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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 02:17:46 UTC

Update Date

2022-03-07 02:56:42 UTC

HMDB ID

HMDB0040718

Secondary Accession Numbers

HMDB40718

Metabolite Identification

Common Name

Zwiebelane B

Description

Zwiebelane B belongs to the class of organic compounds known as thiolanes. These are organic compounds containing thiolane, a five-member saturated ring containing four carbon atoms and a sulfur atom. Zwiebelane B has been detected, but not quantified in, several different foods, such as onion-family vegetables, green onion, garden onions (Allium cepa), welsh onions (Allium fistulosum), and garden onion (var.). This could make zwiebelane b a potential biomarker for the consumption of these foods. Based on a literature review a small amount of articles have been published on Zwiebelane B.

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

C₆H₁₀OS₂

Average Molecular Weight

162.273

Monoisotopic Molecular Weight

162.017306322

IUPAC Name

2,3-dimethyl-5λ⁴,6-dithiabicyclo[2.1.1]hexan-5-one

Traditional Name

2,3-dimethyl-5λ⁴,6-dithiabicyclo[2.1.1]hexan-5-one

CAS Registry Number

120709-22-0

SMILES

CC1C2SC(C1C)S2=O

InChI Identifier

InChI=1S/C6H10OS2/c1-3-4(2)6-8-5(3)9(6)7/h3-6H,1-2H3

InChI Key

MDLUYFYDCNUJHX-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as thiolanes. These are organic compounds containing thiolane, a five-member saturated ring containing four carbon atoms and a sulfur atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Thiolanes

Sub Class

Not Available

Direct Parent

Thiolanes

Alternative Parents

Substituents

Thiolane
Sulfoxide
Dithietane
Dialkylthioether
Sulfinyl compound
Thioether
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0040718)
Cytoplasm (HMDB: HMDB0040718)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0040718)

Source

Exogenous

Exogenous (HMDB: HMDB0040718)

Food

Food (HMDB: HMDB0040718)

Herb and spice

Herb

Welsh onion (FooDB: FOOD00241)

Vegetable

Onion-family vegetable

Garden onion (FooDB: FOOD00006)
Garden onion (var.) (FooDB: FOOD00226)
Onion-family vegetables (FooDB: FOOD00855)
Green onion (FooDB: FOOD00963)
Red onion (FooDB: FOOD00962)

Endogenous

Plant

Plant (HMDB: HMDB0040718)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0040718)

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	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	8.84 g/L	ALOGPS
logP	-0.23	ALOGPS
logP	0.86	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Basic)	-7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	17.07 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	42.12 m³·mol⁻¹	ChemAxon
Polarizability	16.96 Å³	ChemAxon
Number of Rings	2	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
DarkChem	[M+H]+	132.631	31661259
DarkChem	[M-H]-	125.925	31661259
DeepCCS	[M+H]+	132.691	30932474
DeepCCS	[M-H]-	130.075	30932474
DeepCCS	[M-2H]-	166.61	30932474
DeepCCS	[M+Na]+	141.491	30932474
AllCCS	[M+H]+	130.5	32859911
AllCCS	[M+H-H2O]+	126.2	32859911
AllCCS	[M+NH4]+	134.4	32859911
AllCCS	[M+Na]+	135.6	32859911
AllCCS	[M-H]-	133.3	32859911
AllCCS	[M+Na-2H]-	135.1	32859911
AllCCS	[M+HCOO]-	137.1	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	2.67 minutes	32390414
Predicted by Siyang on May 30, 2022	12.9563 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.34 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	305.6 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	662.1 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	321.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	69.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	191.8 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	46.3 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	292.2 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	255.1 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	620.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	616.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	53.9 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	654.4 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	190.3 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	228.2 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	531.2 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	447.3 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	320.3 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Zwiebelane B	CC1C2SC(C1C)S2=O	1957.1	Standard polar	33892256
Zwiebelane B	CC1C2SC(C1C)S2=O	1226.1	Standard non polar	33892256
Zwiebelane B	CC1C2SC(C1C)S2=O	1267.6	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Zwiebelane B GC-MS (Non-derivatized) - 70eV, Positive	splash10-03di-0900000000-42d68e5c9c3a77e5228c	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Zwiebelane B 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 - Zwiebelane B 10V, Positive-QTOF	splash10-03di-0900000000-2dfaa89c576ff4f38ed1	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zwiebelane B 20V, Positive-QTOF	splash10-03di-0900000000-d5e201c1106203addb3e	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zwiebelane B 40V, Positive-QTOF	splash10-0udi-9500000000-cccb3c45b353da4a2c03	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zwiebelane B 10V, Negative-QTOF	splash10-03di-0900000000-7bec9b46520df7fc7650	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zwiebelane B 20V, Negative-QTOF	splash10-03di-0900000000-ec43bef22f1135c357f0	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zwiebelane B 40V, Negative-QTOF	splash10-0006-1900000000-916ada75d73ddde582e2	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zwiebelane B 10V, Negative-QTOF	splash10-03di-0900000000-74cd53dc0fbedfaff1f6	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zwiebelane B 20V, Negative-QTOF	splash10-03di-0900000000-74cd53dc0fbedfaff1f6	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zwiebelane B 40V, Negative-QTOF	splash10-03di-0900000000-3c7eb9d3872ec0a22c20	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zwiebelane B 10V, Positive-QTOF	splash10-03di-0900000000-78b980630fad49dac3fe	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zwiebelane B 20V, Positive-QTOF	splash10-03di-0900000000-78b980630fad49dac3fe	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zwiebelane B 40V, Positive-QTOF	splash10-03di-0900000000-2508797c2c3a036f9dea	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

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

FDB020525

KNApSAcK ID

C00057824

Chemspider ID

10291371

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

85447653

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1885801

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 Zwiebelane B (HMDB0040718)

MOL for HMDB0040718 (Zwiebelane B)

3D MOL for HMDB0040718 (Zwiebelane B)

3D SDF for HMDB0040718 (Zwiebelane B)

3D-SDF for HMDB0040718 (Zwiebelane B)

PDB for HMDB0040718 (Zwiebelane B)

3D PDB for HMDB0040718 (Zwiebelane B)

SMILES for HMDB0040718 (Zwiebelane B)

INCHI for HMDB0040718 (Zwiebelane B)

Structure for HMDB0040718 (Zwiebelane B)

3D Structure for HMDB0040718 (Zwiebelane B)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra