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Record Information
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2019-03-20 17:18:21 UTC
Secondary Accession Numbers
  • HMDB0000487
  • HMDB00487
  • HMDB00646
Metabolite Identification
Common NameL-Arabinose
DescriptionL-Arabinose is a pentose with a sweet taste and one of the most abundant components released by complete hydrolysis of non-starch polysaccharides (NSP) of vegetable origin. However, NSPs are complicated compounds from the point of view of both physical structure and chemical composition, and they include cellulose, hemi-cellulose, pectin, and oligosaccharides. It is well-recognized that NSPs are resistant to the digestive enzymes and pass to the hind-gut where microbial degradation takes place. When L-arabinose is ingested in a digestible form, it is absorbed from the intestinal tract at a lower rate than glucose. A portion of the ingested L-arabinose is excreted in the urine. Although widely present in nature, L-arabinose is rarely used, and its physiological effects in vivo have received little attention. L-Arabinose selectively inhibits intestinal sucrase activity in a noncompetitive manner and suppresses the plasma glucose increase due to sucrose ingestion. Because the intestinal absorption of sucrose is inhibited in the presence of L-arabinose, the absorption of sucrose should be reduced by arabinose ingestion. Most of the studies reported so far on the absorption and utilization of L-arabinose relate to omnivore animal species other than humans. In a rare case of two autistic brothers that were not associated with any known metabolic disease, it was found the median value for their urine samples was 179 umol/mmol creatinine of L-arabinose, nearly six times greater than normal children (PMID: 11238761 , 8931641 , 1390604 , 7628083 ). L-Arabinose is found to be associated with ribose-5-phosphate isomerase deficiency, which is an inborn error of metabolism. L-Arabinose is also a microbial metabolite found in Mycobacterium (PMID: 16232643 ).
L ArabinoseHMDB
Chemical FormulaC5H10O5
Average Molecular Weight150.1299
Monoisotopic Molecular Weight150.05282343
IUPAC Name(3R,4S,5S)-oxane-2,3,4,5-tetrol
Traditional NameL-arabinopyranose
CAS Registry Number5328-37-0
InChI Identifier
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
  • Pentose monosaccharide
  • Oxane
  • Secondary alcohol
  • Hemiacetal
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Hydrocarbon derivative
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors

Route of exposure:


Biological location:

Physical Properties
Experimental Properties
Melting Point158 - 160 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility500 mg/mLNot Available
LogP-3.02HANSCH,C ET AL. (1995)
Predicted Properties
Water Solubility1220 g/LALOGPS
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
Polarizability13.38 ųChemAxon
Number of Rings1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-05al-9300000000-73d0d716ea47fc77a7aeJSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positivesplash10-00g0-9256300000-ae2d57025e3828494249JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0ue9-1900000000-07783f4be8db8a14f6f0JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0f89-1900000000-510acee1186ebf4c526bJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-07s1-9100000000-ff1e6f260ccdb7260dedJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-2900000000-f624316a77fb9d1bc74fJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001j-4900000000-768143fc08314c41644fJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-13182c55ee979014fcfaJSpectraViewer | MoNA
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
Biological Properties
Cellular Locations
  • Extracellular
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Urine
Tissue Locations
  • Prostate
Normal Concentrations
BloodDetected and Quantified2.5 (0.0-5.0) uMAdult (>18 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified19.5 (8.0-38.0) uMAdult (>18 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified8.8 (8.0-31.0) uMAdult (>18 years old)BothNormal details
FecesDetected but not Quantified Adult (>18 years old)Both
FecesDetected but not Quantified Adult (>18 years old)Both
FecesDetected but not Quantified Adult (>18 years old)Both
FecesDetected but not Quantified Adult (>18 years old)Not Specified
UrineDetected and Quantified8.8 (0.8-19.4) umol/mmol creatinineAdult (>18 years old)Both
UrineDetected and Quantified8.75 (6.12-11.84) umol/mmol creatinineAdult (>18 years old)BothNormal
    • Geigy Scientific ...
UrineDetected and Quantified27.483 +/- 18.288 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
    • Mordechai, Hien, ...
UrineDetected but not Quantified Adult (>18 years old)Both
UrineDetected and Quantified13.3 (1.3-22.0) umol/mmol creatinineAdult (>18 years old)Both
Abnormal Concentrations
BloodDetected and Quantified3.0 (0.0-7.0) uMAdult (>18 years old)BothRibose-5-phosphate isomerase deficiency details
Cerebrospinal Fluid (CSF)Detected and Quantified92.0 (66.0-135.0) uMChildren (1-13 years old)BothRibose-5-phosphate isomerase deficiency details
FecesDetected but not Quantified Adult (>18 years old)Both
Colorectal cancer
UrineDetected and Quantified17.07 +/- 14.128 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Mordechai, Hien, ...
UrineDetected and Quantified38.0 (37.0-41.0) umol/mmol creatinineAdult (>18 years old)BothRibose-5-phosphate isomerase deficiency 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 ]
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 ]
Eosinophilic esophagitis
  1. (). Mordechai, Hien, and David S. Wishart. .
Associated OMIM IDs
  • 608611 (Ribose-5-phosphate isomerase deficiency)
  • 114500 (Colorectal cancer)
  • 610247 (Eosinophilic esophagitis)
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012306
KNApSAcK IDC00041349
Chemspider ID388335
KEGG Compound IDC00259
BioCyc IDNot Available
BiGG ID34429
Wikipedia LinkArabinose
PubChem Compound439195
PDB IDNot Available
ChEBI ID17535
Synthesis ReferenceWhistler, Roy L.; Schweiger, Richard. Preparation of D-arabinose from D-glucose with hypochlorite. Journal of the American Chemical Society (1959), 81 5190-2.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
  2. Onkenhout W, Groener JE, Verhoeven NM, Yin C, Laan LA: L-Arabinosuria: a new defect in human pentose metabolism. Mol Genet Metab. 2002 Sep-Oct;77(1-2):80-5. [PubMed:12359133 ]
  3. Lobley RW, Burrows PC, Warwick R, Dawson DJ, Holmes R: Simultaneous assessment of intestinal permeability and lactose tolerance with orally administered raffinose, lactose and L-arabinose. Clin Sci (Lond). 1990 Aug;79(2):175-83. [PubMed:2167807 ]
  4. Osaki S, Kimura T, Sugimoto T, Hizukuri S, Iritani N: L-arabinose feeding prevents increases due to dietary sucrose in lipogenic enzymes and triacylglycerol levels in rats. J Nutr. 2001 Mar;131(3):796-9. [PubMed:11238761 ]
  5. Seri K, Sanai K, Matsuo N, Kawakubo K, Xue C, Inoue S: L-arabinose selectively inhibits intestinal sucrase in an uncompetitive manner and suppresses glycemic response after sucrose ingestion in animals. Metabolism. 1996 Nov;45(11):1368-74. [PubMed:8931641 ]
  6. Schutte JB, de Jong J, van Weerden EJ, Tamminga S: Nutritional implications of L-arabinose in pigs. Br J Nutr. 1992 Jul;68(1):195-207. [PubMed:1390604 ]
  7. Shaw W, Kassen E, Chaves E: Increased urinary excretion of analogs of Krebs cycle metabolites and arabinose in two brothers with autistic features. Clin Chem. 1995 Aug;41(8 Pt 1):1094-104. [PubMed:7628083 ]
  8. TOUSTER O, HARWELL SO: The isolation of L-arabitol from pentosuric urine. J Biol Chem. 1958 Feb;230(2):1031-41. [PubMed:13525419 ]
  9. Ahmed Z, Shimonishi T, Bhuiyan SH, Utamura M, Takada G, Izumori K: Biochemical preparation of L-ribose and L-arabinose from ribitol: a new approach. J Biosci Bioeng. 1999;88(4):444-8. [PubMed:16232643 ]


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:
Uniprot ID:
Molecular weight:
L-Arabitol + NAD → L-Arabinose + NADH + Hydrogen Iondetails
L-Arabitol + NADP → L-Arabinose + NADPH + Hydrogen Iondetails
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:
Uniprot ID:
Molecular weight:
Not Available
L-Arabitol + NAD → L-Arabinose + NADH + Hydrogen Iondetails
L-Arabitol + NADP → L-Arabinose + NADPH + Hydrogen Iondetails