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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2008-09-15 09:55:03 UTC

Update Date

2023-02-21 17:17:24 UTC

HMDB ID

HMDB0010207

Secondary Accession Numbers

HMDB10207

Metabolite Identification

Common Name

L-Rhamnulose

Description

L-Rhamnulose (CAS: 14807-05-7), also known as 6-deoxy-L-fructose, is a breakdown product of L-rhamnose, which is ubiquitous and particularly abundant in some plants, such as buckthorn. Rhamnose is also one of the sugars regularly used to conduct the dual sugar permeability test. Rhamnose is fermented by some colonic bacteria into L-rhamnulose. Three bacterial (gut microflora) enzymes are involved in rhamnose degradation including rhaB (rhamnulose kinase), rhaA (rhamnose isomerase), and rhaD (rhamnulose-1-phosphate aldolase). L-Rhamnulose kinase catalyzes the transfer of the gamma-phosphate group from ATP to the 1-hydroxyl group of L-rhamnulose. L-Rhamnulose has been found in Escherichia (PMID: 4975916 ).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
6-Deoxy-L-arabino-hex-2-ulose	HMDB
6-Deoxy-L-fructose	HMDB
6-Deoxy-beta-D-fructofuranose	HMDB
6-Deoxy-β-D-fructofuranose	HMDB
L-Rhamnulose	HMDB

Chemical Formula

C₆H₁₂O₅

Average Molecular Weight

164.157

Monoisotopic Molecular Weight

164.068473486

IUPAC Name

(2R,3S,4S,5R)-2-(hydroxymethyl)-5-methyloxolane-2,3,4-triol

Traditional Name

(2R,3S,4S,5R)-2-(hydroxymethyl)-5-methyloxolane-2,3,4-triol

CAS Registry Number

470-21-3

SMILES

C[C@H]1O[C@](O)(CO)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C6H12O5/c1-3-4(8)5(9)6(10,2-7)11-3/h3-5,7-10H,2H2,1H3/t3-,4-,5+,6-/m1/s1

InChI Key

CJJCPDZKQKUXSS-ARQDHWQXSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

Alternative Parents

Substituents

Pentose monosaccharide
Oxolane
Secondary alcohol
Hemiacetal
1,2-diol
Oxacycle
Organoheterocyclic compound
Polyol
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 18953024)

Cellular substructure

Cytoplasm (HMDB: HMDB0010207)
Cell membrane (HMDB: HMDB0010207)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0010207)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0010207)

Source

Endogenous

Endogenous (HMDB: HMDB0010207)

Animal

Animal (HMDB: HMDB0010207)

Microbe

Microbe (HMDB: HMDB0010207)
Escherichia coli (HMDB: HMDB0010207)

Exogenous

Food

Food (HMDB: HMDB0010207)

Animal origin

Poultry

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Exogenous (HMDB: HMDB0010207)

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid Peroxidation (HMDB: HMDB0010207)

Biochemical pathway

Metabolic pathway

Fatty Acid Metabolism (HMDB: HMDB0010207)

Lipid metabolism pathway (HMDB: HMDB0010207)

Biochemical process

Lipid transport (HMDB: HMDB0010207)

Role

Biological role

Energy source (HMDB: HMDB0010207)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	388 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-1.7	ChemAxon
logS	0.85	ALOGPS
pKa (Strongest Acidic)	10.29	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	90.15 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	34.82 m³·mol⁻¹	ChemAxon
Polarizability	15.31 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	135.146	30932474
DeepCCS	[M-H]-	132.877	30932474
DeepCCS	[M-2H]-	167.445	30932474
DeepCCS	[M+Na]+	141.633	30932474

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
L-Rhamnulose	C[C@H]1O[C@](O)(CO)[C@@H](O)[C@@H]1O	3147.3	Standard polar	33892256
L-Rhamnulose	C[C@H]1O[C@](O)(CO)[C@@H](O)[C@@H]1O	1466.0	Standard non polar	33892256
L-Rhamnulose	C[C@H]1O[C@](O)(CO)[C@@H](O)[C@@H]1O	1446.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
L-Rhamnulose,1TMS,isomer #1	C[C@H]1O[C@@](CO)(O[Si](C)(C)C)[C@@H](O)[C@@H]1O	1510.6	Semi standard non polar	33892256
L-Rhamnulose,1TMS,isomer #2	C[C@H]1O[C@](O)(CO[Si](C)(C)C)[C@@H](O)[C@@H]1O	1457.6	Semi standard non polar	33892256
L-Rhamnulose,1TMS,isomer #3	C[C@H]1O[C@](O)(CO)[C@@H](O[Si](C)(C)C)[C@@H]1O	1486.6	Semi standard non polar	33892256
L-Rhamnulose,1TMS,isomer #4	C[C@H]1O[C@](O)(CO)[C@@H](O)[C@@H]1O[Si](C)(C)C	1480.6	Semi standard non polar	33892256
L-Rhamnulose,2TMS,isomer #1	C[C@H]1O[C@@](CO[Si](C)(C)C)(O[Si](C)(C)C)[C@@H](O)[C@@H]1O	1556.1	Semi standard non polar	33892256
L-Rhamnulose,2TMS,isomer #2	C[C@H]1O[C@@](CO)(O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@@H]1O	1553.9	Semi standard non polar	33892256
L-Rhamnulose,2TMS,isomer #3	C[C@H]1O[C@@](CO)(O[Si](C)(C)C)[C@@H](O)[C@@H]1O[Si](C)(C)C	1573.0	Semi standard non polar	33892256
L-Rhamnulose,2TMS,isomer #4	C[C@H]1O[C@](O)(CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@@H]1O	1543.0	Semi standard non polar	33892256
L-Rhamnulose,2TMS,isomer #5	C[C@H]1O[C@](O)(CO[Si](C)(C)C)[C@@H](O)[C@@H]1O[Si](C)(C)C	1550.1	Semi standard non polar	33892256
L-Rhamnulose,2TMS,isomer #6	C[C@H]1O[C@](O)(CO)[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	1540.8	Semi standard non polar	33892256
L-Rhamnulose,3TMS,isomer #1	C[C@H]1O[C@@](CO[Si](C)(C)C)(O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@@H]1O	1598.9	Semi standard non polar	33892256
L-Rhamnulose,3TMS,isomer #2	C[C@H]1O[C@@](CO[Si](C)(C)C)(O[Si](C)(C)C)[C@@H](O)[C@@H]1O[Si](C)(C)C	1620.6	Semi standard non polar	33892256
L-Rhamnulose,3TMS,isomer #3	C[C@H]1O[C@@](CO)(O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	1599.2	Semi standard non polar	33892256
L-Rhamnulose,3TMS,isomer #4	C[C@H]1O[C@](O)(CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	1588.2	Semi standard non polar	33892256
L-Rhamnulose,4TMS,isomer #1	C[C@H]1O[C@@](CO[Si](C)(C)C)(O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	1639.3	Semi standard non polar	33892256
L-Rhamnulose,1TBDMS,isomer #1	C[C@H]1O[C@@](CO)(O[Si](C)(C)C(C)(C)C)[C@@H](O)[C@@H]1O	1729.3	Semi standard non polar	33892256
L-Rhamnulose,1TBDMS,isomer #2	C[C@H]1O[C@](O)(CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@@H]1O	1682.8	Semi standard non polar	33892256
L-Rhamnulose,1TBDMS,isomer #3	C[C@H]1O[C@](O)(CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	1706.8	Semi standard non polar	33892256
L-Rhamnulose,1TBDMS,isomer #4	C[C@H]1O[C@](O)(CO)[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	1699.5	Semi standard non polar	33892256
L-Rhamnulose,2TBDMS,isomer #1	C[C@H]1O[C@@](CO[Si](C)(C)C(C)(C)C)(O[Si](C)(C)C(C)(C)C)[C@@H](O)[C@@H]1O	1990.8	Semi standard non polar	33892256
L-Rhamnulose,2TBDMS,isomer #2	C[C@H]1O[C@@](CO)(O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	2007.7	Semi standard non polar	33892256
L-Rhamnulose,2TBDMS,isomer #3	C[C@H]1O[C@@](CO)(O[Si](C)(C)C(C)(C)C)[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	2018.8	Semi standard non polar	33892256
L-Rhamnulose,2TBDMS,isomer #4	C[C@H]1O[C@](O)(CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	1999.1	Semi standard non polar	33892256
L-Rhamnulose,2TBDMS,isomer #5	C[C@H]1O[C@](O)(CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	1996.5	Semi standard non polar	33892256
L-Rhamnulose,2TBDMS,isomer #6	C[C@H]1O[C@](O)(CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	2000.9	Semi standard non polar	33892256
L-Rhamnulose,3TBDMS,isomer #1	C[C@H]1O[C@@](CO[Si](C)(C)C(C)(C)C)(O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	2275.9	Semi standard non polar	33892256
L-Rhamnulose,3TBDMS,isomer #2	C[C@H]1O[C@@](CO[Si](C)(C)C(C)(C)C)(O[Si](C)(C)C(C)(C)C)[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	2302.2	Semi standard non polar	33892256
L-Rhamnulose,3TBDMS,isomer #3	C[C@H]1O[C@@](CO)(O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	2285.9	Semi standard non polar	33892256
L-Rhamnulose,3TBDMS,isomer #4	C[C@H]1O[C@](O)(CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	2290.0	Semi standard non polar	33892256
L-Rhamnulose,4TBDMS,isomer #1	C[C@H]1O[C@@](CO[Si](C)(C)C(C)(C)C)(O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	2520.7	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - L-Rhamnulose GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-Rhamnulose GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Rhamnulose 10V, Positive-QTOF	splash10-004i-0900000000-c557a6ada681319e4326	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Rhamnulose 20V, Positive-QTOF	splash10-00os-4900000000-7546c548a54ffc75a988	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Rhamnulose 40V, Positive-QTOF	splash10-0a4j-9000000000-356d820473476bdd32b8	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Rhamnulose 10V, Negative-QTOF	splash10-03di-4900000000-3eb1e9a5b306e08a73fc	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Rhamnulose 20V, Negative-QTOF	splash10-052f-9300000000-cc1fa1d93325a6d9590f	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Rhamnulose 40V, Negative-QTOF	splash10-0a4l-9000000000-e52bd33409aa2c7fd52f	2021-09-23	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	0.000437 +/- 0.000028 uM	Adult (>18 years old)	Not Specified	Normal	18953024	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

15559441

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

RML

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Petrich K, Ludwig P, Kuhn H, Schewe T: The suppression of 5-lipoxygenation of arachidonic acid in human polymorphonuclear leucocytes by the 15-lipoxygenase product (15S)-hydroxy-(5Z,8Z,11Z,13E)-eicosatetraenoic acid: structure-activity relationship and mechanism of action. Biochem J. 1996 Mar 15;314 ( Pt 3):911-6. [PubMed:8615788 ]
Haviv F, Ratajczyk JD, DeNet RW, Martin YC, Dyer RD, Carter GW: Structural requirements for the inhibition of 5-lipoxygenase by 15-hydroxyeicosa-5,8,11,13-tetraenoic acid analogues. J Med Chem. 1987 Feb;30(2):254-63. [PubMed:3806609 ]
Chiu TH, Feingold DS: L-rhamnulose 1-phosphate aldolase from Escherichia coli. Crystallization and properties. Biochemistry. 1969 Jan;8(1):98-108. [PubMed:4975916 ]

Showing metabocard for L-Rhamnulose (HMDB0010207)

MOL for HMDB0010207 (L-Rhamnulose)

3D MOL for HMDB0010207 (L-Rhamnulose)

3D SDF for HMDB0010207 (L-Rhamnulose)

3D-SDF for HMDB0010207 (L-Rhamnulose)

PDB for HMDB0010207 (L-Rhamnulose)

3D PDB for HMDB0010207 (L-Rhamnulose)

SMILES for HMDB0010207 (L-Rhamnulose)

INCHI for HMDB0010207 (L-Rhamnulose)

Structure for HMDB0010207 (L-Rhamnulose)

3D Structure for HMDB0010207 (L-Rhamnulose)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra