MiMeDB: Showing metabocard for L-Arabinose (MMDBc0000130)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-10-27 23:36:58 UTC

Update Date

2022-08-30 23:58:09 UTC

Metabolite ID

MMDBc0000130

Metabolite Identification

Common Name

L-Arabinose

Description

L-Arabinose (CAS: 5328-37-0) 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, hemicellulose, 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 non-competitive 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 ).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

Synonyms

Value	Source
BETA-L-ARABINOSE	ChEBI
WURCS=2.0/1,1,0/[a211h-1b_1-5]/1/	ChEBI
b-L-ARABINOSE	Generator
Β-L-arabinose	Generator
b-L-Arabinopyranose	HMDB
Β-L-arabinopyranose	HMDB
L-Arabinopyranose	HMDB
Pectinose	HMDB
beta-L-Arabinopyranose	HMDB
Arabinopyranose	HMDB
Arabinose	HMDB
L-Arabinose	HMDB

Molecular Formula

C₅H₁₀O₅

Average Mass

150.1299

Monoisotopic Mass

150.05282343

IUPAC Name

(2S,3R,4S,5S)-oxane-2,3,4,5-tetrol

Traditional Name

β-L-arabinopyranose

CAS Registry Number

7296-56-2

SMILES

O[C@H]1CO[C@H](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-/m0/s1

InChI Key

SRBFZHDQGSBBOR-KLVWXMOXSA-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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

Alternative Parents

Substituents

Pentose monosaccharide
Oxane
Secondary alcohol
Hemiacetal
Oxacycle
Organoheterocyclic compound
Polyol
Hydrocarbon derivative
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

L-arabinopyranose (CHEBI:40886 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	1220 g/L	ALOGPS
logP	-2.6	ALOGPS
logP	-2.3	ChemAxon
logS	0.91	ALOGPS
pKa (Strongest Acidic)	11.31	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	90.15 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	29.96 m³·mol⁻¹	ChemAxon
Polarizability	13.37 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Extracellular

Biospecimen Locations

Blood
Cerebrospinal Fluid (CSF)
Feces
Prostate
Urine

Tissue Locations

Prostate

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0191761	Aldose reductase	Unknown	P15121	Homo_sapiens
MMDBp0196682	Aldo-keto reductase family 1 member B10	Unknown	O60218

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference
Ribose-5-phosphate isomerase deficiency	Slight Increase	Association	Human Blood	HMDB	14988808
Ribose-5-phosphate isomerase deficiency	Increased	Association	Human Urine	HMDB	14988808
Ribose-5-phosphate isomerase deficiency		Association	Human Cerebrospinal Fluid (CSF)	HMDB	14988808
Eosinophilic esophagitis	Slight Decrease	Association	Human Urine	HMDB	Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work)

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	321	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human sputum; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Cattle ; River trout	Microbial culture; Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Firmicutes	763	Human ; Human feces; Human dental plaque; Human pleural fluid plaque; Pig ; Cattle	Microbial culture; Metabolic reconstruction; Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria	Bacteroidetes	219	Human ; Human feces; Human subgingival plaque; Human appendix biopsy	Microbial culture; Metabolic reconstruction
Bacteria	Spirochaetes	4	Human feces	Microbial culture; Metabolic reconstruction
Bacteria	Deinococcus-Thermus	1		Microbial culture
Archaea	Crenarchaeota	3	Human feces	Microbial culture; Metabolic reconstruction
Bacteria	Actinobacteria	209	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human	Microbial culture; Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	2	Human feces	Microbial culture; Unknown
Archaea	Thaumarchaeota	1	Human feces	Metabolic reconstruction
Bacteria	Fusobacteria	9	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	3	Human feces	Metabolic reconstruction
Bacteria	Candidatus Melainabacteria	2	Human feces	Metabolic reconstruction
Bacteria	Tenericutes	4	Human feces	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Bacteria	Chloroflexi	1
Bacteria	Acidobacteria	1
Bacteria	Verrucomicrobia	1
Bacteria	Thermotogae	4
Bacteria/NULL	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human sputum; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Cattle ; River trout	Microbial culture; Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Archaea/Archaea	Euryarchaeota	1	Human feces	Metabolic reconstruction
Archaea/Archaea	Crenarchaeota	1	Human feces	Microbial culture; Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified								HMDB
Human	Detected and Quantified	3.0		0.0	7.0	Adult (>18 years old)	Both	Ribose-5-phosphate isomerase deficiency	HMDB	14988808
Human	Detected and Quantified	38.0		37.0	41.0	Adult (>18 years old)	Both	Ribose-5-phosphate isomerase deficiency	HMDB	14988808
Human	Detected and Quantified	92.0		66.0	135.0	Children (1-13 years old)	Both	Ribose-5-phosphate isomerase deficiency	HMDB	14988808
Human	Detected and Quantified	13.3		1.3	22.0	Adult (>18 years old)	Both	Normal	HMDB	24023812
Human	Detected and Quantified	19.5		8.0	38.0	Adult (>18 years old)	Both	Normal	HMDB	12359133
Human	Detected and Quantified	2.5		0.0	5.0	Adult (>18 years old)	Both	Normal	HMDB	14988808
Human	Detected and Quantified	8.8		0.8	19.4	Adult (>18 years old)	Both	Normal	HMDB	24023812
Human	Detected and Quantified	8.8		8.0	31.0	Adult (>18 years old)	Both	Normal	HMDB	12359133
Human	Detected and Quantified	17.07	14.128			Children (1 - 13 years old)	Not Specified	Eosinophilic esophagitis	HMDB	Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work)
Human	Detected and Quantified	27.483	18.288			Children (1 - 13 years old)	Not Specified	Normal	HMDB	Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work)
Human	Detected and Quantified	8.75		6.12	11.84	Adult (>18 years old)	Both	Normal	HMDB	Geigy Scientific Tables, 8th Rev edition, pp. 130. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp. Basel, Switzerland c1981-1992.
Human Prostate	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Urine	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	24023812
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified					Adult (>18 years old)	Not Specified	Normal	HMDB	25985090
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	29808030

External Links

HMDB ID

HMDB0000646

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Arabinose

METLIN ID

Not Available

PubChem Compound

439764

PDB ID

Not Available

ChEBI ID

40886

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

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. doi: 10.1079/bjn19920077. [PubMed:1390604 ]
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. doi: 10.1042/cs0790175. [PubMed:2167807 ]
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 ]
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. doi: 10.1016/s0026-0495(96)90117-1. [PubMed:8931641 ]
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. doi: 10.1093/jn/131.3.796. [PubMed:11238761 ]
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. doi: 10.1016/s1096-7192(02)00125-7. [PubMed:12359133 ]
TOUSTER O, HARWELL SO: The isolation of L-arabitol from pentosuric urine. J Biol Chem. 1958 Feb;230(2):1031-41. [PubMed:13525419 ]
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. doi: 10.1016/s1389-1723(99)80225-4. [PubMed:16232643 ]
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 ]

Showing metabocard for L-Arabinose (MMDBc0000130)

MOL for #<Metabolite:0x0000560be2235f48>

3D MOL for #<Metabolite:0x0000560be2235f48>

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3D-SDF for #<Metabolite:0x0000560be2235f48>

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3D PDB for #<Metabolite:0x0000560be2235f48>

SMILES for #<Metabolite:0x0000560be2235f48>

INCHI for #<Metabolite:0x0000560be2235f48>

Structure for #<Metabolite:0x0000560be2235f48>

3D Structure for #<Metabolite:0x0000560be2235f48>