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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-20 22:13:13 UTC
Update Date2020-06-15 17:04:52 UTC
HMDB IDHMDB0001644
Secondary Accession Numbers
  • HMDB0000654
  • HMDB00654
  • HMDB01644
Metabolite Identification
Common NameD-Xylulose
DescriptionD-Xylulose (CAS: 551-84-8) is a monosaccharide containing five carbon atoms. D-Xylulose is converted from xylitol by the enzyme NAD+-linked xylitol dehydrogenase (EC 1.1.1.9) in the glucuronate pathway, the most important xylitol-handling metabolic pathway in mammals. This activity has been described in human erythrocytes. Most likely, D-xylulose (as well as D-arabinose or D-ribulose) is a precursor of the pentiol D-arabitol, since pentitols are derived from their corresponding pentose phosphate precursors via pentoses. This pathway can play a role in inherited metabolic disorders underlying the accumulation of pentitols (e.g. ribose 5-phosphate isomerase deficiency and transaldolase deficiency). Although pentitols are present in all living organisms, knowledge concerning their metabolism is limited (PMID: 15234337 , Mol Genet Metab. 2004 Jul;82(3):231-7.).
Structure
Data?1583262951
Synonyms
ValueSource
b-D-XylulofuranoseGenerator, HMDB
β-D-XylulofuranoseGenerator, HMDB
D-LyxuloseHMDB
D-XyluloseHMDB
D-threo-2-PentuloseHMDB
D-threo-PentuloseHMDB
XyluloseHMDB
beta-D-threo-2-PentulofuranoseHMDB
beta-D-threo-PentulofuranoseHMDB
β-D-threo-2-PentulofuranoseHMDB
β-D-threo-PentulofuranoseHMDB
Chemical FormulaC5H10O5
Average Molecular Weight150.1299
Monoisotopic Molecular Weight150.05282343
IUPAC Name(2R,3S,4R)-2-(hydroxymethyl)oxolane-2,3,4-triol
Traditional Name(2R,3S,4R)-2-(hydroxymethyl)oxolane-2,3,4-triol
CAS Registry Number20750-28-1
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-/m1/s1
InChI KeyLQXVFWRQNMEDEE-MROZADKFSA-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

Route of exposure:

Source:

Biological location:

Physical Properties
StateLiquid
Experimental Properties
PropertyValueReference
Melting Point15 °CNot 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
Polarizability13.55 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Not Available
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Urine
Tissue Locations
  • Fibroblasts
  • Placenta
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified2.5 (0.0-5.0) uMAdolescent (13-18 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified0.0 - 5.0 uMAdolescent (13-18 years old)BothNormal details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
UrineDetected and Quantified19.7 (6.4-32.6) umol/mmol creatinineAdult (>18 years old)Both
Normal
details
UrineDetected and Quantified<11 umol/mmol creatinineChildren (1 - 13 years old)BothNormal details
UrineDetected and Quantified0.0 - 5.0 umol/mmol creatinineAdolescent (13-18 years old)BothNormal details
UrineDetected but not Quantified Adult (>18 years old)Both
Normal
details
UrineDetected but not Quantified Adult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified7.5 (5.0-10.0) uMAdolescent (13-18 years old)BothRibose-5-phosphate isomerase deficiency details
Cerebrospinal Fluid (CSF)Detected and Quantified88 - 166 uMAdolescent (13-18 years old)BothRibose-5-Phosphate Isomerase Deficiency details
FecesDetected but not Quantified Adult (>18 years old)Both
Colorectal cancer
details
UrineDetected and Quantified39 - 52 umol/mmol creatinineAdolescent (13-18 years old)BothRibose-5-Phosphate Isomerase Deficiency details
UrineDetected but not Quantified Adult (>18 years old)Both
Bladder cancer
details
UrineDetected and Quantified444.0599-2220.299 umol/mmol creatinineChildren (1 - 13 years old)BothPentosuria
    • PENTOSURIA IN CHI...
details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
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 ]
Pentosuria
  1. G.Frauendienst-Egger, Friedrich K. Trefz (2017). MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de). METAGENE consortium.
  2. Alfered E. Fischer, Miriam Reiner (1930). PENTOSURIA IN CHILDRENWITH LABORATORY DATA ON FOUR CASES. Am J Dis Child. 1930;40(6):1193–1207. doi:10.1001/archpedi.1930.01940060033003. Am J Dis Child.
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022698
KNApSAcK IDC00019684
Chemspider ID25059226
KEGG Compound IDC00310
BioCyc IDD-XYLULOSE
BiGG IDNot Available
Wikipedia LinkXylulose
METLIN IDNot Available
PubChem Compound12358757
PDB IDXLF
ChEBI ID17140
Food Biomarker OntologyNot Available
VMH IDXYLU_D
References
Synthesis ReferenceTakeuchi, Sonoko; Tonouchi, Naoto; Yokozeki, Kenzo. Production of xylitol or D-xylulose by fermentation of glucose with Gluconobacter, Acetobacter, and Frateuria. Eur. Pat. Appl. (2000), 10 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Huck JH, Roos B, Jakobs C, van der Knaap MS, Verhoeven NM: Evaluation of pentitol metabolism in mammalian tissues provides new insight into disorders of human sugar metabolism. Mol Genet Metab. 2004 Jul;82(3):231-7. [PubMed:15234337 ]
  2. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Enzymes

General function:
Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:
Not Available
Gene Name:
XYLB
Uniprot ID:
O75191
Molecular weight:
58381.695
Reactions
Adenosine triphosphate + D-Xylulose → ADP + Xylulose 5-phosphatedetails