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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:43:42 UTC

Update Date

2023-02-21 17:20:41 UTC

HMDB ID

HMDB0031501

Secondary Accession Numbers

HMDB31501

Metabolite Identification

Common Name

3-Hexenoic acid

Description

3-Hexenoic acid, also known as (3Z)-3-hexenoate or 6:1, N-3 cis, belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms. Based on a literature review a significant number of articles have been published on 3-Hexenoic acid.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
(3Z)-3-Hexenoic acid	ChEBI
(Z)-3-Hexenoic acid	ChEBI
(Z)-Hex-3-enoic acid	ChEBI
6:1, N-3 cis	ChEBI
C6:1, N-3 cis	ChEBI
cis-3-Hexenoic acid	ChEBI
cis-Hex-3-ensaeure	ChEBI
Hex-3C-enoic acid	ChEBI
(3Z)-3-Hexenoate	Generator
(Z)-3-Hexenoate	Generator
(Z)-Hex-3-enoate	Generator
cis-3-Hexenoate	Generator
Hex-3C-enoate	Generator
3-Hexenoate	Generator
(3E)-3-Hexenoic acid	HMDB
2-Pentene-1-carboxylic acid	HMDB
FEMA 3170	HMDB
Hydrosorbic acid	HMDB
cis-Hex-3-enoate	Generator

Chemical Formula

C₆H₁₀O₂

Average Molecular Weight

114.1424

Monoisotopic Molecular Weight

114.068079564

IUPAC Name

(3Z)-hex-3-enoic acid

Traditional Name

cis-3-hexenoic acid

CAS Registry Number

4219-24-3

SMILES

CC\C=C/CC(O)=O

InChI Identifier

InChI=1S/C6H10O2/c1-2-3-4-5-6(7)8/h3-4H,2,5H2,1H3,(H,7,8)/b4-3-

InChI Key

XXHDAWYDNSXJQM-ARJAWSKDSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Medium-chain fatty acids

Alternative Parents

Substituents

Medium-chain fatty acid
Unsaturated fatty acid
Straight chain fatty acid
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

3-hexenoic acid (CHEBI:49284 )
Unsaturated fatty acids (LMFA01030779 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0031501)
Cytoplasm (HMDB: HMDB0031501)

Source

Endogenous

Endogenous (HMDB: HMDB0031501)

Exogenous

Exogenous (HMDB: HMDB0031501)

Food

Cereal and cereal product

Cereal product

Breakfast cereal (FooDB: FOOD00270)

Cereals and cereal products (FooDB: FOOD00858)

Tea

Fruit

Berry

Red raspberry (FooDB: FOOD00162)

Fruits (FooDB: FOOD00871)

Vegetable

Root vegetable

Burdock (FooDB: FOOD00017)

Cocoa and cocoa product

Cocoa

Cocoa bean (FooDB: FOOD00182)

Cocoa and cocoa products (FooDB: FOOD00860)

Beverage

Alcoholic beverage

Alcoholic beverages (FooDB: FOOD00854)

Process

Not Available

Role

Not Available

Physical Properties

State

Liquid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	12 °C	Not Available
Boiling Point	100.00 °C. @ 4.00 mm Hg	The Good Scents Company Information System
Water Solubility	7069 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	1.344 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	23.8 g/L	ALOGPS
logP	1.42	ALOGPS
logP	1.45	ChemAxon
logS	-0.68	ALOGPS
pKa (Strongest Acidic)	4.93	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	37.3 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	32.19 m³·mol⁻¹	ChemAxon
Polarizability	12.28 Å³	ChemAxon
Number of Rings	0	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]+	126.935	31661259
DarkChem	[M-H]-	121.623	31661259
DeepCCS	[M+H]+	127.98	30932474
DeepCCS	[M-H]-	125.216	30932474
DeepCCS	[M-2H]-	161.511	30932474
DeepCCS	[M+Na]+	136.46	30932474
AllCCS	[M+H]+	127.7	32859911
AllCCS	[M+H-H2O]+	123.3	32859911
AllCCS	[M+NH4]+	131.7	32859911
AllCCS	[M+Na]+	132.9	32859911
AllCCS	[M-H]-	128.2	32859911
AllCCS	[M+Na-2H]-	131.4	32859911
AllCCS	[M+HCOO]-	134.9	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.	3.58 minutes	32390414
Predicted by Siyang on May 30, 2022	11.2532 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.91 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	47.1 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1523.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	346.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	124.7 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	248.7 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	116.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	396.3 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	408.8 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	100.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	917.9 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	352.3 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	1056.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	283.6 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	317.6 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	485.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	300.5 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	59.5 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3-Hexenoic acid	CC\C=C/CC(O)=O	1917.7	Standard polar	33892256
3-Hexenoic acid	CC\C=C/CC(O)=O	946.7	Standard non polar	33892256
3-Hexenoic acid	CC\C=C/CC(O)=O	988.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3-Hexenoic acid,1TMS,isomer #1	CC/C=C\CC(=O)O[Si](C)(C)C	1071.2	Semi standard non polar	33892256
3-Hexenoic acid,1TBDMS,isomer #1	CC/C=C\CC(=O)O[Si](C)(C)C(C)(C)C	1304.1	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - 3-Hexenoic acid EI-B (Non-derivatized)	splash10-07dx-9000000000-1796c6f6412740199482	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 3-Hexenoic acid EI-B (Non-derivatized)	splash10-07dx-9000000000-1796c6f6412740199482	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hexenoic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-014l-9000000000-eb72564cfd5feb1960c7	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hexenoic acid GC-MS (1 TMS) - 70eV, Positive	splash10-00y0-9200000000-56b6bd5e2a77ed8654b2	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hexenoic acid 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 - 3-Hexenoic acid 10V, Positive-QTOF	splash10-014j-9600000000-706d2cd2eb15a01e605e	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hexenoic acid 20V, Positive-QTOF	splash10-014i-9100000000-458c566c19cf4bd17e62	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hexenoic acid 40V, Positive-QTOF	splash10-1003-9000000000-412d1aed22bbc24c8302	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hexenoic acid 10V, Negative-QTOF	splash10-03di-2900000000-8762b18dddd2835fa1a2	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hexenoic acid 20V, Negative-QTOF	splash10-03xr-9800000000-dc5efb5d4456c273153e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hexenoic acid 40V, Negative-QTOF	splash10-0aou-9000000000-f8d506b9b12a169a61dd	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hexenoic acid 10V, Negative-QTOF	splash10-0002-9300000000-319fba10b832c88f088a	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hexenoic acid 20V, Negative-QTOF	splash10-004j-9000000000-dab61623902cf6d314ac	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hexenoic acid 40V, Negative-QTOF	splash10-014i-9000000000-09cfa6130f7c69f8a348	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hexenoic acid 10V, Positive-QTOF	splash10-014j-9000000000-07a2d7995f6679950bec	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hexenoic acid 20V, Positive-QTOF	splash10-00kf-9000000000-21ed5a3e34951b31ff26	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hexenoic acid 40V, Positive-QTOF	splash10-0553-9000000000-777b6e38e565836f5ae1	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-30	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

FDB021772

KNApSAcK ID

Not Available

Chemspider ID

4511190

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5355152

PDB ID

Not Available

ChEBI ID

49284

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1445951

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Showing metabocard for 3-Hexenoic acid (HMDB0031501)

MOL for HMDB0031501 (3-Hexenoic acid)

3D MOL for HMDB0031501 (3-Hexenoic acid)

3D SDF for HMDB0031501 (3-Hexenoic acid)

3D-SDF for HMDB0031501 (3-Hexenoic acid)

PDB for HMDB0031501 (3-Hexenoic acid)

3D PDB for HMDB0031501 (3-Hexenoic acid)

SMILES for HMDB0031501 (3-Hexenoic acid)

INCHI for HMDB0031501 (3-Hexenoic acid)

Structure for HMDB0031501 (3-Hexenoic acid)

3D Structure for HMDB0031501 (3-Hexenoic acid)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra