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

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 18:35:43 UTC

Update Date

2022-03-07 02:53:52 UTC

HMDB ID

HMDB0033821

Secondary Accession Numbers

HMDB33821

Metabolite Identification

Common Name

2-O-Methyl-D-xylose

Description

2-O-Methyl-D-xylose belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. 2-O-Methyl-D-xylose has been detected, but not quantified in, fruits. This could make 2-O-methyl-D-xylose a potential biomarker for the consumption of these foods. Based on a literature review a small amount of articles have been published on 2-O-Methyl-D-xylose.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₆H₁₂O₅

Average Molecular Weight

164.1565

Monoisotopic Molecular Weight

164.068473494

IUPAC Name

5-(hydroxymethyl)-3-methoxyoxolane-2,4-diol

Traditional Name

5-(hydroxymethyl)-3-methoxyoxolane-2,4-diol

CAS Registry Number

7434-28-8

SMILES

COC1C(O)OC(CO)C1O

InChI Identifier

InChI=1S/C6H12O5/c1-10-5-4(8)3(2-7)11-6(5)9/h3-9H,2H2,1H3

InChI Key

STGXGJRRAJKJRG-UHFFFAOYSA-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
Ether
Dialkyl ether
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Ingestion (HMDB: HMDB0033821)

Source

Exogenous

Food

Food (HMDB: HMDB0033821)

Fruit

Fruits (FooDB: FOOD00871)

Endogenous

Plant

Plant (HMDB: HMDB0033821)

