Human Metabolome Database: Showing metabocard for D-Arabitol (HMDB0000568)

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Record Information

Version

4.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2020-10-09 20:59:44 UTC

HMDB ID

HMDB0000568

Secondary Accession Numbers

HMDB00568

Metabolite Identification

Common Name

D-Arabitol

Description

D-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

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
D-Arabinol	ChEBI
D-Lyxitol	ChEBI
D-Arabinitol	Kegg
Arabitol, (D)-isomer	HMDB
Arabitol	HMDB
D-(+)-Arabitol	HMDB
(+--)-Arabitol	HMDB
DL-Arabitol	HMDB
Arabino-pentitol	HMDB
Lyxitol	HMDB
D-Arabitol	ChEBI

Chemical Formula

C₅H₁₂O₅

Average Molecular Weight

152.1458

Monoisotopic Molecular Weight

152.068473494

IUPAC Name

(2R,4R)-pentane-1,2,3,4,5-pentol

Traditional Name

arabitol

CAS Registry Number

488-82-4

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 Key

HEBKCHPVOIAQTA-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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar alcohols

Alternative Parents

Substituents

Sugar alcohol
Monosaccharide
Secondary alcohol
Polyol
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

arabinitol (CHEBI:18333 )

Ontology

Physiological effect

Health effect:

Health condition:

Invasive candidiasis

Disposition

Route of exposure:

Enteral:

Ingestion

Candida pelliculosa

Biological location:

Tissue and substructures:

Placenta

Subcellular:

Cytoplasm

Biofluid and excreta:

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	101 - 104 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	729 mg/mL	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	664 g/L	ALOGPS
logP	-2.5	ALOGPS
logP	-3.1	ChemAxon
logS	0.64	ALOGPS
pKa (Strongest Acidic)	12.76	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	101.15 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	32.44 m³·mol⁻¹	ChemAxon
Polarizability	14.28 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	View
GC-MS	GC-MS Spectrum - GC-MS (5 TMS)	splash10-0gb9-0982000000-4e5007f03273cea8b23e	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-01ba-9500000000-67233150807800e941f0	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-01b9-9000000000-1ff17a8b87bbab9a3622	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-044i-9000000000-e0e330c8a899be718f60	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-00m0-2900000000-c6b1101b88fa522fabd0	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - , negative	splash10-0zmr-9500000000-164d598431954fc1aeae	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - , negative	splash10-0uki-9600000000-b90e9cee04cd0631b599	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-00e9-2900000000-75413a29e8c6b3d9a6a1	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-0udi-0900000000-c5cc931b9156365c4ca7	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-0a5a-0900000000-94cf956e3f47a633d572	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-03k9-0900000000-f0634d5b1d1f523b3caa	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-1900000000-4f856d537cc8252ecc47	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-9300000000-403bacad5117a30582df	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03dl-9000000000-eb879b27e7b182cfe7c0	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udu-9400000000-3db6454ab3e2315aa744	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0btl-9200000000-b84c400427c7e44eb4dd	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9000000000-c37624fb31a8cb33b163	Spectrum
MS	Mass Spectrum (Electron Ionization)	splash10-01vo-9000000000-f065454e8412613f8ecd	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Cerebrospinal Fluid (CSF)
Feces
Urine

Tissue Locations

Placenta

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	3 (0-5) uM	Adolescent (13-18 years old)	Not Specified	Normal	14988808	details
Blood	Detected and Quantified	0 uM	Not Specified	Not Specified	Normal	Geigy Scientific ...	details
Cerebrospinal Fluid (CSF)	Detected and Quantified	19.0 +/- 6.3 uM	Adult (>18 years old)	Both	Normal	Geigy Scientific ...	details
Cerebrospinal Fluid (CSF)	Detected and Quantified	9.0-39.0 uM	Adolescent (13-18 years old)	Both	Normal	14988808	details
Cerebrospinal Fluid (CSF)	Detected and Quantified	19.0 +/- 6.3 uM	Not Specified	Not Specified	Normal	Geigy Scientific ...	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	29808030	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	25037050	details
Urine	Detected and Quantified	16-89 umol/mmol creatinine	Adolescent (13-18 years old)	Both	Normal	14988808	details
Urine	Detected and Quantified	19.0 +/- 6.0 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	Geigy Scientific ...	details
Urine	Detected and Quantified	53.153 +/- 16.798 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Normal	Mordechai, Hien, ...	details
Urine	Detected and Quantified	23 (8-36) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	24023812	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	115 (32 - 198) uM	Adolescent (13-18 years old)	Male	Ribose-5-Phosphate Isomerase Deficiency	14988808	details
Blood	Detected and Quantified	39.4 (0.7-788) uM	Adult (>18 years old)	Both	Invasive candidiasis	493963	details
Cerebrospinal Fluid (CSF)	Detected and Quantified	3342-5535 uM	Adolescent (13-18 years old)	Both	Ribose-5-Phosphate Isomerase Deficiency	14988808	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal cancer	25037050	details
Urine	Detected and Quantified	1021 - 1612 umol/mmol creatinine	Adult (>18 years old)	Both	Ribose-5-Phosphate Isomerase Deficiency	14988808	details
Urine	Detected and Quantified	63.837 +/- 87.775 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Eosinophilic esophagitis	Mordechai, Hien, ...	details

Associated Disorders and Diseases

Disease References

Ribose-5-phosphate isomerase deficiency
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
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
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
(). Mordechai, Hien, and David S. Wishart. .

Associated OMIM IDs

608611 (Ribose-5-phosphate isomerase deficiency)
114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

D-arabinitol

METLIN ID

5551

PubChem Compound

94154

PDB ID

Not Available

ChEBI ID

18333

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

MDB00000189

References

Synthesis Reference

Delobeau, 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

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 ]
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 ]
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 ]
Christensson B, Sigmundsdottir G, Larsson L: D-arabinitol--a marker for invasive candidiasis. Med Mycol. 1999 Dec;37(6):391-6. [PubMed:10647119 ]
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 ]
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 ]

Showing metabocard for D-Arabitol (HMDB0000568)

Structure for HMDB0000568 (D-Arabitol)