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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2009-06-02 16:04:01 UTC

Update Date

2021-09-14 15:45:01 UTC

HMDB ID

HMDB0012325

Secondary Accession Numbers

HMDB12325

Metabolite Identification

Common Name

Arabinofuranose

Description

Arabinofuranose refers to the furanose form of arabinose, which is an optical isomer of arabinose. For biosynthetic reasons, most saccharides are almost always more abundant in nature as the "D" form, or structurally analogous to D-(+)-glyceraldehyde. However, L-arabinose is in fact more common than D-arabinose in nature and is found in nature as a component of biopolymers such as hemicellulose and pectin.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
WURCS=2.0/1,1,0/[a211h-1x_1-4]/1/	ChEBI
L-Arabinofuranose	HMDB
Arabinofuranose	MeSH

Chemical Formula

C₅H₁₀O₅

Average Molecular Weight

150.1299

Monoisotopic Molecular Weight

150.05282343

IUPAC Name

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

Traditional Name

L-arabinofuranose

CAS Registry Number

13221-22-2

SMILES

OC[C@@H]1OC(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-HWQSCIPKSA-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-arabinose (CHEBI:6178 )

Ontology

Not Available

Urine (PMID: 19616694)

Source

Endogenous

Endogenous (HMDB: HMDB0012325)

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular 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	13.51 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	132.603	31661259
DarkChem	[M-H]-	129.007	31661259
DeepCCS	[M+H]+	133.274	30932474
DeepCCS	[M-H]-	131.072	30932474
DeepCCS	[M-2H]-	165.913	30932474
DeepCCS	[M+Na]+	140.298	30932474
AllCCS	[M+H]+	134.3	32859911
AllCCS	[M+H-H2O]+	129.8	32859911
AllCCS	[M+NH4]+	138.5	32859911
AllCCS	[M+Na]+	139.7	32859911
AllCCS	[M-H]-	124.8	32859911
AllCCS	[M+Na-2H]-	126.5	32859911
AllCCS	[M+HCOO]-	128.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Arabinofuranose	OC[C@@H]1OC(O)[C@H](O)[C@H]1O	3078.5	Standard polar	33892256
Arabinofuranose	OC[C@@H]1OC(O)[C@H](O)[C@H]1O	1491.1	Standard non polar	33892256
Arabinofuranose	OC[C@@H]1OC(O)[C@H](O)[C@H]1O	1406.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Arabinofuranose,1TMS,isomer #1	C[Si](C)(C)OC[C@@H]1OC(O)[C@H](O)[C@H]1O	1505.7	Semi standard non polar	33892256
Arabinofuranose,1TMS,isomer #2	C[Si](C)(C)OC1O[C@@H](CO)[C@H](O)[C@H]1O	1544.9	Semi standard non polar	33892256
Arabinofuranose,1TMS,isomer #3	C[Si](C)(C)O[C@H]1C(O)O[C@@H](CO)[C@@H]1O	1526.5	Semi standard non polar	33892256
Arabinofuranose,1TMS,isomer #4	C[Si](C)(C)O[C@H]1[C@H](CO)OC(O)[C@@H]1O	1518.1	Semi standard non polar	33892256
Arabinofuranose,2TMS,isomer #1	C[Si](C)(C)OC[C@@H]1OC(O[Si](C)(C)C)[C@H](O)[C@H]1O	1596.6	Semi standard non polar	33892256
Arabinofuranose,2TMS,isomer #2	C[Si](C)(C)OC[C@@H]1OC(O)[C@H](O[Si](C)(C)C)[C@H]1O	1575.7	Semi standard non polar	33892256
Arabinofuranose,2TMS,isomer #3	C[Si](C)(C)OC[C@@H]1OC(O)[C@H](O)[C@H]1O[Si](C)(C)C	1564.9	Semi standard non polar	33892256
Arabinofuranose,2TMS,isomer #4	C[Si](C)(C)OC1O[C@@H](CO)[C@H](O[Si](C)(C)C)[C@H]1O	1574.0	Semi standard non polar	33892256
Arabinofuranose,2TMS,isomer #5	C[Si](C)(C)OC1O[C@@H](CO)[C@H](O)[C@H]1O[Si](C)(C)C	1572.6	Semi standard non polar	33892256
Arabinofuranose,2TMS,isomer #6	C[Si](C)(C)O[C@H]1[C@H](CO)OC(O)[C@@H]1O[Si](C)(C)C	1563.3	Semi standard non polar	33892256
Arabinofuranose,3TMS,isomer #1	C[Si](C)(C)OC[C@@H]1OC(O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@H]1O	1646.3	Semi standard non polar	33892256
Arabinofuranose,3TMS,isomer #2	C[Si](C)(C)OC[C@@H]1OC(O[Si](C)(C)C)[C@H](O)[C@H]1O[Si](C)(C)C	1623.2	Semi standard non polar	33892256
Arabinofuranose,3TMS,isomer #3	C[Si](C)(C)OC[C@@H]1OC(O)[C@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	1633.0	Semi standard non polar	33892256
Arabinofuranose,3TMS,isomer #4	C[Si](C)(C)OC1O[C@@H](CO)[C@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	1606.1	Semi standard non polar	33892256
Arabinofuranose,4TMS,isomer #1	C[Si](C)(C)OC[C@@H]1OC(O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	1603.5	Semi standard non polar	33892256
Arabinofuranose,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1OC(O)[C@H](O)[C@H]1O	1731.7	Semi standard non polar	33892256
Arabinofuranose,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1O[C@@H](CO)[C@H](O)[C@H]1O	1753.8	Semi standard non polar	33892256
Arabinofuranose,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@H]1C(O)O[C@@H](CO)[C@@H]1O	1746.3	Semi standard non polar	33892256
Arabinofuranose,1TBDMS,isomer #4	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](CO)OC(O)[C@@H]1O	1746.3	Semi standard non polar	33892256
Arabinofuranose,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1OC(O[Si](C)(C)C(C)(C)C)[C@H](O)[C@H]1O	2028.4	Semi standard non polar	33892256
Arabinofuranose,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@@H]1OC(O)[C@H](O[Si](C)(C)C(C)(C)C)[C@H]1O	2021.9	Semi standard non polar	33892256
Arabinofuranose,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@@H]1OC(O)[C@H](O)[C@H]1O[Si](C)(C)C(C)(C)C	2013.5	Semi standard non polar	33892256
Arabinofuranose,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC1O[C@@H](CO)[C@H](O[Si](C)(C)C(C)(C)C)[C@H]1O	2022.7	Semi standard non polar	33892256
Arabinofuranose,2TBDMS,isomer #5	CC(C)(C)[Si](C)(C)OC1O[C@@H](CO)[C@H](O)[C@H]1O[Si](C)(C)C(C)(C)C	2015.4	Semi standard non polar	33892256
Arabinofuranose,2TBDMS,isomer #6	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](CO)OC(O)[C@@H]1O[Si](C)(C)C(C)(C)C	2028.0	Semi standard non polar	33892256
Arabinofuranose,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1OC(O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@H]1O	2304.0	Semi standard non polar	33892256
Arabinofuranose,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@@H]1OC(O[Si](C)(C)C(C)(C)C)[C@H](O)[C@H]1O[Si](C)(C)C(C)(C)C	2306.4	Semi standard non polar	33892256
Arabinofuranose,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@@H]1OC(O)[C@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C	2310.8	Semi standard non polar	33892256
Arabinofuranose,3TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC1O[C@@H](CO)[C@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C	2290.3	Semi standard non polar	33892256
Arabinofuranose,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1OC(O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C	2543.5	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Arabinofuranose GC-MS (Non-derivatized) - 70eV, Positive	splash10-00di-9200000000-8614b5abdf90e5e63d91	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arabinofuranose GC-MS (4 TMS) - 70eV, Positive	splash10-00g0-7349300000-49b1e72358e4fd020b5d	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arabinofuranose GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arabinofuranose GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranose 10V, Negative-QTOF	splash10-0002-1900000000-6c48df798a58fc7029d9	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranose 20V, Negative-QTOF	splash10-001j-2900000000-816419eb5dad5bd99819	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranose 40V, Negative-QTOF	splash10-0006-9200000000-91d11d896b253dfd9693	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranose 10V, Negative-QTOF	splash10-0pc1-5900000000-6953077be254812d8b25	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranose 20V, Negative-QTOF	splash10-0a4i-9100000000-fcc3022a655e16f83b2c	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranose 40V, Negative-QTOF	splash10-0006-9000000000-750ecddfae4eefc71996	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranose 10V, Positive-QTOF	splash10-0ue9-2900000000-6c1199d377747f0e5b49	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranose 20V, Positive-QTOF	splash10-0f89-2900000000-8a9f89ac0a25c323249e	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranose 40V, Positive-QTOF	splash10-052p-9100000000-eaebbbf2fa629ce04160	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranose 10V, Positive-QTOF	splash10-0gc0-1900000000-346af5e1437ac746833b	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranose 20V, Positive-QTOF	splash10-0nc4-9400000000-74fd6af917cb088bef2b	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranose 40V, Positive-QTOF	splash10-0a4i-9000000000-55c82f4fa793a5fd288b	2021-09-23	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	19616694	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Hepatocellular carcinoma	19616694	details

Associated Disorders and Diseases

Disease References

Hepatocellular carcinoma
Wu H, Xue R, Dong L, Liu T, Deng C, Zeng H, Shen X: Metabolomic profiling of human urine in hepatocellular carcinoma patients using gas chromatography/mass spectrometry. Anal Chim Acta. 2009 Aug 19;648(1):98-104. doi: 10.1016/j.aca.2009.06.033. Epub 2009 Jun 21. [PubMed:19616694 ]

Associated OMIM IDs

114550 (Hepatocellular carcinoma)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB028944

KNApSAcK ID

Not Available

Chemspider ID

389751

KEGG Compound ID

C06115

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

440921

PDB ID

Not Available

ChEBI ID

6178

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Mao YY, Bai JQ, Chen JH, Shou ZF, He Q, Wu JY, Chen Y, Cheng YY: A pilot study of GC/MS-based serum metabolic profiling of acute rejection in renal transplantation. Transpl Immunol. 2008 Apr;19(1):74-80. doi: 10.1016/j.trim.2008.01.006. Epub 2008 Feb 22. [PubMed:18346641 ]

Showing metabocard for Arabinofuranose (HMDB0012325)

MOL for HMDB0012325 (Arabinofuranose)

3D MOL for HMDB0012325 (Arabinofuranose)

3D SDF for HMDB0012325 (Arabinofuranose)

3D-SDF for HMDB0012325 (Arabinofuranose)

PDB for HMDB0012325 (Arabinofuranose)

3D PDB for HMDB0012325 (Arabinofuranose)

SMILES for HMDB0012325 (Arabinofuranose)

INCHI for HMDB0012325 (Arabinofuranose)

Structure for HMDB0012325 (Arabinofuranose)

3D Structure for HMDB0012325 (Arabinofuranose)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra