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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 21:31:12 UTC

Update Date

2022-03-07 02:54:54 UTC

HMDB ID

HMDB0036382

Secondary Accession Numbers

HMDB36382

Metabolite Identification

Common Name

6-Deoxyfagomine

Description

6-Deoxyfagomine 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. Based on a literature review very few articles have been published on 6-Deoxyfagomine.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
(-)-6-Deoxy-fagomine	HMDB
6-Deoxy-fagomine	HMDB

Chemical Formula

C₆H₁₃NO₂

Average Molecular Weight

131.1729

Monoisotopic Molecular Weight

131.094628665

IUPAC Name

2-methylpiperidine-3,4-diol

Traditional Name

2-methylpiperidine-3,4-diol

CAS Registry Number

197449-09-5

SMILES

CC1NCCC(O)C1O

InChI Identifier

InChI=1S/C6H13NO2/c1-4-6(9)5(8)2-3-7-4/h4-9H,2-3H2,1H3

InChI Key

RMJCALHKIHCSMY-UHFFFAOYSA-N

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

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0036382)
Cytoplasm (HMDB: HMDB0036382)

Source

Exogenous

Food

Food (HMDB: HMDB0036382)

Not Available

Nutrient (HMDB: HMDB0036382)

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	1000000 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	542 g/L	ALOGPS
logP	-0.93	ALOGPS
logP	-1.1	ChemAxon
logS	0.62	ALOGPS
pKa (Strongest Acidic)	13.51	ChemAxon
pKa (Strongest Basic)	9.21	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	52.49 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	33.93 m³·mol⁻¹	ChemAxon
Polarizability	14.09 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]+	127.361	31661259
DarkChem	[M-H]-	120.611	31661259
DeepCCS	[M+H]+	132.113	30932474
DeepCCS	[M-H]-	130.007	30932474
DeepCCS	[M-2H]-	165.982	30932474
DeepCCS	[M+Na]+	140.787	30932474
AllCCS	[M+H]+	129.5	32859911
AllCCS	[M+H-H2O]+	124.8	32859911
AllCCS	[M+NH4]+	133.9	32859911
AllCCS	[M+Na]+	135.2	32859911
AllCCS	[M-H]-	125.6	32859911
AllCCS	[M+Na-2H]-	127.8	32859911
AllCCS	[M+HCOO]-	130.2	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
6-Deoxyfagomine	CC1NCCC(O)C1O	2266.0	Standard polar	33892256
6-Deoxyfagomine	CC1NCCC(O)C1O	1241.3	Standard non polar	33892256
6-Deoxyfagomine	CC1NCCC(O)C1O	1230.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
6-Deoxyfagomine,1TMS,isomer #1	CC1NCCC(O[Si](C)(C)C)C1O	1279.8	Semi standard non polar	33892256
6-Deoxyfagomine,1TMS,isomer #2	CC1NCCC(O)C1O[Si](C)(C)C	1315.0	Semi standard non polar	33892256
6-Deoxyfagomine,1TMS,isomer #3	CC1C(O)C(O)CCN1[Si](C)(C)C	1370.1	Semi standard non polar	33892256
6-Deoxyfagomine,2TMS,isomer #1	CC1NCCC(O[Si](C)(C)C)C1O[Si](C)(C)C	1386.8	Semi standard non polar	33892256
6-Deoxyfagomine,2TMS,isomer #2	CC1C(O)C(O[Si](C)(C)C)CCN1[Si](C)(C)C	1420.4	Semi standard non polar	33892256
6-Deoxyfagomine,2TMS,isomer #3	CC1C(O[Si](C)(C)C)C(O)CCN1[Si](C)(C)C	1432.3	Semi standard non polar	33892256
6-Deoxyfagomine,3TMS,isomer #1	CC1C(O[Si](C)(C)C)C(O[Si](C)(C)C)CCN1[Si](C)(C)C	1510.4	Semi standard non polar	33892256
6-Deoxyfagomine,3TMS,isomer #1	CC1C(O[Si](C)(C)C)C(O[Si](C)(C)C)CCN1[Si](C)(C)C	1531.9	Standard non polar	33892256
6-Deoxyfagomine,1TBDMS,isomer #1	CC1NCCC(O[Si](C)(C)C(C)(C)C)C1O	1527.7	Semi standard non polar	33892256
6-Deoxyfagomine,1TBDMS,isomer #2	CC1NCCC(O)C1O[Si](C)(C)C(C)(C)C	1548.9	Semi standard non polar	33892256
6-Deoxyfagomine,1TBDMS,isomer #3	CC1C(O)C(O)CCN1[Si](C)(C)C(C)(C)C	1630.7	Semi standard non polar	33892256
6-Deoxyfagomine,2TBDMS,isomer #1	CC1NCCC(O[Si](C)(C)C(C)(C)C)C1O[Si](C)(C)C(C)(C)C	1812.8	Semi standard non polar	33892256
6-Deoxyfagomine,2TBDMS,isomer #2	CC1C(O)C(O[Si](C)(C)C(C)(C)C)CCN1[Si](C)(C)C(C)(C)C	1876.5	Semi standard non polar	33892256
6-Deoxyfagomine,2TBDMS,isomer #3	CC1C(O[Si](C)(C)C(C)(C)C)C(O)CCN1[Si](C)(C)C(C)(C)C	1871.2	Semi standard non polar	33892256
6-Deoxyfagomine,3TBDMS,isomer #1	CC1C(O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)CCN1[Si](C)(C)C(C)(C)C	2143.7	Semi standard non polar	33892256
6-Deoxyfagomine,3TBDMS,isomer #1	CC1C(O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)CCN1[Si](C)(C)C(C)(C)C	2196.6	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 6-Deoxyfagomine GC-MS (Non-derivatized) - 70eV, Positive	splash10-074l-9300000000-210e4186cd3d9465ee03	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 6-Deoxyfagomine GC-MS (2 TMS) - 70eV, Positive	splash10-074r-9850000000-64dd3aa9ea80f5546765	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 6-Deoxyfagomine 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 - 6-Deoxyfagomine 10V, Positive-QTOF	splash10-001i-1900000000-1eed61863fa3097ecbed	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6-Deoxyfagomine 20V, Positive-QTOF	splash10-01qa-7900000000-d962f68c93310b620284	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6-Deoxyfagomine 40V, Positive-QTOF	splash10-052e-9000000000-1458ad075ed40e44ec53	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6-Deoxyfagomine 10V, Negative-QTOF	splash10-001i-1900000000-d4c42898a0463209568f	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6-Deoxyfagomine 20V, Negative-QTOF	splash10-001i-7900000000-d169935340cb740ca359	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6-Deoxyfagomine 40V, Negative-QTOF	splash10-052f-9000000000-0c3793268633c265e290	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6-Deoxyfagomine 10V, Positive-QTOF	splash10-01q9-2900000000-d5b2f71dde168c0a84a1	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6-Deoxyfagomine 20V, Positive-QTOF	splash10-0ac3-9300000000-3504d3b510ac2d8e24bc	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6-Deoxyfagomine 40V, Positive-QTOF	splash10-0a4m-9000000000-8bbcfd71e2421f1be2fd	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6-Deoxyfagomine 10V, Negative-QTOF	splash10-001i-0900000000-a42e42c2c7f8ddcd644f	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6-Deoxyfagomine 20V, Negative-QTOF	splash10-059x-9400000000-3efa73ad5a65160c607b	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6-Deoxyfagomine 40V, Negative-QTOF	splash10-052f-9000000000-d2335899b725a6fb1789	2021-09-23	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

Cytoplasm
Extracellular

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

FDB015260

KNApSAcK ID

C00036613

Chemspider ID

35014134

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

57449463

PDB ID

Not Available

ChEBI ID

172323

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1854901

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 6-Deoxyfagomine (HMDB0036382)

MOL for HMDB0036382 (6-Deoxyfagomine)

3D MOL for HMDB0036382 (6-Deoxyfagomine)

3D SDF for HMDB0036382 (6-Deoxyfagomine)

3D-SDF for HMDB0036382 (6-Deoxyfagomine)

PDB for HMDB0036382 (6-Deoxyfagomine)

3D PDB for HMDB0036382 (6-Deoxyfagomine)

SMILES for HMDB0036382 (6-Deoxyfagomine)

INCHI for HMDB0036382 (6-Deoxyfagomine)

Structure for HMDB0036382 (6-Deoxyfagomine)

3D Structure for HMDB0036382 (6-Deoxyfagomine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra