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Record Information
Version4.0
Creation Date2005-11-16 15:48:42 UTC
Update Date2017-09-27 06:51:41 UTC
HMDB IDHMDB0000098
Secondary Accession Numbers
  • HMDB00098
  • HMDB03763
Metabolite Identification
Common NameD-Xylose
DescriptionXylose or wood sugar is an aldopentose - a monosaccharide containing five carbon atoms and an aldehyde functional group. It has chemical formula C5H10O5 and is 40% as sweet as sucrose. Xylose is found in the embryos of most edible plants. The polysaccharide xylan, which is closely associated with cellulose, consists practically entirely of d-xylose. Corncobs, cottonseed hulls, pecan shells, and straw contain considerable amounts of this sugar. Xylose is also found in mucopolysaccharides of connective tissue and sometimes in the urine. Xylose is the first sugar added to serine or threonine residues during proteoglycan type O-glycosylation. Therefore xylose is involved in the biosythetic pathways of most anionic polysaccharides such as heparan sulphate and chondroitin sulphate. In medicine, xylose is used to test for malabsorption by administering a xylose solution to the patient after fasting. If xylose is detected in the blood and/or urine within the next few hours, it has been absorbed by the intestines. Xylose is said to be one of eight sugars which are essential for human nutrition, the others being galactose, glucose, mannose, N-acetylglucosamine, N-acetylgalactosamine, fucose, and sialic acid. (Wikipedia). Xylose in the urine is a biomarker for the consumption of apples and other fruits.
Structure
Thumb
Synonyms
ValueSource
(3R,4S,5R)-tetrahydro-2H-Pyran-2,3,4,5-tetrolChEBI
D-(+)-XyloseChEBI
D-XylopentoseChEBI
Wood sugarChEBI
D-xylo-PentoseHMDB
xylo-PfanHMDB
XylomedHMDB
XyloseHMDB
XylosideHMDB
XylopyranoseMeSH
D XyloseMeSH
D-XylopyranoseMeSH
Chemical FormulaC5H10O5
Average Molecular Weight150.1299
Monoisotopic Molecular Weight150.05282343
IUPAC Name(3R,4S,5R)-oxane-2,3,4,5-tetrol
Traditional Named-xylose
CAS Registry Number58-86-6
SMILES
O[C@@H]1COC(O)[C@H](O)[C@H]1O
InChI Identifier
InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3+,4-,5?/m1/s1
InChI KeySRBFZHDQGSBBOR-IOVATXLUSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
KingdomChemical entities
Super ClassOrganic compounds
ClassOrganic oxygen compounds
Sub ClassOrganooxygen compounds
Direct ParentPentoses
Alternative Parents
Substituents
  • Pentose monosaccharide
  • Oxane
  • Secondary alcohol
  • Hemiacetal
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Hydrocarbon derivative
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect

Health effect:

  Health condition:

    Cancer:

Disposition

Biological Location:

  Subcellular:

  Biofluid and excreta:

  Organ and components:

Source:

Process

Naturally occurring process:

  Biological process:

    Biochemical pathway:

Role

Indirect biological role:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point90.5 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility555 mg/mLNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility1220 g/LALOGPS
logP-2.6ALOGPS
logP-2.3ChemAxon
logS0.91ALOGPS
pKa (Strongest Acidic)11.31ChemAxon
pKa (Strongest Basic)-3.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area90.15 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity29.96 m³·mol⁻¹ChemAxon
Polarizability13.44 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MSNot Available
Predicted GC-MSPredicted GC-MS Spectrum - GC-MSNot Available
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0udi-2900000000-5a95e26ce7a03eeb4a1cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-00kr-9200000000-ffce45222cab00a0c302View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0udr-5900000000-8d1e329345725c7495d0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR13C NMR SpectrumNot Available
2D NMR[1H,1H] 2D NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Lysosome
Biofluid Locations
  • Blood
  • Feces
  • Saliva
  • Urine
Tissue Location
  • Erythrocyte
  • Small Intestine
PathwaysNot Available
NameSMPDB/PathwhizKEGG
No entries found
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified3088.7 +/- 527.9 uMAdult (>18 years old)Not Specified
Normal
details
BloodDetected and Quantified1797.5 +/- 328.2 uMAdult (>18 years old)Not Specified
Normal
details
BloodDetected and Quantified1797.33 (1458.74 - 2357.96) uMNot AvailableNot Available
Normal
details
FecesDetected but not Quantified Infant (0-1 year old)Both
Normal
details
FecesDetected but not Quantified Not SpecifiedNot Specified
Normal
details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
SalivaDetected but not Quantified Adult (>18 years old)Both
Normal
    • Zerihun T. Dame, ...
details
SalivaDetected but not Quantified Adult (>18 years old)Male
Normal
details
SalivaDetected but not Quantified Adult (>18 years old)Male
Normal
details
SalivaDetected but not Quantified Adult (>18 years old)Male
Normal
details
SalivaDetected but not Quantified Adult (>18 years old)Male
Normal
details
SalivaDetected but not Quantified Adult (>18 years old)Male
Normal
details
SalivaDetected but not Quantified Adult (>18 years old)Male
Normal
details
SalivaDetected but not Quantified Adult (>18 years old)Male
Normal
details
SalivaDetected but not Quantified Adult (>18 years old)Male
Normal
details
SalivaDetected but not Quantified Adult (>18 years old)Male
Normal
details
SalivaDetected but not Quantified Adult (>18 years old)Male
Normal
details
UrineDetected and Quantified26.7 +/- 23.7 umol/mmol creatinineInfant (0-1 year old)BothNormal details
UrineDetected and Quantified5.26 (4.0-7.0) umol/mmol creatinineAdult (>18 years old)BothNormal
    • Geigy Scientific ...
details
UrineDetected but not Quantified Adult (>18 years old)BothNormal details
UrineDetected and Quantified20.1 (2.9-102) umol/mmol creatinineAdult (>18 years old)Both
Normal
details
UrineDetected and Quantified51.19 umol/mmol creatinineAdult (>18 years old)Male
Normal
    • Shaykhutdinov RA,...
details
UrineDetected but not Quantified Adult (>18 years old)Both
Normal
details
UrineDetected and Quantified22.674 +/- 14.809 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal
    • Mordechai, Hien, ...
details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified652.8 +/- 273.1 uMAdult (>18 years old)Not Specified
Small intestinal malabsorption, HIV, & diarrhea
details
BloodDetected and Quantified2911.1 +/- 752.4 uMAdult (>18 years old)Not Specified
Kidney disease
details
BloodDetected and Quantified519.6 +/- 213.2 uMAdult (>18 years old)Not Specified
Small intestinal malabsorption, HIV, & diarrhea
details
BloodDetected and Quantified399.8 +/- 139.9 uMAdult (>18 years old)Not Specified
Small intestinal malabsorption, scleroderma, & bacterial overgrowth
details
BloodDetected and Quantified886.0 +/- 18.8 uMAdult (>18 years old)Not Specified
Small intestinal malabsorption, scleroderma, & bacterial overgrowth
details
BloodDetected and Quantified483.0 +/- 14.1 uMAdult (>18 years old)Not Specified
Small intestinal malabsorption, HIV, & cryptosporidiosis
details
BloodDetected and Quantified799.4 +/- 358.0 uMAdult (>18 years old)Not Specified
Small intestinal malabsorption, HIV, & cryptosporidiosis
details
BloodDetected and Quantified2867.1 +/- 917.0 uMAdult (>18 years old)Not Specified
Kidney disease
details
BloodDetected and Quantified3188.7 +/- 790.1 uMAdult (>18 years old)Not Specified
Small intestinal bacterial overgrowth
details
BloodDetected and Quantified2373.7 +/- 238.0 uMAdult (>18 years old)Not Specified
Small intestinal bacterial overgrowth
details
BloodDetected and Quantified3134.3 +/- 1248.3 uMAdult (>18 years old)Not Specified
Crohn's disease
details
BloodDetected and Quantified2817.8 +/- 904.4 uMAdult (>18 years old)Not Specified
HIV and diarrhea
details
BloodDetected and Quantified2684.6 +/- 913.8 uMAdult (>18 years old)Not Specified
HIV and diarrhea
details
BloodDetected and Quantified2704.3 uMNot AvailableNot Available
Crohn's disease
