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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2012-09-11 17:33:42 UTC

Update Date

2023-02-21 17:19:23 UTC

HMDB ID

HMDB0029942

Secondary Accession Numbers

HMDB29942

Metabolite Identification

Common Name

D-Arabinose

Description

D-Arabinose, also known as arabinopyranose or pectinose, belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. D-Arabinose is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review very few articles have been published on D-Arabinose.

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/[a122h-1b_1-5]/1/	ChEBI
b-D-Arabinopyranose	HMDB
Β-D-arabinopyranose	HMDB
Arabinopyranose	HMDB
Arabinose	HMDB
D-Arabinopyranose	HMDB
Pectinose	HMDB
beta-D-Arabinopyranose	HMDB
beta-D-Arabinose	HMDB
Β-D-arabinose	HMDB
D-Arabinose	HMDB

Chemical Formula

C₅H₁₀O₅

Average Molecular Weight

150.13

Monoisotopic Molecular Weight

150.052823422

IUPAC Name

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

Traditional Name

D-arabinopyranose

CAS Registry Number

6748-95-4

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-/m1/s1

InChI Key

SRBFZHDQGSBBOR-SQOUGZDYSA-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

D-arabinopyranose (CHEBI:46996 )

Ontology

Not Available

Physical Properties

State

Not Available

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	380 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	13.42 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
DeepCCS	[M+H]+	134.601	30932474
DeepCCS	[M-H]-	132.379	30932474
DeepCCS	[M-2H]-	166.982	30932474
DeepCCS	[M+Na]+	141.124	30932474
AllCCS	[M+H]+	134.2	32859911
AllCCS	[M+H-H2O]+	129.6	32859911
AllCCS	[M+NH4]+	138.4	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
D-Arabinose	O[C@@H]1CO[C@@H](O)[C@@H](O)[C@@H]1O	3000.0	Standard polar	33892256
D-Arabinose	O[C@@H]1CO[C@@H](O)[C@@H](O)[C@@H]1O	1530.6	Standard non polar	33892256
D-Arabinose	O[C@@H]1CO[C@@H](O)[C@@H](O)[C@@H]1O	1384.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
D-Arabinose,1TMS,isomer #1	C[Si](C)(C)O[C@@H]1CO[C@@H](O)[C@@H](O)[C@@H]1O	1494.4	Semi standard non polar	33892256
D-Arabinose,1TMS,isomer #2	C[Si](C)(C)O[C@@H]1OC[C@@H](O)[C@@H](O)[C@@H]1O	1456.1	Semi standard non polar	33892256
D-Arabinose,1TMS,isomer #3	C[Si](C)(C)O[C@@H]1[C@H](O)OC[C@@H](O)[C@H]1O	1492.8	Semi standard non polar	33892256
D-Arabinose,1TMS,isomer #4	C[Si](C)(C)O[C@H]1[C@H](O)[C@H](O)OC[C@H]1O	1501.0	Semi standard non polar	33892256
D-Arabinose,2TMS,isomer #1	C[Si](C)(C)O[C@@H]1OC[C@@H](O[Si](C)(C)C)[C@@H](O)[C@@H]1O	1519.1	Semi standard non polar	33892256
D-Arabinose,2TMS,isomer #2	C[Si](C)(C)O[C@@H]1[C@H](O)OC[C@@H](O[Si](C)(C)C)[C@H]1O	1515.9	Semi standard non polar	33892256
D-Arabinose,2TMS,isomer #3	C[Si](C)(C)O[C@H]1[C@H](O)[C@H](O)OC[C@H]1O[Si](C)(C)C	1471.6	Semi standard non polar	33892256
D-Arabinose,2TMS,isomer #4	C[Si](C)(C)O[C@@H]1OC[C@@H](O)[C@@H](O[Si](C)(C)C)[C@@H]1O	1518.4	Semi standard non polar	33892256
D-Arabinose,2TMS,isomer #5	C[Si](C)(C)O[C@@H]1OC[C@@H](O)[C@@H](O)[C@@H]1O[Si](C)(C)C	1477.7	Semi standard non polar	33892256
D-Arabinose,2TMS,isomer #6	C[Si](C)(C)O[C@@H]1[C@H](O)OC[C@@H](O)[C@H]1O[Si](C)(C)C	1495.9	Semi standard non polar	33892256
D-Arabinose,3TMS,isomer #1	C[Si](C)(C)O[C@@H]1OC[C@@H](O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@@H]1O	1560.9	Semi standard non polar	33892256
D-Arabinose,3TMS,isomer #2	C[Si](C)(C)O[C@@H]1OC[C@@H](O[Si](C)(C)C)[C@@H](O)[C@@H]1O[Si](C)(C)C	1548.5	Semi standard non polar	33892256
D-Arabinose,3TMS,isomer #3	C[Si](C)(C)O[C@@H]1[C@H](O)OC[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	1553.8	Semi standard non polar	33892256
D-Arabinose,3TMS,isomer #4	C[Si](C)(C)O[C@@H]1OC[C@@H](O)[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	1576.0	Semi standard non polar	33892256
D-Arabinose,4TMS,isomer #1	C[Si](C)(C)O[C@@H]1OC[C@@H](O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	1645.4	Semi standard non polar	33892256
D-Arabinose,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@@H]1CO[C@@H](O)[C@@H](O)[C@@H]1O	1744.5	Semi standard non polar	33892256
D-Arabinose,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@@H]1OC[C@@H](O)[C@@H](O)[C@@H]1O	1707.1	Semi standard non polar	33892256
D-Arabinose,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@@H]1[C@H](O)OC[C@@H](O)[C@H]1O	1726.7	Semi standard non polar	33892256
D-Arabinose,1TBDMS,isomer #4	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O)[C@H](O)OC[C@H]1O	1732.8	Semi standard non polar	33892256
D-Arabinose,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@@H]1OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](O)[C@@H]1O	1990.7	Semi standard non polar	33892256
D-Arabinose,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@@H]1[C@H](O)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O	1979.0	Semi standard non polar	33892256
D-Arabinose,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O)[C@H](O)OC[C@H]1O[Si](C)(C)C(C)(C)C	1956.2	Semi standard non polar	33892256
D-Arabinose,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)O[C@@H]1OC[C@@H](O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	1976.0	Semi standard non polar	33892256
D-Arabinose,2TBDMS,isomer #5	CC(C)(C)[Si](C)(C)O[C@@H]1OC[C@@H](O)[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	1949.6	Semi standard non polar	33892256
D-Arabinose,2TBDMS,isomer #6	CC(C)(C)[Si](C)(C)O[C@@H]1[C@H](O)OC[C@@H](O)[C@H]1O[Si](C)(C)C(C)(C)C	1958.4	Semi standard non polar	33892256
D-Arabinose,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@@H]1OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	2254.8	Semi standard non polar	33892256
D-Arabinose,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@@H]1OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	2238.9	Semi standard non polar	33892256
D-Arabinose,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@@H]1[C@H](O)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C	2250.2	Semi standard non polar	33892256
D-Arabinose,3TBDMS,isomer #4	CC(C)(C)[Si](C)(C)O[C@@H]1OC[C@@H](O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	2239.3	Semi standard non polar	33892256
D-Arabinose,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@@H]1OC[C@@H](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	2479.8	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 - D-Arabinose GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Arabinose 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 - D-Arabinose 10V, Negative-QTOF	splash10-0002-7900000000-524214992b29f1ff9b80	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Arabinose 20V, Negative-QTOF	splash10-0a4i-9000000000-f758a7d33dac04b06275	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Arabinose 40V, Negative-QTOF	splash10-0a4l-9000000000-4b3e154b12c2ee07bf58	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Arabinose 10V, Positive-QTOF	splash10-0gc0-1900000000-e784a3fdca89dcb59c12	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Arabinose 20V, Positive-QTOF	splash10-0m4p-9100000000-fc295e2732f55a0a18c1	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Arabinose 40V, Positive-QTOF	splash10-0007-9000000000-ba5f29c2c79df8d0956f	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Blood
Feces
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	34436864	details
Feces	Detected and Quantified	1041.0984 +/- 657.431 nmol/g wet feces	Not Specified	Not Specified	Normal	20669995	details
Feces	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	20669995	details
Feces	Detected but not Quantified	Not Quantified	Infant (0-1 year old)	Both	Normal	22411374	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	34436864	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal Cancer	27275383	details

Associated Disorders and Diseases

Disease References

Colorectal cancer
Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]

Associated OMIM IDs

114500 (Colorectal cancer)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB001219

KNApSAcK ID

C00001115

Chemspider ID

392169

KEGG Compound ID

Not Available

BioCyc ID

CPD-12049

BiGG ID

Not Available

Wikipedia Link

Arabinose

METLIN ID

Not Available

PubChem Compound

444173

PDB ID

Not Available

ChEBI ID

46996

Food Biomarker Ontology

Not Available

VMH ID

ARAB_D

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for D-Arabinose (HMDB0029942)

MOL for HMDB0029942 (D-Arabinose)

3D MOL for HMDB0029942 (D-Arabinose)

3D SDF for HMDB0029942 (D-Arabinose)

3D-SDF for HMDB0029942 (D-Arabinose)

PDB for HMDB0029942 (D-Arabinose)

3D PDB for HMDB0029942 (D-Arabinose)

SMILES for HMDB0029942 (D-Arabinose)

INCHI for HMDB0029942 (D-Arabinose)

Structure for HMDB0029942 (D-Arabinose)

3D Structure for HMDB0029942 (D-Arabinose)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra