sub ClassMedium-chain keto acids and derivatives
Direct ParentMedium-chain keto acids and derivatives
Alternative Parents
Substituents
  • Medium-chain keto acid
  • Alpha-keto acid
  • Beta-hydroxy ketone
  • 1,2-diol
  • Ketone
  • Secondary alcohol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Alcohol
  • Carbonyl group
  • Organic oxide
  • Organic oxygen compound
  • Organooxygen compound
  • Organic anion
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
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-1.2ALOGPS
logP-0.73ChemAxon
logS0.35ALOGPS
pKa (Strongest Acidic)3.06ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area97.66 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity45.61 m³·mol⁻¹ChemAxon
Polarizability14.18 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
AllCCS[M+H]+136.79732859911
AllCCS[M+H-H2O]+132.80832859911
AllCCS[M+Na]+141.58332859911
AllCCS[M+NH4]+140.51232859911
AllCCS[M-H]-126.68532859911
AllCCS[M+Na-2H]-128.38632859911
AllCCS[M+HCOO]-130.31232859911
DeepCCS[M+H]+134.01930932474
DeepCCS[M-H]-131.62330932474
DeepCCS[M-2H]-165.55630932474
DeepCCS[M+Na]+140.19130932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-keto-3-deoxy-L-rhamnonate,3TMS,isomer #1C[C@H](O[Si](C)(C)C)[C@@H](C=C(O[Si](C)(C)C)C(=O)[O-])O[Si](C)(C)C1603.7Semi standard non polar33892256
2-keto-3-deoxy-L-rhamnonate,3TMS,isomer #1C[C@H](O[Si](C)(C)C)[C@@H](C=C(O[Si](C)(C)C)C(=O)[O-])O[Si](C)(C)C1569.1Standard non polar33892256
2-keto-3-deoxy-L-rhamnonate,3TMS,isomer #1C[C@H](O[Si](C)(C)C)[C@@H](C=C(O[Si](C)(C)C)C(=O)[O-])O[Si](C)(C)C1617.9Standard polar33892256
2-keto-3-deoxy-L-rhamnonate,3TBDMS,isomer #1C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](C=C(O[Si](C)(C)C(C)(C)C)C(=O)[O-])O[Si](C)(C)C(C)(C)C2267.6Semi standard non polar33892256
2-keto-3-deoxy-L-rhamnonate,3TBDMS,isomer #1C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](C=C(O[Si](C)(C)C(C)(C)C)C(=O)[O-])O[Si](C)(C)C(C)(C)C2197.1Standard non polar33892256
2-keto-3-deoxy-L-rhamnonate,3TBDMS,isomer #1C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](C=C(O[Si](C)(C)C(C)(C)C)C(=O)[O-])O[Si](C)(C)C(C)(C)C2007.6Standard polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-keto-3-deoxy-L-rhamnonate 10V, Negative-QTOFsplash10-0006-4900000000-f5de63a8818661bad9e02019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-keto-3-deoxy-L-rhamnonate 20V, Negative-QTOFsplash10-00y0-9200000000-4bdcb6f3f08609462c2d2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-keto-3-deoxy-L-rhamnonate 40V, Negative-QTOFsplash10-00dl-9000000000-7efc926d60d895e310572019-02-23Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030341
KNApSAcK IDNot Available
Chemspider ID26331139
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID58371
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 ReferencesNot Available