Not Available

Nutrient (HMDB: HMDB0033821)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	137 - 138 °C	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	971 g/L	ALOGPS
logP	-1.7	ALOGPS
logP	-1.7	ChemAxon
logS	0.77	ALOGPS
pKa (Strongest Acidic)	11.33	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	79.15 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	34.71 m³·mol⁻¹	ChemAxon
Polarizability	15.71 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]+	134.99	31661259
DarkChem	[M-H]-	131.966	31661259
DeepCCS	[M+H]+	141.296	30932474
DeepCCS	[M-H]-	137.983	30932474
DeepCCS	[M-2H]-	175.166	30932474
DeepCCS	[M+Na]+	150.406	30932474
AllCCS	[M+H]+	137.9	32859911
AllCCS	[M+H-H2O]+	133.6	32859911
AllCCS	[M+NH4]+	141.9	32859911
AllCCS	[M+Na]+	143.1	32859911
AllCCS	[M-H]-	131.6	32859911
AllCCS	[M+Na-2H]-	133.1	32859911
AllCCS	[M+HCOO]-	134.7	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-O-Methyl-D-xylose	COC1C(O)OC(CO)C1O	3238.0	Standard polar	33892256
2-O-Methyl-D-xylose	COC1C(O)OC(CO)C1O	1481.5	Standard non polar	33892256
2-O-Methyl-D-xylose	COC1C(O)OC(CO)C1O	1424.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2-O-Methyl-D-xylose,1TMS,isomer #1	COC1C(O[Si](C)(C)C)OC(CO)C1O	1470.3	Semi standard non polar	33892256
2-O-Methyl-D-xylose,1TMS,isomer #2	COC1C(O)OC(CO[Si](C)(C)C)C1O	1467.3	Semi standard non polar	33892256
2-O-Methyl-D-xylose,1TMS,isomer #3	COC1C(O)OC(CO)C1O[Si](C)(C)C	1477.9	Semi standard non polar	33892256
2-O-Methyl-D-xylose,2TMS,isomer #1	COC1C(O[Si](C)(C)C)OC(CO[Si](C)(C)C)C1O	1547.8	Semi standard non polar	33892256
2-O-Methyl-D-xylose,2TMS,isomer #2	COC1C(O[Si](C)(C)C)OC(CO)C1O[Si](C)(C)C	1533.6	Semi standard non polar	33892256
2-O-Methyl-D-xylose,2TMS,isomer #3	COC1C(O)OC(CO[Si](C)(C)C)C1O[Si](C)(C)C	1545.6	Semi standard non polar	33892256
2-O-Methyl-D-xylose,3TMS,isomer #1	COC1C(O[Si](C)(C)C)OC(CO[Si](C)(C)C)C1O[Si](C)(C)C	1589.9	Semi standard non polar	33892256
2-O-Methyl-D-xylose,1TBDMS,isomer #1	COC1C(O[Si](C)(C)C(C)(C)C)OC(CO)C1O	1705.5	Semi standard non polar	33892256
2-O-Methyl-D-xylose,1TBDMS,isomer #2	COC1C(O)OC(CO[Si](C)(C)C(C)(C)C)C1O	1697.7	Semi standard non polar	33892256
2-O-Methyl-D-xylose,1TBDMS,isomer #3	COC1C(O)OC(CO)C1O[Si](C)(C)C(C)(C)C	1712.6	Semi standard non polar	33892256
2-O-Methyl-D-xylose,2TBDMS,isomer #1	COC1C(O[Si](C)(C)C(C)(C)C)OC(CO[Si](C)(C)C(C)(C)C)C1O	1973.3	Semi standard non polar	33892256
2-O-Methyl-D-xylose,2TBDMS,isomer #2	COC1C(O[Si](C)(C)C(C)(C)C)OC(CO)C1O[Si](C)(C)C(C)(C)C	1975.6	Semi standard non polar	33892256
2-O-Methyl-D-xylose,2TBDMS,isomer #3	COC1C(O)OC(CO[Si](C)(C)C(C)(C)C)C1O[Si](C)(C)C(C)(C)C	1981.7	Semi standard non polar	33892256
2-O-Methyl-D-xylose,3TBDMS,isomer #1	COC1C(O[Si](C)(C)C(C)(C)C)OC(CO[Si](C)(C)C(C)(C)C)C1O[Si](C)(C)C(C)(C)C	2240.2	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 - 2-O-Methyl-D-xylose GC-MS (Non-derivatized) - 70eV, Positive	splash10-00dl-9200000000-a002eed1a3ad8caa80a2	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-O-Methyl-D-xylose GC-MS (3 TMS) - 70eV, Positive	splash10-0g12-4792000000-1e94d4aac52f27b30297	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-O-Methyl-D-xylose 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 - 2-O-Methyl-D-xylose 10V, Positive-QTOF	splash10-014i-1900000000-cd6d21623be74add8f05	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methyl-D-xylose 20V, Positive-QTOF	splash10-014j-2900000000-7e1417c50404d72ae92d	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methyl-D-xylose 40V, Positive-QTOF	splash10-00mn-9200000000-b86a807f8566713a9417	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methyl-D-xylose 10V, Negative-QTOF	splash10-03di-1900000000-a69e46b5087ef06cd884	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methyl-D-xylose 20V, Negative-QTOF	splash10-03dj-2900000000-19da9b3024d14fadfa3b	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methyl-D-xylose 40V, Negative-QTOF	splash10-0006-9200000000-cd2f590bd6f08b9cf2e6	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methyl-D-xylose 10V, Positive-QTOF	splash10-015a-0900000000-a37820cd17dcca50d0ad	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methyl-D-xylose 20V, Positive-QTOF	splash10-00tb-9400000000-9177fdc441a75b65ab29	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methyl-D-xylose 40V, Positive-QTOF	splash10-052b-9000000000-91cecb7a2de20bb1564a	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methyl-D-xylose 10V, Negative-QTOF	splash10-03k9-4900000000-991b351c3df2017362d1	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methyl-D-xylose 20V, Negative-QTOF	splash10-0a4u-9400000000-b63f7b65e2ad27951e5d	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methyl-D-xylose 40V, Negative-QTOF	splash10-0a4l-9000000000-60dbbcd817a65d0aaafb	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

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

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB011986

KNApSAcK ID

Not Available

Chemspider ID

486947

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

560157

PDB ID

Not Available

ChEBI ID

Not Available

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

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

Showing metabocard for 2-O-Methyl-D-xylose (HMDB0033821)

MOL for HMDB0033821 (2-O-Methyl-D-xylose)

3D MOL for HMDB0033821 (2-O-Methyl-D-xylose)

3D SDF for HMDB0033821 (2-O-Methyl-D-xylose)

3D-SDF for HMDB0033821 (2-O-Methyl-D-xylose)

PDB for HMDB0033821 (2-O-Methyl-D-xylose)

3D PDB for HMDB0033821 (2-O-Methyl-D-xylose)

SMILES for HMDB0033821 (2-O-Methyl-D-xylose)

INCHI for HMDB0033821 (2-O-Methyl-D-xylose)

Structure for HMDB0033821 (2-O-Methyl-D-xylose)

3D Structure for HMDB0033821 (2-O-Methyl-D-xylose)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra