MiMeDB: Showing metabocard for 1-Deoxyxylonojirimycin (MMDBc0030114)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:54:26 UTC

Update Date

2022-08-31 17:39:49 UTC

Metabolite ID

MMDBc0030114

Metabolite Identification

Common Name

1-Deoxyxylonojirimycin

Description

1-deoxyxylonojirimycin belongs to the class of Piperidines. These are compounds containing a piperidine ring, which is a saturated aliphatic six-member ring with one nitrogen atom and five carbon atoms. (inferred from compound structure)

Structure

MOL SDF PDB SMILES InChI

Synonyms

Not Available

Molecular Formula

C₅H₁₂NO₃

Average Mass

134.1537

Monoisotopic Mass

134.081718255

IUPAC Name

3,4,5-trihydroxypiperidin-1-ium

Traditional Name

3,4,5-trihydroxypiperidin-1-ium

CAS Registry Number

Not Available

SMILES

OC1C[NH2+]CC(O)C1O

InChI Identifier

InChI=1S/C5H11NO3/c7-3-1-6-2-4(8)5(3)9/h3-9H,1-2H2/p+1

InChI Key

RMCNETIHECSPMZ-UHFFFAOYSA-O

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as piperidines. Piperidines are compounds containing a piperidine ring, which is a saturated aliphatic six-member ring with one nitrogen atom and five carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Piperidines

Sub Class

Not Available

Direct Parent

Piperidines

Alternative Parents

Substituents

Piperidine
Secondary alcohol
1,2-aminoalcohol
Azacycle
Secondary amine
Polyol
Secondary aliphatic amine
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
Organic cation
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	279 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.3	ChemAxon
logS	0.22	ALOGPS
pKa (Strongest Acidic)	12.98	ChemAxon
pKa (Strongest Basic)	8.53	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	77.3 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	42.03 m³·mol⁻¹	ChemAxon
Polarizability	13.34 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 LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0900000000-28c94ee9bdc56fd88bf5	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-2900000000-74d8bcf57e7f969f79fe	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0007-9000000000-5914d2bb4d16ee7404d9	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-4900000000-21e4b578b9b525b3f0d1	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001l-9700000000-b85d0fc57580c20c11dc	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-72ec05557c464bcb9e56	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-23	486.2
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	395.2
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-23	40.4
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	219.8
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	281.3
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	314.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	435.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	816.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	729.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	181.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	568.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	196.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	33.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	329.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	775.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	80.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	288.4
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	663.8
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	547.2

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_1	C[Si](C)(C)OC1C[NH2+]CC(O)C1O	standard non polar	2025-10-24	1775.8
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_2	C[Si](C)(C)OC1C(O)C[NH2+]CC1O	standard non polar	2025-10-24	1895.27
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_3	C[Si](C)(C)[NH+]1CC(O)C(O)C(O)C1	standard non polar	2025-10-24	2058.75
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_4	C[Si](C)(C)OC1C[NH2+]CC(O[Si](C)(C)C)C1O	standard non polar	2025-10-24	2274.37
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_5	C[Si](C)(C)OC1C[NH2+]CC(O)C1O[Si](C)(C)C	standard non polar	2025-10-24	2363.07
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_6	C[Si](C)(C)OC1C[NH+]([Si](C)(C)C)CC(O)C1O	standard non polar	2025-10-24	1976.47
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_7	C[Si](C)(C)OC1C(O)C[NH+]([Si](C)(C)C)CC1O	standard non polar	2025-10-24	2091.87
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_8	C[Si](C)(C)[N+]1([Si](C)(C)C)CC(O)C(O)C(O)C1	standard non polar	2025-10-24	1637.45
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_9	C[Si](C)(C)OC1C[NH2+]CC(O[Si](C)(C)C)C1O[Si](C)(C)C	standard non polar	2025-10-24	2098.12
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_10	C[Si](C)(C)OC1C[NH+]([Si](C)(C)C)CC(O[Si](C)(C)C)C1O	standard non polar	2025-10-24	2417.8
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_11	C[Si](C)(C)OC1C[NH+]([Si](C)(C)C)CC(O)C1O[Si](C)(C)C	standard non polar	2025-10-24	2515.08
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_12	C[Si](C)(C)OC1C[N+]([Si](C)(C)C)([Si](C)(C)C)CC(O)C1O	standard non polar	2025-10-24	1526.32
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_13	C[Si](C)(C)OC1C(O)C[N+]([Si](C)(C)C)([Si](C)(C)C)CC1O	standard non polar	2025-10-24	1554.4
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_14	C[Si](C)(C)OC1C[NH+]([Si](C)(C)C)CC(O[Si](C)(C)C)C1O[Si](C)(C)C	standard non polar	2025-10-24	1779.73
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_15	C[Si](C)(C)OC1C[N+]([Si](C)(C)C)([Si](C)(C)C)CC(O[Si](C)(C)C)C1O	standard non polar	2025-10-24	1414.55
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_16	C[Si](C)(C)OC1C[N+]([Si](C)(C)C)([Si](C)(C)C)CC(O)C1O[Si](C)(C)C	standard non polar	2025-10-24	2737.3
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_17	C[Si](C)(C)OC1C[N+]([Si](C)(C)C)([Si](C)(C)C)CC(O[Si](C)(C)C)C1O[Si](C)(C)C	standard non polar	2025-10-24	2605.07
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_1	C[Si](C)(C)OC1C[NH2+]CC(O)C1O	standard polar	2025-10-24	2407.78
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_2	C[Si](C)(C)OC1C(O)C[NH2+]CC1O	standard polar	2025-10-24	1950.08
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_3	C[Si](C)(C)[NH+]1CC(O)C(O)C(O)C1	standard polar	2025-10-24	1638.52
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_4	C[Si](C)(C)OC1C[NH2+]CC(O[Si](C)(C)C)C1O	standard polar	2025-10-24	2041.18
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_5	C[Si](C)(C)OC1C[NH2+]CC(O)C1O[Si](C)(C)C	standard polar	2025-10-24	1965.78
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_6	C[Si](C)(C)OC1C[NH+]([Si](C)(C)C)CC(O)C1O	standard polar	2025-10-24	2486.53
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_7	C[Si](C)(C)OC1C(O)C[NH+]([Si](C)(C)C)CC1O	standard polar	2025-10-24	2085.47
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_8	C[Si](C)(C)[N+]1([Si](C)(C)C)CC(O)C(O)C(O)C1	standard polar	2025-10-24	2081.07
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_9	C[Si](C)(C)OC1C[NH2+]CC(O[Si](C)(C)C)C1O[Si](C)(C)C	standard polar	2025-10-24	1711.77
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_10	C[Si](C)(C)OC1C[NH+]([Si](C)(C)C)CC(O[Si](C)(C)C)C1O	standard polar	2025-10-24	2080.18
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_11	C[Si](C)(C)OC1C[NH+]([Si](C)(C)C)CC(O)C1O[Si](C)(C)C	standard polar	2025-10-24	1624.41
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_12	C[Si](C)(C)OC1C[N+]([Si](C)(C)C)([Si](C)(C)C)CC(O)C1O	standard polar	2025-10-24	1884.09
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_13	C[Si](C)(C)OC1C(O)C[N+]([Si](C)(C)C)([Si](C)(C)C)CC1O	standard polar	2025-10-24	1983.83
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_14	C[Si](C)(C)OC1C[NH+]([Si](C)(C)C)CC(O[Si](C)(C)C)C1O[Si](C)(C)C	standard polar	2025-10-24	1724.52
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_15	C[Si](C)(C)OC1C[N+]([Si](C)(C)C)([Si](C)(C)C)CC(O[Si](C)(C)C)C1O	standard polar	2025-10-24	1681.75
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_16	C[Si](C)(C)OC1C[N+]([Si](C)(C)C)([Si](C)(C)C)CC(O)C1O[Si](C)(C)C	standard polar	2025-10-24	2008.71
Gas Chromatography	1-Deoxyxylonojirimycin_TMS_17	C[Si](C)(C)OC1C[N+]([Si](C)(C)C)([Si](C)(C)C)CC(O[Si](C)(C)C)C1O[Si](C)(C)C	standard polar	2025-10-24	2092.71

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25203271

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muniz-Rascado L, Bonavides-Martinez C, Paley S, Krummenacker M, Altman T, Kaipa P, Spaulding A, Pacheco J, Latendresse M, Fulcher C, Sarker M, Shearer AG, Mackie A, Paulsen I, Gunsalus RP, Karp PD: EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 2011 Jan;39(Database issue):D583-90. doi: 10.1093/nar/gkq1143. Epub 2010 Nov 21. [PubMed:21097882 ]

Showing metabocard for 1-Deoxyxylonojirimycin (MMDBc0030114)

MOL for #<Metabolite:0x0000561537563090>

3D MOL for #<Metabolite:0x0000561537563090>

3D SDF for #<Metabolite:0x0000561537563090>

3D-SDF for #<Metabolite:0x0000561537563090>

PDB for #<Metabolite:0x0000561537563090>

3D PDB for #<Metabolite:0x0000561537563090>

SMILES for #<Metabolite:0x0000561537563090>

INCHI for #<Metabolite:0x0000561537563090>

Structure for #<Metabolite:0x0000561537563090>

3D Structure for #<Metabolite:0x0000561537563090>