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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (1) Show 1 protein XML

enzymes (1) Show 1 protein

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2009-02-04 10:13:48 UTC

Update Date

2023-02-21 17:17:33 UTC

HMDB ID

HMDB0011676

Secondary Accession Numbers

HMDB11676

Metabolite Identification

Common Name

D-Xylono-1,5-lactone

Description

D-xylonolactone is a lactone derivative of xylonic acid. It is an intermediate in the pentose and glucuronate interconversion pathway and can be formed from either D-xylonic acid or D-xylose. D-xylose is a simple 5 carbon sugar that is found in a variety of edible plants. It is also frequently used in intestinal absorption tests to help diagnose problems that prevent the small intestine from absorbing nutrients in food. Xylose is also the first saccharide added to the serine or threonine in the proteoglycan type O-glycosylation and so it is the first saccharide in biosynthetic pathways of most anionic polysaccharides such as heparan sulfate and chondroitin sulfate. D-xylose is normally easily absorbed by the intestines where it can be converted to D-xylonolactone by intestinal D-xylose 1-dehydrogenase (EC 1.1.1.175).

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
D-Xylonolactone	ChEBI
Xylonolactone	HMDB

Chemical Formula

C₅H₈O₅

Average Molecular Weight

148.114

Monoisotopic Molecular Weight

148.037173366

IUPAC Name

(3R,4S,5R)-3,4,5-trihydroxyoxan-2-one

Traditional Name

D-xylonolactone

CAS Registry Number

Not Available

SMILES

O[C@@H]1COC(=O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C5H8O5/c6-2-1-10-5(9)4(8)3(2)7/h2-4,6-8H,1H2/t2-,3+,4-/m1/s1

InChI Key

XXBSUZSONOQQGK-FLRLBIABSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as delta valerolactones. These are cyclic organic compounds containing an oxan-2- one moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Lactones

Sub Class

Delta valerolactones

Direct Parent

Delta valerolactones

Alternative Parents

Substituents

Delta valerolactone
Delta_valerolactone
Oxane
Carboxylic acid ester
Secondary alcohol
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Oxacycle
Polyol
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

xylonolactone (CHEBI:15867 )

Ontology

Not Available

Endogenous (HMDB: HMDB0011676)

Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)
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)

Equine

Horse (FooDB: FOOD00378)

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)

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	830 g/L	ALOGPS
logP	-2.1	ALOGPS
logP	-2.1	ChemAxon
logS	0.75	ALOGPS
pKa (Strongest Acidic)	11.63	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	86.99 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	28.82 m³·mol⁻¹	ChemAxon
Polarizability	12.53 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	130.843	31661259
DarkChem	[M-H]-	126.797	31661259
DeepCCS	[M+H]+	134.173	30932474
DeepCCS	[M-H]-	132.057	30932474
DeepCCS	[M-2H]-	167.06	30932474
DeepCCS	[M+Na]+	140.992	30932474
AllCCS	[M+H]+	133.1	32859911
AllCCS	[M+H-H2O]+	128.5	32859911
AllCCS	[M+NH4]+	137.4	32859911
AllCCS	[M+Na]+	138.7	32859911
AllCCS	[M-H]-	123.9	32859911
AllCCS	[M+Na-2H]-	125.5	32859911
AllCCS	[M+HCOO]-	127.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
D-Xylono-1,5-lactone	O[C@@H]1COC(=O)[C@H](O)[C@H]1O	2724.9	Standard polar	33892256
D-Xylono-1,5-lactone	O[C@@H]1COC(=O)[C@H](O)[C@H]1O	1343.0	Standard non polar	33892256
D-Xylono-1,5-lactone	O[C@@H]1COC(=O)[C@H](O)[C@H]1O	1516.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
D-Xylono-1,5-lactone,1TMS,isomer #1	C[Si](C)(C)O[C@@H]1COC(=O)[C@H](O)[C@H]1O	1461.3	Semi standard non polar	33892256
D-Xylono-1,5-lactone,1TMS,isomer #2	C[Si](C)(C)O[C@H]1C(=O)OC[C@@H](O)[C@@H]1O	1499.2	Semi standard non polar	33892256
D-Xylono-1,5-lactone,1TMS,isomer #3	C[Si](C)(C)O[C@H]1[C@H](O)COC(=O)[C@@H]1O	1493.5	Semi standard non polar	33892256
D-Xylono-1,5-lactone,2TMS,isomer #1	C[Si](C)(C)O[C@@H]1COC(=O)[C@H](O[Si](C)(C)C)[C@H]1O	1574.7	Semi standard non polar	33892256
D-Xylono-1,5-lactone,2TMS,isomer #2	C[Si](C)(C)O[C@@H]1COC(=O)[C@H](O)[C@H]1O[Si](C)(C)C	1533.6	Semi standard non polar	33892256
D-Xylono-1,5-lactone,2TMS,isomer #3	C[Si](C)(C)O[C@H]1[C@H](O)COC(=O)[C@@H]1O[Si](C)(C)C	1561.9	Semi standard non polar	33892256
D-Xylono-1,5-lactone,3TMS,isomer #1	C[Si](C)(C)O[C@H]1[C@H](O[Si](C)(C)C)COC(=O)[C@@H]1O[Si](C)(C)C	1608.1	Semi standard non polar	33892256
D-Xylono-1,5-lactone,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@@H]1COC(=O)[C@H](O)[C@H]1O	1717.6	Semi standard non polar	33892256
D-Xylono-1,5-lactone,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1C(=O)OC[C@@H](O)[C@@H]1O	1731.6	Semi standard non polar	33892256
D-Xylono-1,5-lactone,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O)COC(=O)[C@@H]1O	1733.7	Semi standard non polar	33892256
D-Xylono-1,5-lactone,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@@H]1COC(=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@H]1O	2008.1	Semi standard non polar	33892256
D-Xylono-1,5-lactone,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@@H]1COC(=O)[C@H](O)[C@H]1O[Si](C)(C)C(C)(C)C	1977.3	Semi standard non polar	33892256
D-Xylono-1,5-lactone,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O)COC(=O)[C@@H]1O[Si](C)(C)C(C)(C)C	1982.9	Semi standard non polar	33892256
D-Xylono-1,5-lactone,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O[Si](C)(C)C(C)(C)C)COC(=O)[C@@H]1O[Si](C)(C)C(C)(C)C	2255.2	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 - D-Xylono-1,5-lactone GC-MS (Non-derivatized) - 70eV, Positive	splash10-006x-9200000000-9be356e915f5897a8457	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylono-1,5-lactone GC-MS (3 TMS) - 70eV, Positive	splash10-0umr-5393000000-7965b784b3d72826f0d8	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylono-1,5-lactone 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-Xylono-1,5-lactone 10V, Positive-QTOF	splash10-000t-0900000000-76be85e7ac9842da922d	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Xylono-1,5-lactone 20V, Positive-QTOF	splash10-001j-0900000000-6503dfb28a322525b19b	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Xylono-1,5-lactone 40V, Positive-QTOF	splash10-0006-9000000000-6d2c25a921117df43c23	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Xylono-1,5-lactone 10V, Negative-QTOF	splash10-0002-1900000000-553611cef4b5ef504aaa	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Xylono-1,5-lactone 20V, Negative-QTOF	splash10-0092-4900000000-6160c263002249bb2798	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Xylono-1,5-lactone 40V, Negative-QTOF	splash10-0006-9000000000-778239485e740a0bac20	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Xylono-1,5-lactone 10V, Negative-QTOF	splash10-0002-3900000000-e1d13fcaf4a10f71b067	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Xylono-1,5-lactone 20V, Negative-QTOF	splash10-052f-9000000000-6244519c64b48d453565	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Xylono-1,5-lactone 40V, Negative-QTOF	splash10-0a4l-9000000000-66b1430247d75367a183	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Xylono-1,5-lactone 10V, Positive-QTOF	splash10-01x0-4900000000-2a8ed88211a98056f83b	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Xylono-1,5-lactone 20V, Positive-QTOF	splash10-00di-9000000000-824a8872c2d8c7415b9f	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Xylono-1,5-lactone 40V, Positive-QTOF	splash10-0006-9000000000-1f8660ec1076805bcc2d	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)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	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

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

FDB028364

KNApSAcK ID

Not Available

Chemspider ID

388758

KEGG Compound ID

C02266

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439692

PDB ID

Not Available

ChEBI ID

15867

Food Biomarker Ontology

Not Available

VMH ID

M01757

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Enzymes

Enzyme Details

1. Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase

General function:: Involved in catalytic activity
Specific function:: Not Available
Gene Name:: DHDH
Uniprot ID:: Q9UQ10
Molecular weight:: 36381.705

Reactions

D-Xylose + NADP → D-Xylono-1,5-lactone + NADPH	details
D-Xylose + NADP → D-Xylono-1,5-lactone + NADPH + Hydrogen Ion	details

Showing metabocard for D-Xylono-1,5-lactone (HMDB0011676)

MOL for HMDB0011676 (D-Xylono-1,5-lactone)

3D MOL for HMDB0011676 (D-Xylono-1,5-lactone)

3D SDF for HMDB0011676 (D-Xylono-1,5-lactone)

3D-SDF for HMDB0011676 (D-Xylono-1,5-lactone)

PDB for HMDB0011676 (D-Xylono-1,5-lactone)

3D PDB for HMDB0011676 (D-Xylono-1,5-lactone)

SMILES for HMDB0011676 (D-Xylono-1,5-lactone)

INCHI for HMDB0011676 (D-Xylono-1,5-lactone)

Structure for HMDB0011676 (D-Xylono-1,5-lactone)

3D Structure for HMDB0011676 (D-Xylono-1,5-lactone)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra

Enzymes

Reactions