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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 18:11:15 UTC

Update Date

2023-02-21 17:23:19 UTC

HMDB ID

HMDB0033453

Secondary Accession Numbers

HMDB33453

Metabolite Identification

Common Name

Fagomine

Description

Fagomine is an alkaloid found in the seeds of Castanospermum australe (commonly known as the Black Bean or the Moreton Bay Chestnut) (PMID: 25583438 ). Castanospermum australe is a large evergreen tree of the legume family native to the east coast of Australia in Queensland and New South Wales, and to the Pacific islands of Vanuatu, New Caledonia, and the island of New Britain (Papua New Guinea). The seeds are poisonous, but become edible when carefully prepared by roasting, cutting up into small pieces, leaching with running water for several days, and pounding into flour (Wikipedia).

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-Fagomine	ChEMBL, HMDB
Fagomine	MeSH
1,2,5-Trideoxy-1,5-imino-D-arabino-hexitol	MeSH, HMDB
(2R,3R,4R)-2-(Hydroxymethyl)-3,4-piperidinediol	PhytoBank

Chemical Formula

C₆H₁₃NO₃

Average Molecular Weight

147.174

Monoisotopic Molecular Weight

147.089543283

IUPAC Name

(2R,3R,4R)-2-(hydroxymethyl)piperidine-3,4-diol

Traditional Name

fagomine

CAS Registry Number

53185-12-9

SMILES

OC[C@H]1NCC[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C6H13NO3/c8-3-4-6(10)5(9)1-2-7-4/h4-10H,1-3H2/t4-,5-,6-/m1/s1

InChI Key

YZNNBIPIQWYLDM-HSUXUTPPSA-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
Secondary alcohol
Secondary aliphatic amine
Azacycle
Secondary amine
Organic nitrogen compound
Hydrocarbon derivative
Primary alcohol
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Amine
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

piperidines (CHEBI:4969 )
Piperidine alkaloids (C10144 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0033453)
Cytoplasm (HMDB: HMDB0033453)

Source

Exogenous

Food

Cereal and cereal product

Cereal product

Breakfast cereal (FooDB: FOOD00270)

Cereal

Common buckwheat (FooDB: FOOD00079)

Cereals and cereal products (FooDB: FOOD00858)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	186 - 188 °C	Not Available
Boiling Point	315.00 to 316.00 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	1000000 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	-0.880 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	573 g/L	ALOGPS
logP	-1.6	ALOGPS
logP	-2.2	ChemAxon
logS	0.59	ALOGPS
pKa (Strongest Acidic)	13.43	ChemAxon
pKa (Strongest Basic)	8.63	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	72.72 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	35.48 m³·mol⁻¹	ChemAxon
Polarizability	15.06 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
DeepCCS	[M+H]+	134.665	30932474
DeepCCS	[M-H]-	132.499	30932474
DeepCCS	[M-2H]-	167.514	30932474
DeepCCS	[M+Na]+	141.965	30932474
AllCCS	[M+H]+	133.2	32859911
AllCCS	[M+H-H2O]+	128.7	32859911
AllCCS	[M+NH4]+	137.5	32859911
AllCCS	[M+Na]+	138.7	32859911
AllCCS	[M-H]-	127.3	32859911
AllCCS	[M+Na-2H]-	129.0	32859911
AllCCS	[M+HCOO]-	130.9	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Fagomine	OC[C@H]1NCC[C@@H](O)[C@@H]1O	2737.0	Standard polar	33892256
Fagomine	OC[C@H]1NCC[C@@H](O)[C@@H]1O	1458.7	Standard non polar	33892256
Fagomine	OC[C@H]1NCC[C@@H](O)[C@@H]1O	1525.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Fagomine,1TMS,isomer #1	C[Si](C)(C)OC[C@H]1NCC[C@@H](O)[C@@H]1O	1515.5	Semi standard non polar	33892256
Fagomine,1TMS,isomer #2	C[Si](C)(C)O[C@@H]1CCN[C@H](CO)[C@H]1O	1519.7	Semi standard non polar	33892256
Fagomine,1TMS,isomer #3	C[Si](C)(C)O[C@H]1[C@H](O)CCN[C@@H]1CO	1500.1	Semi standard non polar	33892256
Fagomine,1TMS,isomer #4	C[Si](C)(C)N1CC[C@@H](O)[C@H](O)[C@H]1CO	1448.2	Semi standard non polar	33892256
Fagomine,2TMS,isomer #1	C[Si](C)(C)OC[C@H]1NCC[C@@H](O[Si](C)(C)C)[C@@H]1O	1581.8	Semi standard non polar	33892256
Fagomine,2TMS,isomer #2	C[Si](C)(C)OC[C@H]1NCC[C@@H](O)[C@@H]1O[Si](C)(C)C	1555.1	Semi standard non polar	33892256
Fagomine,2TMS,isomer #3	C[Si](C)(C)OC[C@@H]1[C@@H](O)[C@H](O)CCN1[Si](C)(C)C	1568.7	Semi standard non polar	33892256
Fagomine,2TMS,isomer #4	C[Si](C)(C)O[C@@H]1CCN[C@H](CO)[C@H]1O[Si](C)(C)C	1524.3	Semi standard non polar	33892256
Fagomine,2TMS,isomer #5	C[Si](C)(C)O[C@@H]1CCN([Si](C)(C)C)[C@H](CO)[C@H]1O	1520.4	Semi standard non polar	33892256
Fagomine,2TMS,isomer #6	C[Si](C)(C)O[C@H]1[C@H](O)CCN([Si](C)(C)C)[C@@H]1CO	1533.5	Semi standard non polar	33892256
Fagomine,3TMS,isomer #1	C[Si](C)(C)OC[C@H]1NCC[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	1600.1	Semi standard non polar	33892256
Fagomine,3TMS,isomer #2	C[Si](C)(C)OC[C@@H]1[C@@H](O)[C@H](O[Si](C)(C)C)CCN1[Si](C)(C)C	1625.2	Semi standard non polar	33892256
Fagomine,3TMS,isomer #3	C[Si](C)(C)OC[C@@H]1[C@@H](O[Si](C)(C)C)[C@H](O)CCN1[Si](C)(C)C	1637.4	Semi standard non polar	33892256
Fagomine,3TMS,isomer #4	C[Si](C)(C)O[C@@H]1CCN([Si](C)(C)C)[C@H](CO)[C@H]1O[Si](C)(C)C	1599.8	Semi standard non polar	33892256
Fagomine,4TMS,isomer #1	C[Si](C)(C)OC[C@@H]1[C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)CCN1[Si](C)(C)C	1698.6	Semi standard non polar	33892256
Fagomine,4TMS,isomer #1	C[Si](C)(C)OC[C@@H]1[C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)CCN1[Si](C)(C)C	1792.0	Standard non polar	33892256
Fagomine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1NCC[C@@H](O)[C@@H]1O	1761.4	Semi standard non polar	33892256
Fagomine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@@H]1CCN[C@H](CO)[C@H]1O	1756.7	Semi standard non polar	33892256
Fagomine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O)CCN[C@@H]1CO	1748.7	Semi standard non polar	33892256
Fagomine,1TBDMS,isomer #4	CC(C)(C)[Si](C)(C)N1CC[C@@H](O)[C@H](O)[C@H]1CO	1735.6	Semi standard non polar	33892256
Fagomine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1NCC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	2025.5	Semi standard non polar	33892256
Fagomine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1NCC[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	2004.7	Semi standard non polar	33892256
Fagomine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@@H]1[C@@H](O)[C@H](O)CCN1[Si](C)(C)C(C)(C)C	2032.1	Semi standard non polar	33892256
Fagomine,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)O[C@@H]1CCN[C@H](CO)[C@H]1O[Si](C)(C)C(C)(C)C	1985.5	Semi standard non polar	33892256
Fagomine,2TBDMS,isomer #5	CC(C)(C)[Si](C)(C)O[C@@H]1CCN([Si](C)(C)C(C)(C)C)[C@H](CO)[C@H]1O	2008.3	Semi standard non polar	33892256
Fagomine,2TBDMS,isomer #6	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O)CCN([Si](C)(C)C(C)(C)C)[C@@H]1CO	2005.6	Semi standard non polar	33892256
Fagomine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1NCC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	2257.2	Semi standard non polar	33892256
Fagomine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@@H]1[C@@H](O)[C@H](O[Si](C)(C)C(C)(C)C)CCN1[Si](C)(C)C(C)(C)C	2304.0	Semi standard non polar	33892256
Fagomine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@@H]1[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)CCN1[Si](C)(C)C(C)(C)C	2289.8	Semi standard non polar	33892256
Fagomine,3TBDMS,isomer #4	CC(C)(C)[Si](C)(C)O[C@@H]1CCN([Si](C)(C)C(C)(C)C)[C@H](CO)[C@H]1O[Si](C)(C)C(C)(C)C	2271.3	Semi standard non polar	33892256
Fagomine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)CCN1[Si](C)(C)C(C)(C)C	2563.6	Semi standard non polar	33892256
Fagomine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)CCN1[Si](C)(C)C(C)(C)C	2608.9	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Fagomine GC-MS (Non-derivatized) - 70eV, Positive	splash10-00ri-9400000000-3b8a5882645861b88c33	2017-07-27	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Fagomine 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 - Fagomine 10V, Positive-QTOF	splash10-000t-0900000000-1cd0371a246b72560112	2017-06-28	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Fagomine 20V, Positive-QTOF	splash10-01q9-1900000000-bf1bf8f8fc28cdba567f	2017-06-28	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Fagomine 40V, Positive-QTOF	splash10-03dl-9600000000-eb5b3f84b34a61c5ea29	2017-06-28	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Fagomine 10V, Negative-QTOF	splash10-0002-1900000000-d532dc64bdef94e8ec0a	2017-06-28	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Fagomine 20V, Negative-QTOF	splash10-00mn-9700000000-01b152f05c6f3ed1cd4c	2017-06-28	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Fagomine 40V, Negative-QTOF	splash10-0a4l-9000000000-c81ae5d7d7853799165f	2017-06-28	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Fagomine 10V, Negative-QTOF	splash10-0002-0900000000-f139716f16d745072c5a	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Fagomine 20V, Negative-QTOF	splash10-0a4j-9400000000-8a791e320b3bb834d1b6	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Fagomine 40V, Negative-QTOF	splash10-0a4l-9000000000-54b85f2d100a98c86df4	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Fagomine 10V, Positive-QTOF	splash10-03e9-0900000000-af1e57e01fc85eeb862f	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Fagomine 20V, Positive-QTOF	splash10-001j-5900000000-f038cfecd4438da4f325	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Fagomine 40V, Positive-QTOF	splash10-0a4i-9200000000-6fdcd83134b6d7537397	2021-09-24	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

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX 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

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

72259

PDB ID

Not Available

ChEBI ID

4969

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1629151

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Kato A, Hirokami Y, Kinami K, Tsuji Y, Miyawaki S, Adachi I, Hollinshead J, Nash RJ, Kiappes JL, Zitzmann N, Cha JK, Molyneux RJ, Fleet GW, Asano N: Isolation and SAR studies of bicyclic iminosugars from Castanospermum australe as glycosidase inhibitors. Phytochemistry. 2015 Mar;111:124-31. doi: 10.1016/j.phytochem.2014.12.011. Epub 2015 Jan 9. [PubMed:25583438 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for Fagomine (HMDB0033453)

MOL for HMDB0033453 (Fagomine)

3D MOL for HMDB0033453 (Fagomine)

3D SDF for HMDB0033453 (Fagomine)

3D-SDF for HMDB0033453 (Fagomine)

PDB for HMDB0033453 (Fagomine)

3D PDB for HMDB0033453 (Fagomine)

SMILES for HMDB0033453 (Fagomine)

INCHI for HMDB0033453 (Fagomine)

Structure for HMDB0033453 (Fagomine)

3D Structure for HMDB0033453 (Fagomine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra