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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (1) Show 1 protein XML

enzymes (1) Show 1 protein

Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2021-09-14 15:45:03 UTC

HMDB ID

HMDB0000751

Secondary Accession Numbers

HMDB0002245
HMDB00751
HMDB02245

Metabolite Identification

Common Name

L-Xylulose

Description

L-Xylulose, also known as L-lyxulose or L-threo-pentulose, belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. L-Xylulose 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 L-xylulose a potential biomarker for the consumption of these foods. L-Xylulose is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. L-Xylulose, with regard to humans, has been found to be associated with the diseases such as leukoencephalopathy; L-xylulose has also been linked to the inborn metabolic disorder ribose-5-phosphate isomerase deficiency. Based on a literature review very few articles have been published on L-Xylulose.

Structure

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

View in JSmol View Stereo Labels

Synonyms

Value	Source
L-Lyxulose	HMDB
L-Threo-pentulose	HMDB
L-Threo-2-pentulose	HMDB
Xylulose	HMDB
beta-L-Threo-pentulofuranose	HMDB
beta-L-Threo-2-pentulofuranose	HMDB
Β-L-threo-pentulofuranose	HMDB
Β-L-threo-2-pentulofuranose	HMDB
L-Xylulose	HMDB

Chemical Formula

C₅H₁₀O₅

Average Molecular Weight

150.13

Monoisotopic Molecular Weight

150.052823422

IUPAC Name

(2S,3R,4S)-2-(hydroxymethyl)oxolane-2,3,4-triol

Traditional Name

(2S,3R,4S)-2-(hydroxymethyl)oxolane-2,3,4-triol

CAS Registry Number

1932596-80-9

SMILES

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

InChI Identifier

InChI=1S/C5H10O5/c6-2-5(9)4(8)3(7)1-10-5/h3-4,6-9H,1-2H2/t3-,4+,5-/m0/s1

InChI Key

LQXVFWRQNMEDEE-LMVFSUKVSA-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
Oxacycle
Organoheterocyclic compound
Polyol
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Disposition

Biological location

Excreta

Cellular substructure

Macromolecular complex

Blood

Cytoplasm

Ingestion

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 Spectral Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	678 g/L	ALOGPS
logP	10^(-2.2) g/L	ALOGPS
logP	10^(-2.1) g/L	ChemAxon
logS	10^(0.94) g/L	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	30.4 m³·mol⁻¹	ChemAxon
Polarizability	13.61 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 Spectral Properties

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
L-Xylulose,1TMS,#1	C[Si](C)(C)OC[C@]1(O)OC[C@H](O)[C@H]1O	1470.7	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,1TMS,#2	C[Si](C)(C)O[C@@]1(CO)OC[C@H](O)[C@H]1O	1512.4	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,1TMS,#3	C[Si](C)(C)O[C@H]1CO[C@@](O)(CO)[C@@H]1O	1488.0	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,1TMS,#4	C[Si](C)(C)O[C@@H]1[C@@H](O)CO[C@@]1(O)CO	1491.9	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,2TMS,#1	C[Si](C)(C)OC[C@]1(O[Si](C)(C)C)OC[C@H](O)[C@H]1O	1543.5	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,2TMS,#2	C[Si](C)(C)OC[C@]1(O)OC[C@H](O[Si](C)(C)C)[C@H]1O	1522.1	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,2TMS,#3	C[Si](C)(C)OC[C@]1(O)OC[C@H](O)[C@H]1O[Si](C)(C)C	1533.5	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,2TMS,#4	C[Si](C)(C)O[C@H]1CO[C@](CO)(O[Si](C)(C)C)[C@@H]1O	1550.1	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,2TMS,#5	C[Si](C)(C)O[C@@H]1[C@@H](O)CO[C@]1(CO)O[Si](C)(C)C	1551.0	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,2TMS,#6	C[Si](C)(C)O[C@H]1CO[C@@](O)(CO)[C@@H]1O[Si](C)(C)C	1523.5	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,3TMS,#1	C[Si](C)(C)OC[C@]1(O[Si](C)(C)C)OC[C@H](O[Si](C)(C)C)[C@H]1O	1594.3	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,3TMS,#2	C[Si](C)(C)OC[C@]1(O[Si](C)(C)C)OC[C@H](O)[C@H]1O[Si](C)(C)C	1591.6	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,3TMS,#3	C[Si](C)(C)OC[C@]1(O)OC[C@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	1569.2	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,3TMS,#4	C[Si](C)(C)O[C@H]1CO[C@](CO)(O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	1576.3	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,4TMS,#1	C[Si](C)(C)OC[C@]1(O[Si](C)(C)C)OC[C@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	1597.8	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,1TBDMS,#1	CC(C)(C)[Si](C)(C)OC[C@]1(O)OC[C@H](O)[C@H]1O	1695.6	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,1TBDMS,#2	CC(C)(C)[Si](C)(C)O[C@@]1(CO)OC[C@H](O)[C@H]1O	1739.3	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,1TBDMS,#3	CC(C)(C)[Si](C)(C)O[C@H]1CO[C@@](O)(CO)[C@@H]1O	1683.0	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,1TBDMS,#4	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](O)CO[C@@]1(O)CO	1707.3	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,2TBDMS,#1	CC(C)(C)[Si](C)(C)OC[C@]1(O[Si](C)(C)C(C)(C)C)OC[C@H](O)[C@H]1O	1978.8	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,2TBDMS,#2	CC(C)(C)[Si](C)(C)OC[C@]1(O)OC[C@H](O[Si](C)(C)C(C)(C)C)[C@H]1O	1957.4	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,2TBDMS,#3	CC(C)(C)[Si](C)(C)OC[C@]1(O)OC[C@H](O)[C@H]1O[Si](C)(C)C(C)(C)C	1980.1	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,2TBDMS,#4	CC(C)(C)[Si](C)(C)O[C@H]1CO[C@](CO)(O[Si](C)(C)C(C)(C)C)[C@@H]1O	2000.0	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,2TBDMS,#5	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](O)CO[C@]1(CO)O[Si](C)(C)C(C)(C)C	2002.1	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,2TBDMS,#6	CC(C)(C)[Si](C)(C)O[C@H]1CO[C@@](O)(CO)[C@@H]1O[Si](C)(C)C(C)(C)C	1966.2	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,3TBDMS,#1	CC(C)(C)[Si](C)(C)OC[C@]1(O[Si](C)(C)C(C)(C)C)OC[C@H](O[Si](C)(C)C(C)(C)C)[C@H]1O	2278.8	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,3TBDMS,#2	CC(C)(C)[Si](C)(C)OC[C@]1(O[Si](C)(C)C(C)(C)C)OC[C@H](O)[C@H]1O[Si](C)(C)C(C)(C)C	2266.1	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,3TBDMS,#3	CC(C)(C)[Si](C)(C)OC[C@]1(O)OC[C@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C	2267.0	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,3TBDMS,#4	CC(C)(C)[Si](C)(C)O[C@H]1CO[C@](CO)(O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	2275.9	Semi standard non polar	https://arxiv.org/abs/1905.12712
L-Xylulose,4TBDMS,#1	CC(C)(C)[Si](C)(C)OC[C@]1(O[Si](C)(C)C(C)(C)C)OC[C@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C	2519.1	Semi standard non polar	https://arxiv.org/abs/1905.12712

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - L-Xylulose GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-Xylulose 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-Xylulose 10V, Positive-QTOF	splash10-001i-2900000000-d014866a9eaa4bcc1c15	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Xylulose 20V, Positive-QTOF	splash10-05fv-9000000000-fac868271cf0145b751c	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Xylulose 40V, Positive-QTOF	splash10-052e-9000000000-3310acb8673d3f763bfa	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Xylulose 10V, Negative-QTOF	splash10-052b-8900000000-6174ea340f73118a4e71	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Xylulose 20V, Negative-QTOF	splash10-056r-9000000000-3155b6a3b975db3bc626	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Xylulose 40V, Negative-QTOF	splash10-052f-9000000000-cc7ea805a3871cd388b5	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm (predicted from logP)

Biospecimen Locations

Blood
Cerebrospinal Fluid (CSF)
Feces
Urine

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	9.0 +/- 12.0 uM	Adult (>18 years old)	Both	Normal	Geigy Scientific ...	details
Cerebrospinal Fluid (CSF)	Detected and Quantified	< 5.0 uM	Children (1-13 years old)	Both	Normal	14988808	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	29808030	details
Urine	Detected and Quantified	0.0-0.5 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	14988808	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	5.0 (0.0-10.0) uM	Adult (>18 years old)	Both	Ribose-5-phosphate isomerase deficiency	14988808	details
Cerebrospinal Fluid (CSF)	Detected and Quantified	254.0 (88.0-166.0) uM	Adult (>18 years old)	Both	Leukoencephalopathy and peripheral neuropathy	14988808	details

Associated Disorders and Diseases

Disease References

Ribose-5-phosphate isomerase deficiency
Huck JH, Verhoeven NM, Struys EA, Salomons GS, Jakobs C, van der Knaap MS: Ribose-5-phosphate isomerase deficiency: new inborn error in the pentose phosphate pathway associated with a slowly progressive leukoencephalopathy. Am J Hum Genet. 2004 Apr;74(4):745-51. Epub 2004 Feb 25. [PubMed:14988808 ]
Leukoencephalopathy
Huck JH, Verhoeven NM, Struys EA, Salomons GS, Jakobs C, van der Knaap MS: Ribose-5-phosphate isomerase deficiency: new inborn error in the pentose phosphate pathway associated with a slowly progressive leukoencephalopathy. Am J Hum Genet. 2004 Apr;74(4):745-51. Epub 2004 Feb 25. [PubMed:14988808 ]

Associated OMIM IDs

608611 (Ribose-5-phosphate isomerase deficiency)

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

Xylulose

METLIN ID

Not Available

PubChem Compound

89810215

PDB ID

Not Available

ChEBI ID

17399

Food Biomarker Ontology

Not Available

VMH ID

XYLU_L

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Ashwell, Gilbert; Kanfer, Julian; Burns, J. J. Mechanism of L-xylulose formation by kidney enzymes. Journal of Biological Chemistry (1959), 234 472-5.

Material Safety Data Sheet (MSDS)

Not Available

General References

Oka H, Suzuki S, Suzuki H, Oda T: Increased urinary excretion of L-xylulose in patients with liver cirrhosis. Clin Chim Acta. 1976 Mar 1;67(2):131-6. [PubMed:1248150 ]

Enzymes

Enzyme Details

1. L-xylulose reductase

General function:: Involved in oxidoreductase activity
Specific function:: Catalyzes the NADPH-dependent reduction of several pentoses, tetroses, trioses, alpha-dicarbonyl compounds and L-xylulose. Participates in the uronate cycle of glucose metabolism. May play a role in the water absorption and cellular osmoregulation in the proximal renal tubules by producing xylitol, an osmolyte, thereby preventing osmolytic stress from occurring in the renal tubules.
Gene Name:: DCXR
Uniprot ID:: Q7Z4W1
Molecular weight:: 25742.665

Reactions

D-Xylitol + NADP → L-Xylulose + NADPH	details
D-Xylitol + NADP → L-Xylulose + NADPH + Hydrogen Ion	details

Showing metabocard for L-Xylulose (HMDB0000751)

MOL for HMDB0000751 (L-Xylulose)

3D MOL for HMDB0000751 (L-Xylulose)

3D SDF for HMDB0000751 (L-Xylulose)

3D-SDF for HMDB0000751 (L-Xylulose)

PDB for HMDB0000751 (L-Xylulose)

3D PDB for HMDB0000751 (L-Xylulose)

SMILES for HMDB0000751 (L-Xylulose)

INCHI for HMDB0000751 (L-Xylulose)

Structure for HMDB0000751 (L-Xylulose)

3D Structure for HMDB0000751 (L-Xylulose)

Predicted Kovats Retention Indices

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

Reactions