details
BloodDetected and Quantified1998.3 uMNot AvailableNot Available
Crohn's disease, short bowel
details
BloodDetected and Quantified1432.1 uMNot AvailableNot Available
Crohn's disease, bowel obstruction
details
FecesDetected but not Quantified Not SpecifiedNot Specified
Cryptosporidium infection
details
FecesDetected but not Quantified Adult (>18 years old)BothColorectal Cancer details
UrineDetected and Quantified3.0 (0.0-17.0) umol/mmol creatinineNot SpecifiedBothLung cancer details
UrineDetected and Quantified14.794 +/- 14.096 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Mordechai, Hien, ...
details
Associated Disorders and Diseases
Disease References
AIDS
  1. Ehrenpreis ED, Salvino M, Craig RM: Improving the serum D-xylose test for the identification of patients with small intestinal malabsorption. J Clin Gastroenterol. 2001 Jul;33(1):36-40. [PubMed:11418788 ]
Crohn's disease
  1. Ehrenpreis ED, Salvino M, Craig RM: Improving the serum D-xylose test for the identification of patients with small intestinal malabsorption. J Clin Gastroenterol. 2001 Jul;33(1):36-40. [PubMed:11418788 ]
Kidney disease
  1. Ehrenpreis ED, Salvino M, Craig RM: Improving the serum D-xylose test for the identification of patients with small intestinal malabsorption. J Clin Gastroenterol. 2001 Jul;33(1):36-40. [PubMed:11418788 ]
Lung Cancer
  1. Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S, Mandal R, Sinelnikov I, Xia J, Jia L, Cruz JA, Lim E, Sobsey CA, Shrivastava S, Huang P, Liu P, Fang L, Peng J, Fradette R, Cheng D, Tzur D, Clements M, Lewis A, De Souza A, Zuniga A, Dawe M, Xiong Y, Clive D, Greiner R, Nazyrova A, Shaykhutdinov R, Li L, Vogel HJ, Forsythe I: HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res. 2009 Jan;37(Database issue):D603-10. doi: 10.1093/nar/gkn810. Epub 2008 Oct 25. [PubMed:18953024 ]
Small intestinal malabsorption
  1. Ehrenpreis ED, Salvino M, Craig RM: Improving the serum D-xylose test for the identification of patients with small intestinal malabsorption. J Clin Gastroenterol. 2001 Jul;33(1):36-40. [PubMed:11418788 ]
Small bowel bacterial overgrowth syndrome
  1. Ehrenpreis ED, Salvino M, Craig RM: Improving the serum D-xylose test for the identification of patients with small intestinal malabsorption. J Clin Gastroenterol. 2001 Jul;33(1):36-40. [PubMed:11418788 ]
Associated OMIM IDs
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB001136
KNApSAcK IDC00007290
Chemspider ID119104
KEGG Compound IDC00181
BioCyc IDXYLOSE
BiGG ID34162
Wikipedia Link Wood sugar
METLIN ID314
PubChem Compound135191
PDB IDNot Available
ChEBI ID53455
References
Synthesis ReferenceLavarack, B. P.; Griffin, G.; Rodman, D. Optimizing the autohydrolysis of bagasse to extract D-xylose. Proceedings of the Conference of the Australian Society of Sugar Cane Technologists (1999), 21st 394-400.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Shoemaker JD, Elliott WH: Automated screening of urine samples for carbohydrates, organic and amino acids after treatment with urease. J Chromatogr. 1991 Jan 2;562(1-2):125-38. [PubMed:2026685 ]
  2. Saliba F, Hagipantelli R, Misset JL, Bastian G, Vassal G, Bonnay M, Herait P, Cote C, Mahjoubi M, Mignard D, Cvitkovic E: Pathophysiology and therapy of irinotecan-induced delayed-onset diarrhea in patients with advanced colorectal cancer: a prospective assessment. J Clin Oncol. 1998 Aug;16(8):2745-51. [PubMed:9704727 ]
  3. Weiner R, Dietze F, Laue R: Age-dependent alterations of intestinal absorption. II. A clinical study using a modified D-xylose absorption test. Arch Gerontol Geriatr. 1984 Jul;3(2):97-108. [PubMed:6548110 ]
  4. Molina JM, Tourneur M, Sarfati C, Chevret S, de Gouvello A, Gobert JG, Balkan S, Derouin F: Fumagillin treatment of intestinal microsporidiosis. N Engl J Med. 2002 Jun 20;346(25):1963-9. [PubMed:12075057 ]
  5. Kost S, Keinert K, Glaser FH: [D-xylose test of resorption as a method to determine radiation side effects in the small intestine]. Strahlenther Onkol. 1998 Sep;174(9):462-7. [PubMed:9765687 ]
  6. Weiner R, Laue R, Dietze F: [Enteral resorption kinetics in the aging process]. Z Gesamte Inn Med. 1986 Mar 1;41(5):152-8. [PubMed:3716508 ]
  7. Ehrenpreis ED, Salvino M, Craig RM: Improving the serum D-xylose test for the identification of patients with small intestinal malabsorption. J Clin Gastroenterol. 2001 Jul;33(1):36-40. [PubMed:11418788 ]
  8. Weiner R: [Characteristics of disease and involution-induced changes in intestinal absorption]. Z Alternsforsch. 1986 Jul-Aug;41(4):219-24. [PubMed:3751145 ]
  9. Weiner R, Laue R, Dietze F, Hartig W: A modified D-xylose absorption test. Infusionsther Klin Ernahr. 1984 Dec;11(6):333-7. [PubMed:6526497 ]
  10. Horvath K, Horn G, Bingadeem H, Nemes Nagy A, Bodanszky H: [The value of the d-xylose loading test in the diagnosis of malabsorption syndromes]. Orv Hetil. 1990 Aug 19;131(33):1803-6, 1809. [PubMed:2204861 ]
  11. Wang SC, You RD: [Clinical and experimental study on treatment of anorexy in children with the activating spleen prescription]. Zhong Xi Yi Jie He Za Zhi. 1991 Feb;11(2):75-8, 67. [PubMed:2060054 ]

Enzymes

General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the NADPH-dependent reduction of a wide variety of carbonyl-containing compounds to their corresponding alcohols with a broad range of catalytic efficiencies.
Gene Name:
AKR1B1
Uniprot ID:
P15121
Molecular weight:
35853.125
Reactions
D-Xylitol + NADP → D-Xylose + NADPH + Hydrogen Iondetails
General function:
Involved in catalytic activity
Specific function:
Not Available
Gene Name:
DHDH
Uniprot ID:
Q9UQ10
Molecular weight:
36381.705
Reactions
D-Xylose + NADP → D-Xylono-1,5-lactone + NADPHdetails
D-Xylose + NADP → D-Xylono-1,5-lactone + NADPH + Hydrogen Iondetails
General function:
Involved in transporter activity
Specific function:
Involved in the sodium-dependent cotransport of myo-inositol (MI) with a Na(+):MI stoichiometry of 2:1. Exclusively responsible for apical MI transport and absorption in intestine. Also can transport D-chiro-inositol (DCI) but not L-fructose. Exhibits stereospecific cotransport of both D-glucose and D-xylose. May induce apoptosis through the TNF-alpha, PDCD1 pathway. May play a role in the regulation of MI concentration in serum, involving reabsorption in at least the proximal tubule of the kidney.
Gene Name:
SLC5A11
Uniprot ID:
Q8WWX8
Molecular weight:
69906.495
General function:
Not Available
Specific function:
Acts as all-trans-retinaldehyde reductase. Can efficiently reduce aliphatic and aromatic aldehydes, and is less active on hexoses (in vitro). May be responsible for detoxification of reactive aldehydes in the digested food before the nutrients are passed on to other organs.
Gene Name:
AKR1B10
Uniprot ID:
O60218
Molecular weight:
Not Available
Reactions
D-Xylitol + NADP → D-Xylose + NADPH + Hydrogen Iondetails
General function:
Not Available
Specific function:
Responsible for the 2-O-phosphorylation of xylose in the glycosaminoglycan-protein linkage region of proteoglycans thereby regulating the amount of mature GAG chains. Sulfated glycosaminoglycans (GAGs), including heparan sulfate and chondroitin sulfate, are synthesized on the so-called common GAG-protein linkage region (GlcUAbeta1-3Galbeta1-3Galbeta1-4Xylbeta1-O-Ser) of core proteins, which is formed by the stepwise addition of monosaccharide residues by the respective specific glycosyltransferases. Xylose 2-o-phosphorylation may influence the catalytic activity of B3GAT3 (GlcAT-I) which completes the precursor tetrasaccharide of GAG-protein linkage regions on which the repeating disaccharide region is synthesized.
Gene Name:
FAM20B
Uniprot ID:
O75063
Molecular weight:
46432.04
Reactions
Adenosine triphosphate + D-Xylose → ADP + D-xylose 2-phosphatedetails