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Showing metabocard for L-Xylulose (HMDB0000751)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
enzymes (1) Show 1 protein
Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-06-15 17:04:51 UTC
HMDB IDHMDB0000751
Secondary Accession Numbers
  • HMDB0002245
  • HMDB00751
  • HMDB02245
Metabolite Identification
Common NameL-Xylulose
DescriptionL-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. Xylulose is a ketopentose, a monosaccharide containing five carbon atoms, and including a ketone functional group. L-Xylulose accumulates in the urine in patients with pentosuria, due to a deficiency in L-xylulose reductase. L-Xylulose is an extremely weak basic (essentially neutral) compound (based on its pKa). 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. It has the chemical formula C5H10O5. In nature, it occurs in both the L- and D-enantiomers. Since L-xylulose is a reducing sugar like D-glucose, pentosuria patients have been wrongly diagnosed in the past to be diabetic.
Structure
Data?1582752154
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
L-LyxuloseHMDB
L-Threo-pentuloseHMDB
L-Threo-2-pentuloseHMDB
XyluloseHMDB
beta-L-Threo-pentulofuranoseHMDB
beta-L-Threo-2-pentulofuranoseHMDB
Β-L-threo-pentulofuranoseHMDB
Β-L-threo-2-pentulofuranoseHMDB
L-XyluloseHMDB
Chemical FormulaC5H10O5
Average Molecular Weight150.13
Monoisotopic Molecular Weight150.052823422
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 Number1932596-80-9
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 KeyLQXVFWRQNMEDEE-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.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentoses
Alternative Parents
Substituents
  • Pentose monosaccharide
  • Oxolane
  • Secondary alcohol
  • Hemiacetal
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect

Health effect:

Disposition

Source:

Biological location:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility678 g/LALOGPS
logP-2.2ALOGPS
logP-2.1ChemAxon
logS0.94ALOGPS
pKa (Strongest Acidic)10.29ChemAxon
pKa (Strongest Basic)-3.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area90.15 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity30.4 m³·mol⁻¹ChemAxon
Polarizability13.61 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Not Available
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified9.0 +/- 12.0 uMAdult (>18 years old)BothNormal
    • Geigy Scientific ...
 details
Cerebrospinal Fluid (CSF)Detected and Quantified< 5.0 uMChildren (1-13 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified0.0-0.5 umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified5.0 (0.0-10.0) uMAdult (>18 years old)BothRibose-5-phosphate isomerase deficiency details
Cerebrospinal Fluid (CSF)Detected and Quantified254.0 (88.0-166.0) uMAdult (>18 years old)BothLeukoencephalopathy and peripheral neuropathy details
Associated Disorders and Diseases
Disease References
Ribose-5-phosphate isomerase deficiency
  1. 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
  1. 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)
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022223
KNApSAcK IDNot Available
Chemspider ID61612021
KEGG Compound IDC00312
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkXylulose
METLIN IDNot Available
PubChem Compound89810215
PDB IDNot Available
ChEBI ID17399
Food Biomarker OntologyNot Available
VMH IDXYLU_L
MarkerDB ID
References
Synthesis ReferenceAshwell, 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
  1. 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 + NADPHdetails
D-Xylitol + NADP → L-Xylulose + NADPH + Hydrogen Iondetails