MiMeDB: Showing metabocard for beta-L-arabinofuranose (MMDBc0054365)

Pharmaceutical

Xenobiotic

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:09:09 UTC

Update Date

2025-10-07 16:08:29 UTC

Metabolite ID

MMDBc0054365

Metabolite Identification

Common Name

beta-L-arabinofuranose

Description

beta-L-arabinofuranose is a carbohydrate belonging to the class of pentoses, specifically a furanose form of L-arabinose. Its chemical structure features a five-membered ring containing four carbon atoms and one oxygen atom, with hydroxyl groups attached to the carbon atoms. This sugar plays a role in various biochemical pathways, including the synthesis of nucleosides, as demonstrated in the synthesis of 1-(5'-amino-3',5'-dideoxy-alpha-L-arabinofuranosyl)uracil, a component of dihydropacidamycin D (PMID:11909731 ). Additionally, beta-L-arabinofuranose is involved in the biosynthesis of polysaccharides and glycoproteins, contributing to cellular structure and function. Its unique configuration and reactivity make it a valuable building block in carbohydrate chemistry and biochemistry, facilitating the development of complex biomolecules.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
b-Arabinose	Generator
Β-arabinose	Generator
b-L-Arabinose	HMDB
Β-L-arabinose	HMDB

Molecular Formula

C₅H₁₀O₅

Average Mass

150.1299

Monoisotopic Mass

150.05282343

IUPAC Name

(2S,3R,4R,5S)-5-(hydroxymethyl)oxolane-2,3,4-triol

Traditional Name

β-L-arabinofuranose

CAS Registry Number

Not Available

SMILES

OC[C@@H]1O[C@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4+,5-/m0/s1

InChI Key

HMFHBZSHGGEWLO-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
Tetrahydrofuran
Secondary alcohol
Hemiacetal
Oxacycle
Organoheterocyclic compound
Polyol
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

L-arabinofuranose (CHEBI:28272 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	1070 g/L	ALOGPS
logP	-2.6	ALOGPS
logP	-2.3	ChemAxon
logS	0.85	ALOGPS
pKa (Strongest Acidic)	11.31	ChemAxon
pKa (Strongest Basic)	-3	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	1	ChemAxon
Refractivity	29.96 m³·mol⁻¹	ChemAxon
Polarizability	13.53 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-05cu-9300000000-e24e80da64b2475ddfd8	2017-08-28	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positive	splash10-00g0-7349300000-49b1e72358e4fd020b5d	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0ue9-2900000000-6c1199d377747f0e5b49	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0f89-2900000000-8a9f89ac0a25c323249e	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052p-9100000000-eaebbbf2fa629ce04160	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-1900000000-6c48df798a58fc7029d9	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001j-2900000000-816419eb5dad5bd99819	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9200000000-91d11d896b253dfd9693	2017-07-26	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	415.3
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	266.2
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	40.6
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	221.2
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	279.8
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	315.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	650.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	660.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	777.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	171.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	328.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	189.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	39.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	292.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	605.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	70.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	245.2
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	758.1
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	569.8

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	beta-L-arabinofuranose_TMS_1	C[Si](C)(C)OC[C@@H]1O[C@H](O)[C@H](O)[C@H]1O	standard non polar	2025-10-24	1983.99
Gas Chromatography	beta-L-arabinofuranose_TMS_2	C[Si](C)(C)O[C@H]1O[C@@H](CO)[C@H](O)[C@H]1O	standard non polar	2025-10-24	1481.52
Gas Chromatography	beta-L-arabinofuranose_TMS_3	C[Si](C)(C)O[C@H]1[C@@H](O)O[C@@H](CO)[C@@H]1O	standard non polar	2025-10-24	1633.26
Gas Chromatography	beta-L-arabinofuranose_TMS_4	C[Si](C)(C)O[C@H]1[C@H](CO)O[C@H](O)[C@@H]1O	standard non polar	2025-10-24	1726.91
Gas Chromatography	beta-L-arabinofuranose_TMS_5	C[Si](C)(C)OC[C@@H]1O[C@H](O[Si](C)(C)C)[C@H](O)[C@H]1O	standard non polar	2025-10-24	1889.74
Gas Chromatography	beta-L-arabinofuranose_TMS_6	C[Si](C)(C)OC[C@@H]1O[C@H](O)[C@H](O[Si](C)(C)C)[C@H]1O	standard non polar	2025-10-24	1638.9
Gas Chromatography	beta-L-arabinofuranose_TMS_7	C[Si](C)(C)OC[C@@H]1O[C@H](O)[C@H](O)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1986.66
Gas Chromatography	beta-L-arabinofuranose_TMS_8	C[Si](C)(C)O[C@H]1O[C@@H](CO)[C@H](O[Si](C)(C)C)[C@H]1O	standard non polar	2025-10-24	1773.66
Gas Chromatography	beta-L-arabinofuranose_TMS_9	C[Si](C)(C)O[C@H]1O[C@@H](CO)[C@H](O)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1754.31
Gas Chromatography	beta-L-arabinofuranose_TMS_10	C[Si](C)(C)O[C@H]1[C@H](CO)O[C@H](O)[C@@H]1O[Si](C)(C)C	standard non polar	2025-10-24	2005.25
Gas Chromatography	beta-L-arabinofuranose_TMS_11	C[Si](C)(C)OC[C@@H]1O[C@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@H]1O	standard non polar	2025-10-24	1857.84
Gas Chromatography	beta-L-arabinofuranose_TMS_12	C[Si](C)(C)OC[C@@H]1O[C@H](O[Si](C)(C)C)[C@H](O)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1789.41
Gas Chromatography	beta-L-arabinofuranose_TMS_13	C[Si](C)(C)OC[C@@H]1O[C@H](O)[C@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	2378.45
Gas Chromatography	beta-L-arabinofuranose_TMS_14	C[Si](C)(C)O[C@H]1[C@H](CO)O[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	standard non polar	2025-10-24	2189.52
Gas Chromatography	beta-L-arabinofuranose_TMS_15	C[Si](C)(C)OC[C@@H]1O[C@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	2006.82
Gas Chromatography	beta-L-arabinofuranose_TMS_1	C[Si](C)(C)OC[C@@H]1O[C@H](O)[C@H](O)[C@H]1O	standard polar	2025-10-24	2201.21
Gas Chromatography	beta-L-arabinofuranose_TMS_2	C[Si](C)(C)O[C@H]1O[C@@H](CO)[C@H](O)[C@H]1O	standard polar	2025-10-24	2277.93
Gas Chromatography	beta-L-arabinofuranose_TMS_3	C[Si](C)(C)O[C@H]1[C@@H](O)O[C@@H](CO)[C@@H]1O	standard polar	2025-10-24	2139.63
Gas Chromatography	beta-L-arabinofuranose_TMS_4	C[Si](C)(C)O[C@H]1[C@H](CO)O[C@H](O)[C@@H]1O	standard polar	2025-10-24	1975.5
Gas Chromatography	beta-L-arabinofuranose_TMS_5	C[Si](C)(C)OC[C@@H]1O[C@H](O[Si](C)(C)C)[C@H](O)[C@H]1O	standard polar	2025-10-24	2337.35
Gas Chromatography	beta-L-arabinofuranose_TMS_6	C[Si](C)(C)OC[C@@H]1O[C@H](O)[C@H](O[Si](C)(C)C)[C@H]1O	standard polar	2025-10-24	1878.14
Gas Chromatography	beta-L-arabinofuranose_TMS_7	C[Si](C)(C)OC[C@@H]1O[C@H](O)[C@H](O)[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	1792.44
Gas Chromatography	beta-L-arabinofuranose_TMS_8	C[Si](C)(C)O[C@H]1O[C@@H](CO)[C@H](O[Si](C)(C)C)[C@H]1O	standard polar	2025-10-24	1890.17
Gas Chromatography	beta-L-arabinofuranose_TMS_9	C[Si](C)(C)O[C@H]1O[C@@H](CO)[C@H](O)[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	2504.11
Gas Chromatography	beta-L-arabinofuranose_TMS_10	C[Si](C)(C)O[C@H]1[C@H](CO)O[C@H](O)[C@@H]1O[Si](C)(C)C	standard polar	2025-10-24	1548.69
Gas Chromatography	beta-L-arabinofuranose_TMS_11	C[Si](C)(C)OC[C@@H]1O[C@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@H]1O	standard polar	2025-10-24	2279.43
Gas Chromatography	beta-L-arabinofuranose_TMS_12	C[Si](C)(C)OC[C@@H]1O[C@H](O[Si](C)(C)C)[C@H](O)[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	1869.5
Gas Chromatography	beta-L-arabinofuranose_TMS_13	C[Si](C)(C)OC[C@@H]1O[C@H](O)[C@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	2287.51
Gas Chromatography	beta-L-arabinofuranose_TMS_14	C[Si](C)(C)O[C@H]1[C@H](CO)O[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	standard polar	2025-10-24	1854.99
Gas Chromatography	beta-L-arabinofuranose_TMS_15	C[Si](C)(C)OC[C@@H]1O[C@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	2270.33

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

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

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Actinobacteria	1	Human ; Human feces

Exposure Sources

Other Exposures

Source Type	Data Source	Reference
Drugs - Antimicrobial	U.S. Environmental Protection Agency	CompTox
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

HMDB0094694

DrugBank ID

DB03246

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C20569

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6857384

PDB ID

Not Available

ChEBI ID

28272

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for beta-L-arabinofuranose (MMDBc0054365)

MOL for #<Metabolite:0x0000564322870738>

3D MOL for #<Metabolite:0x0000564322870738>

3D SDF for #<Metabolite:0x0000564322870738>

3D-SDF for #<Metabolite:0x0000564322870738>

PDB for #<Metabolite:0x0000564322870738>

3D PDB for #<Metabolite:0x0000564322870738>

SMILES for #<Metabolite:0x0000564322870738>

INCHI for #<Metabolite:0x0000564322870738>

Structure for #<Metabolite:0x0000564322870738>

3D Structure for #<Metabolite:0x0000564322870738>