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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 02:43:47 UTC

Update Date

2023-02-21 17:28:34 UTC

HMDB ID

HMDB0041084

Secondary Accession Numbers

HMDB41084

Metabolite Identification

Common Name

Raphanusamide

Description

Raphanusamide belongs to the class of organic compounds known as thiolactams. These are cyclic thioamides, obtained by replacing the oxygen atom from a lactam ring with sulfur. Raphanusamide has been detected, but not quantified in, brassicas. This could make raphanusamide a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Raphanusamide.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₆H₉NOS

Average Molecular Weight

143.207

Monoisotopic Molecular Weight

143.040484605

IUPAC Name

(3Z)-3-(methoxymethylidene)pyrrolidine-2-thione

Traditional Name

(3Z)-3-(methoxymethylidene)pyrrolidine-2-thione

CAS Registry Number

104730-65-6

SMILES

CO\C=C1\CCNC1=S

InChI Identifier

InChI=1S/C6H9NOS/c1-8-4-5-2-3-7-6(5)9/h4H,2-3H2,1H3,(H,7,9)/b5-4-

InChI Key

FXKRKZYGKOWUNE-PLNGDYQASA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as thiolactams. These are cyclic thioamides, obtained by replacing the oxygen atom from a lactam ring with sulfur.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Thiolactams

Sub Class

Not Available

Direct Parent

Thiolactams

Alternative Parents

Substituents

Thiolactam
Pyrrolidine
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Thiocarbonyl group
Organosulfur compound
Organooxygen compound
Organonitrogen 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: HMDB0041084)
Cytoplasm (HMDB: HMDB0041084)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0041084)

Source

Exogenous

Food

Food (HMDB: HMDB0041084)

Vegetable

Brassica

Brassicas (FooDB: FOOD00857)

Endogenous

Plant

Plant (HMDB: HMDB0041084)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0041084)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	150 - 151 °C	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	1.7 g/L	ALOGPS
logP	0.18	ALOGPS
logP	0.28	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	11.7	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	21.26 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	41.36 m³·mol⁻¹	ChemAxon
Polarizability	14.88 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	130.362	30932474
DeepCCS	[M-H]-	128.3	30932474
DeepCCS	[M-2H]-	164.167	30932474
DeepCCS	[M+Na]+	138.875	30932474
AllCCS	[M+H]+	129.9	32859911
AllCCS	[M+H-H2O]+	125.4	32859911
AllCCS	[M+NH4]+	134.2	32859911
AllCCS	[M+Na]+	135.4	32859911
AllCCS	[M-H]-	129.3	32859911
AllCCS	[M+Na-2H]-	131.6	32859911
AllCCS	[M+HCOO]-	134.2	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Raphanusamide	CO\C=C1\CCNC1=S	2268.4	Standard polar	33892256
Raphanusamide	CO\C=C1\CCNC1=S	1407.6	Standard non polar	33892256
Raphanusamide	CO\C=C1\CCNC1=S	1618.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Raphanusamide,1TMS,isomer #1	CO/C=C1/CCN([Si](C)(C)C)C1=S	1537.1	Semi standard non polar	33892256
Raphanusamide,1TMS,isomer #1	CO/C=C1/CCN([Si](C)(C)C)C1=S	1404.7	Standard non polar	33892256
Raphanusamide,1TBDMS,isomer #1	CO/C=C1/CCN([Si](C)(C)C(C)(C)C)C1=S	1743.0	Semi standard non polar	33892256
Raphanusamide,1TBDMS,isomer #1	CO/C=C1/CCN([Si](C)(C)C(C)(C)C)C1=S	1659.1	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Raphanusamide GC-MS (Non-derivatized) - 70eV, Positive	splash10-03gl-9600000000-3060b21423bfaf9c8c89	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Raphanusamide 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 - Raphanusamide 10V, Positive-QTOF	splash10-0006-0900000000-ec873858b38124a7de2b	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Raphanusamide 20V, Positive-QTOF	splash10-01p6-9800000000-0a73eab2e86bab75c151	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Raphanusamide 40V, Positive-QTOF	splash10-0f6x-9000000000-57a0c505368aa8f21ed3	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Raphanusamide 10V, Negative-QTOF	splash10-0006-0900000000-89c099fbb0b7703f832d	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Raphanusamide 20V, Negative-QTOF	splash10-0a4m-5900000000-0b615ad70edd31058b5d	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Raphanusamide 40V, Negative-QTOF	splash10-0a4j-9000000000-ea9bac1a82e3fcb4601f	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Raphanusamide 10V, Positive-QTOF	splash10-0006-0900000000-3d5daa4753871c561b5b	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Raphanusamide 20V, Positive-QTOF	splash10-0006-6900000000-9674f892e6170b405c19	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Raphanusamide 40V, Positive-QTOF	splash10-01oy-9200000000-c458c0bebbd7b82f0790	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Raphanusamide 10V, Negative-QTOF	splash10-0002-9200000000-ec6d44c7da11d6896485	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Raphanusamide 20V, Negative-QTOF	splash10-0002-9000000000-5a080aab77c9dddccb7a	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Raphanusamide 40V, Negative-QTOF	splash10-052b-9000000000-94b6b82c8c4452653a0f	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	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

FDB020962

KNApSAcK ID

C00056391

Chemspider ID

30777534

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

131753019

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

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 Raphanusamide (HMDB0041084)

MOL for HMDB0041084 (Raphanusamide)

3D MOL for HMDB0041084 (Raphanusamide)

3D SDF for HMDB0041084 (Raphanusamide)

3D-SDF for HMDB0041084 (Raphanusamide)

PDB for HMDB0041084 (Raphanusamide)

3D PDB for HMDB0041084 (Raphanusamide)

SMILES for HMDB0041084 (Raphanusamide)

INCHI for HMDB0041084 (Raphanusamide)

Structure for HMDB0041084 (Raphanusamide)

3D Structure for HMDB0041084 (Raphanusamide)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra