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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:43:43 UTC

Update Date

2023-02-21 17:20:41 UTC

HMDB ID

HMDB0031504

Secondary Accession Numbers

HMDB31504

Metabolite Identification

Common Name

Methyl (Z)-3-hexenoate

Description

Methyl (Z)-3-hexenoate belongs to the class of organic compounds known as fatty acid methyl esters. Fatty acid methyl esters are compounds containing a fatty acid that is esterified with a methyl group. They have the general structure RC(=O)OR', where R=fatty aliphatic tail or organyl group and R'=methyl group. Based on a literature review a small amount of articles have been published on Methyl (Z)-3-hexenoate.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Methyl (Z)-3-hexenoic acid	Generator
3-Hexenoic acid, methyl ester	HMDB
FEMA 3364	HMDB
Methyl (3E)-3-hexenoate	HMDB
Methyl (e)-hex-3-enoate	HMDB
Methyl 3-hexenoate	HMDB
Methyl ester(3E)-3-hexenoic acid	HMDB
Methyl ester(e)-3-hexenoic acid	HMDB
Methyl hex-3-enoate	HMDB
Methyl hydrosorbate	HMDB
Methyl trans-3-hexenoate	HMDB
Methyl (e)-3-hexenoic acid	Generator

Chemical Formula

C₇H₁₂O₂

Average Molecular Weight

128.169

Monoisotopic Molecular Weight

128.083729628

IUPAC Name

methyl (3Z)-hex-3-enoate

Traditional Name

methyl (3Z)-hex-3-enoate

CAS Registry Number

2396-78-3

SMILES

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

InChI Identifier

InChI=1S/C7H12O2/c1-3-4-5-6-7(8)9-2/h4-5H,3,6H2,1-2H3/b5-4-

InChI Key

XEAIHUDTEINXFG-PLNGDYQASA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as fatty acid methyl esters. Fatty acid methyl esters are compounds containing a fatty acid that is esterified with a methyl group. They have the general structure RC(=O)OR', where R=fatty aliphatic tail or organyl group and R'=methyl group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acid esters

Direct Parent

Fatty acid methyl esters

Alternative Parents

Substituents

Fatty acid methyl ester
Methyl ester
Carboxylic acid ester
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Sweet

Disposition

Biological location

Cellular substructure

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0031504)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0031504)

Source

Endogenous

Endogenous (HMDB: HMDB0031504)

Animal

Animal (HMDB: HMDB0031504)

Exogenous

Food

Food (HMDB: HMDB0031504)

Fruit

Fruits (FooDB: FOOD00871)

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid Peroxidation (HMDB: HMDB0031504)

Biochemical pathway

Metabolic pathway

Fatty Acid Metabolism (HMDB: HMDB0031504)

Lipid metabolism pathway (HMDB: HMDB0031504)

Cellular process

Cell signaling (HMDB: HMDB0031504)

Biochemical process

Lipid transport (HMDB: HMDB0031504)

Role

Biological role

Energy source (HMDB: HMDB0031504)

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0031504)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	168.00 to 169.00 °C. @ 760.00 mm Hg	The Good Scents Company Information System
Water Solubility	1439 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	2.316 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	3.85 g/L	ALOGPS
logP	2.08	ALOGPS
logP	1.59	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Basic)	-7.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	26.3 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	36.96 m³·mol⁻¹	ChemAxon
Polarizability	14.66 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]+	131.239	31661259
DarkChem	[M-H]-	126.573	31661259
DeepCCS	[M+H]+	123.66	30932474
DeepCCS	[M-H]-	120.307	30932474
DeepCCS	[M-2H]-	156.817	30932474
DeepCCS	[M+Na]+	132.217	30932474
AllCCS	[M+H]+	131.6	32859911
AllCCS	[M+H-H2O]+	127.3	32859911
AllCCS	[M+NH4]+	135.5	32859911
AllCCS	[M+Na]+	136.6	32859911
AllCCS	[M-H]-	131.6	32859911
AllCCS	[M+Na-2H]-	134.4	32859911
AllCCS	[M+HCOO]-	137.4	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.	4.84 minutes	32390414
Predicted by Siyang on May 30, 2022	13.4555 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	4.12 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	28.4 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1908.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	411.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	166.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	301.8 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	108.3 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	482.8 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	526.5 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	86.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1155.4 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	417.4 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	1156.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	325.1 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	344.5 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	455.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	406.5 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	31.3 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Methyl (Z)-3-hexenoate	CC\C=C/CC(=O)OC	1276.2	Standard polar	33892256
Methyl (Z)-3-hexenoate	CC\C=C/CC(=O)OC	896.9	Standard non polar	33892256
Methyl (Z)-3-hexenoate	CC\C=C/CC(=O)OC	964.3	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 - Methyl (Z)-3-hexenoate GC-MS (Non-derivatized) - 70eV, Positive	splash10-05mo-9100000000-e39300cbb58274acd402	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Methyl (Z)-3-hexenoate 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 - Methyl (Z)-3-hexenoate 10V, Positive-QTOF	splash10-004j-9700000000-a2e9f766a1b0e19b7b52	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (Z)-3-hexenoate 20V, Positive-QTOF	splash10-05r1-9300000000-affd5717272722910280	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (Z)-3-hexenoate 40V, Positive-QTOF	splash10-0pbc-9000000000-00d33188a50c63305807	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (Z)-3-hexenoate 10V, Negative-QTOF	splash10-004i-5900000000-d635e296f9d2e5493310	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (Z)-3-hexenoate 20V, Negative-QTOF	splash10-004j-9700000000-c892169952088134cf01	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (Z)-3-hexenoate 40V, Negative-QTOF	splash10-0006-9000000000-fe7bde94fcb26ef10ef7	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (Z)-3-hexenoate 10V, Negative-QTOF	splash10-0002-9400000000-dab7248b81babaec7227	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (Z)-3-hexenoate 20V, Negative-QTOF	splash10-004m-9000000000-e15227da60fe307ba866	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (Z)-3-hexenoate 40V, Negative-QTOF	splash10-014i-9000000000-b13a811c5eb2f432df30	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (Z)-3-hexenoate 10V, Positive-QTOF	splash10-0691-9100000000-010c61161a9815254265	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (Z)-3-hexenoate 20V, Positive-QTOF	splash10-00mo-9000000000-90571345ad7e68e3ee74	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (Z)-3-hexenoate 40V, Positive-QTOF	splash10-00ko-9000000000-84e5bb862f0ca8d17e65	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)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	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+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular
Membrane

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

FDB008095

KNApSAcK ID

Not Available

Chemspider ID

4515284

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5362819

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1035941

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 Methyl (Z)-3-hexenoate (HMDB0031504)

MOL for HMDB0031504 (Methyl (Z)-3-hexenoate)

3D MOL for HMDB0031504 (Methyl (Z)-3-hexenoate)

3D SDF for HMDB0031504 (Methyl (Z)-3-hexenoate)

3D-SDF for HMDB0031504 (Methyl (Z)-3-hexenoate)

PDB for HMDB0031504 (Methyl (Z)-3-hexenoate)

3D PDB for HMDB0031504 (Methyl (Z)-3-hexenoate)

SMILES for HMDB0031504 (Methyl (Z)-3-hexenoate)

INCHI for HMDB0031504 (Methyl (Z)-3-hexenoate)

Structure for HMDB0031504 (Methyl (Z)-3-hexenoate)

3D Structure for HMDB0031504 (Methyl (Z)-3-hexenoate)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra