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Showing metabocard for D-Arabitol (HMDB0000568)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-02-26 21:22:20 UTC
HMDB IDHMDB0000568
Secondary Accession Numbers
  • HMDB00568
Metabolite Identification
Common NameD-Arabitol
DescriptionD-Arabitol is a polyol. Polyols are sugar alcohols linked to the pentose phosphate pathway (PPP). They are classified on the basis of the number of carbon atoms. Polyols occur in body fluids. A patient with leukoencephalopathy and peripheral neuropathy has been identified as suffering from ribose-5-phosphate isomerase (RPI) deficiency, a defect in the PPP. In this disorder, highly elevated concentrations of the C5 polyols such as D-arabitol are found in body fluids. In addition, transaldolase deficiency, another defect in the PPP, has been diagnosed in a patient with mainly liver problems among others. This patient had increased concentrations of polyols, mainly D-arabitol. So far, the pathophysiological role of polyols is relatively unknown. It is thought that D-arabitol is a metabolic end-product in humans. The strong brain-CSF-plasma gradient of polyols in the patient with RPI deficiency suggested a primary metabolic disorder. The mechanisms of brain and neuronal damage in RPI deficiency remain to be elucidated. A neurotoxic effect due to the accumulation of the polyols may play a role. D-Arabitol is a product of the enzyme D-arabinitol 4-dehydrogenase (EC 1.1.1.11) in the pentose and glucuronate interconversion pathway (PMID: 16435225 , J Inherit Metab Dis. 2005;28(6):1181-3). D-Arabitol has also been found to be a fungal metabolite, urinary D-Arabinitol is a marker for invasive candidiasis or infection by Candida fungal species (PMID: 15183861 ; PMID: 10647119 ). It can also a metabolite in Debaryomyces, Pichia and Zygosaccharomyces (PMID: 25809659 ).
Structure
Data?1582752140
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
D-ArabinolChEBI
D-LyxitolChEBI
D-ArabinitolKegg
Arabitol, (D)-isomerHMDB
ArabitolHMDB
D-(+)-ArabitolHMDB
(+--)-ArabitolHMDB
DL-ArabitolHMDB
Arabino-pentitolHMDB
LyxitolHMDB
D-ArabitolChEBI
Chemical FormulaC5H12O5
Average Molecular Weight152.1458
Monoisotopic Molecular Weight152.068473494
IUPAC Name(2R,4R)-pentane-1,2,3,4,5-pentol
Traditional Namearabitol
CAS Registry Number488-82-4
SMILES
OC[C@@H](O)C(O)[C@H](O)CO
InChI Identifier
InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4-/m1/s1
InChI KeyHEBKCHPVOIAQTA-QWWZWVQMSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as sugar alcohols. These are hydrogenated forms of carbohydrate in which the carbonyl group (aldehyde or ketone, reducing sugar) has been reduced to a primary or secondary hydroxyl group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentSugar alcohols
Alternative Parents
Substituents
  • Sugar alcohol
  • Monosaccharide
  • Secondary alcohol
  • Polyol
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect

Health effect:

Disposition

Route of exposure:

Source:

Biological location:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point101 - 104 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility729 mg/mLNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility664 g/LALOGPS
logP-2.5ALOGPS
logP-3.1ChemAxon
logS0.64ALOGPS
pKa (Strongest Acidic)12.76ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area101.15 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity32.44 m³·mol⁻¹ChemAxon
Polarizability14.28 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-MS (5 TMS)splash10-0gb9-0982000000-4e5007f03273cea8b23eSpectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-01ba-9500000000-67233150807800e941f0Spectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-01b9-9000000000-1ff17a8b87bbab9a3622Spectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-044i-9000000000-e0e330c8a899be718f60Spectrum
LC-MS/MSLC-MS/MS Spectrum - Linear Ion Trap , negativesplash10-00m0-2900000000-c6b1101b88fa522fabd0Spectrum
LC-MS/MSLC-MS/MS Spectrum - , negativesplash10-0zmr-9500000000-164d598431954fc1aeaeSpectrum
LC-MS/MSLC-MS/MS Spectrum - , negativesplash10-0uki-9600000000-b90e9cee04cd0631b599Spectrum
LC-MS/MSLC-MS/MS Spectrum - Linear Ion Trap , positivesplash10-00e9-2900000000-75413a29e8c6b3d9a6a1Spectrum
LC-MS/MSLC-MS/MS Spectrum - Linear Ion Trap , positivesplash10-0udi-0900000000-c5cc931b9156365c4ca7Spectrum
LC-MS/MSLC-MS/MS Spectrum - Linear Ion Trap , positivesplash10-0a5a-0900000000-94cf956e3f47a633d572Spectrum
LC-MS/MSLC-MS/MS Spectrum - Linear Ion Trap , positivesplash10-03k9-0900000000-f0634d5b1d1f523b3caaSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-1900000000-4f856d537cc8252ecc47Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-9300000000-403bacad5117a30582dfSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03dl-9000000000-eb879b27e7b182cfe7c0Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udu-9400000000-3db6454ab3e2315aa744Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0btl-9200000000-b84c400427c7e44eb4ddSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4l-9000000000-c37624fb31a8cb33b163Spectrum
MSMass Spectrum (Electron Ionization)splash10-01vo-9000000000-f065454e8412613f8ecdSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableSpectrum
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Urine
Tissue Locations
  • Placenta
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified3 (0-5) uMAdolescent (13-18 years old)Not Specified
Normal		 details
BloodDetected and Quantified0 uMNot SpecifiedNot SpecifiedNormal
    • Geigy Scientific ...
 details
Cerebrospinal Fluid (CSF)Detected and Quantified19.0 +/- 6.3 uMAdult (>18 years old)BothNormal
    • Geigy Scientific ...
 details
Cerebrospinal Fluid (CSF)Detected and Quantified9.0-39.0 uMAdolescent (13-18 years old)Both
Normal		 details
Cerebrospinal Fluid (CSF)Detected and Quantified19.0 +/- 6.3 uMNot SpecifiedNot SpecifiedNormal
    • Geigy Scientific ...
 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 Quantified16-89 umol/mmol creatinineAdolescent (13-18 years old)Both
Normal		 details
UrineDetected and Quantified19.0 +/- 6.0 umol/mmol creatinineAdult (>18 years old)BothNormal
    • Geigy Scientific ...
 details
UrineDetected and Quantified53.153 +/- 16.798 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal
    • Mordechai, Hien, ...
 details
UrineDetected and Quantified23 (8-36) umol/mmol creatinineAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified115 (32 - 198) uMAdolescent (13-18 years old)MaleRibose-5-Phosphate Isomerase Deficiency details
BloodDetected and Quantified39.4 (0.7-788) uMAdult (>18 years old)Both
Invasive candidiasis		 details
Cerebrospinal Fluid (CSF)Detected and Quantified3342-5535 uMAdolescent (13-18 years old)Both
Ribose-5-Phosphate Isomerase Deficiency		 details
FecesDetected but not Quantified Adult (>18 years old)Both
Colorectal cancer		 details
UrineDetected and Quantified1021 - 1612 umol/mmol creatinineAdult (>18 years old)Both
Ribose-5-Phosphate Isomerase Deficiency		 details
UrineDetected and Quantified63.837 +/- 87.775 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Mordechai, Hien, ...
 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 ]
Invasive candidiasis
  1. Kiehn TE, Bernard EM, Gold JW, Armstrong D: Candidiasis: detection by gas-liquid chromatography of D-arabinitol, a fungal metabolite, in human serum. Science. 1979 Nov 2;206(4418):577-80. [PubMed:493963 ]
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
FooDB IDFDB001475
KNApSAcK IDC00001156
Chemspider ID84971
KEGG Compound IDC01904
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkD-arabinitol
METLIN ID5551
PubChem Compound94154
PDB IDNot Available
ChEBI ID18333
Food Biomarker OntologyNot Available
VMH IDNot Available
References
Synthesis ReferenceDelobeau, Didier; Moine, Didier. Process for the preparation of d-arabitol from lactose. Eur. Pat. Appl. (1997), 9 pp.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Kiehn TE, Bernard EM, Gold JW, Armstrong D: Candidiasis: detection by gas-liquid chromatography of D-arabinitol, a fungal metabolite, in human serum. Science. 1979 Nov 2;206(4418):577-80. [PubMed:493963 ]
  2. Klusmann A, Fleischer W, Waldhaus A, Siebler M, Mayatepek E: Influence of D-arabitol and ribitol on neuronal network activity. J Inherit Metab Dis. 2005;28(6):1181-3. [PubMed:16435225 ]
  3. Hui M, Cheung SW, Chin ML, Chu KC, Chan RC, Cheng AF: Development and application of a rapid diagnostic method for invasive Candidiasis by the detection of D-/L-arabinitol using gas chromatography/mass spectrometry. Diagn Microbiol Infect Dis. 2004 Jun;49(2):117-23. doi: 10.1016/j.diagmicrobio.2004.02.006. [PubMed:15183861 ]
  4. Christensson B, Sigmundsdottir G, Larsson L: D-arabinitol--a marker for invasive candidiasis. Med Mycol. 1999 Dec;37(6):391-6. [PubMed:10647119 ]
  5. Kordowska-Wiater M: Production of arabitol by yeasts: current status and future prospects. J Appl Microbiol. 2015 Aug;119(2):303-14. doi: 10.1111/jam.12807. Epub 2015 Apr 8. [PubMed:25809659 ]
  6. 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 ]