MiMeDB: Showing metabocard for D-Xylono-1,5-lactone (MMDBc0048868)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:12:26 UTC

Update Date

2024-04-30 20:37:37 UTC

Metabolite ID

MMDBc0048868

Metabolite Identification

Common Name

D-Xylono-1,5-lactone

Description

D-Xylono-1,5-lactone, also known as D-xylonolactone, belongs to the class of organic compounds known as delta valerolactones. These are cyclic organic compounds containing an oxan-2- one moiety. D-Xylono-1,5-lactone has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make D-xylono-1,5-lactone a potential biomarker for the consumption of these foods. D-Xylono-1,5-lactone 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-Xylono-1,5-lactone.

Structure

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

Synonyms

Value	Source
D-Xylonolactone	ChEBI
Xylonolactone	HMDB

Molecular Formula

C₅H₈O₅

Average Mass

148.114

Monoisotopic Mass

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 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted 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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-006x-9200000000-9be356e915f5897a8457	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0umr-5393000000-7965b784b3d72826f0d8	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000t-0900000000-76be85e7ac9842da922d	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001j-0900000000-6503dfb28a322525b19b	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9000000000-6d2c25a921117df43c23	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-1900000000-553611cef4b5ef504aaa	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0092-4900000000-6160c263002249bb2798	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-778239485e740a0bac20	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-3900000000-e1d13fcaf4a10f71b067	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-052f-9000000000-6244519c64b48d453565	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9000000000-66b1430247d75367a183	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01x0-4900000000-2a8ed88211a98056f83b	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00di-9000000000-824a8872c2d8c7415b9f	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9000000000-1f8660ec1076805bcc2d	2021-09-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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
MMDBp0192149	Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase	Enzyme	Q9UQ10	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0010291	NADP	Hydrogen Ion	Dihydrodiol dehydrogenase (dimeric)	D-Xylose:NADP+ 1-Oxidoreductase	VMH; KEGG	30371894
MMDBr0013259	D-Xylose	D-Xylono-1,5-lactone	D-xylose 1-dehydrogenase	Dehydrogenation	RHEA	34755880
MMDBr0014163	D-Xylose	D-Xylono-1,5-lactone	D-xylose 1-dehydrogenase (NADP(+))	Dehydrogenation	RHEA	34755880
MMDBr0016994	D-Xylose	D-Xylono-1,5-lactone	Carbohydrate oxidase	Oxidation	RHEA	34755880

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
Bacteria	Proteobacteria	1
Bacteria/NULL	Actinobacteria	1
Eukaryota/Fungi	Ascomycota	3
Archaea/Archaea	Euryarchaeota	1

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0011676

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

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
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 D-Xylono-1,5-lactone (MMDBc0048868)

MOL for #<Metabolite:0x00007fa4d2db0230>

3D MOL for #<Metabolite:0x00007fa4d2db0230>

3D SDF for #<Metabolite:0x00007fa4d2db0230>

3D-SDF for #<Metabolite:0x00007fa4d2db0230>

PDB for #<Metabolite:0x00007fa4d2db0230>

3D PDB for #<Metabolite:0x00007fa4d2db0230>

SMILES for #<Metabolite:0x00007fa4d2db0230>

INCHI for #<Metabolite:0x00007fa4d2db0230>

Structure for #<Metabolite:0x00007fa4d2db0230>

3D Structure for #<Metabolite:0x00007fa4d2db0230>