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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:44:04 UTC

Update Date

2023-02-21 17:20:50 UTC

HMDB ID

HMDB0031562

Secondary Accession Numbers

HMDB31562

Metabolite Identification

Common Name

2-Methyl-3-pentenoic acid

Description

2-Methyl-3-pentenoic acid belongs to the class of organic compounds known as methyl-branched fatty acids. These are fatty acids with an acyl chain that has a methyl branch. Usually, they are saturated and contain only one or more methyl group. However, branches other than methyl may be present. Based on a literature review a significant number of articles have been published on 2-Methyl-3-pentenoic 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
2-Methyl-3-pentenoate	Generator
2-Methylpent-3-en-1-Oic acid	HMDB
2-Pentene-4-carboxylic acid	HMDB
FEMA 3464	HMDB
(3Z)-2-Methylpent-3-enoate	Generator

Chemical Formula

C₆H₁₀O₂

Average Molecular Weight

114.1424

Monoisotopic Molecular Weight

114.068079564

IUPAC Name

(3Z)-2-methylpent-3-enoic acid

Traditional Name

(3Z)-2-methylpent-3-enoic acid

CAS Registry Number

37674-63-8

SMILES

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

InChI Identifier

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

InChI Key

NFRJJFMXYKSRPK-ARJAWSKDSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as methyl-branched fatty acids. These are fatty acids with an acyl chain that has a methyl branch. Usually, they are saturated and contain only one or more methyl group. However, branches other than methyl may be present.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Methyl-branched fatty acids

Alternative Parents

Substituents

Methyl-branched fatty acid
Unsaturated 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

Not Available

Ontology

Cellular substructure

Organelle

Adiposome (HMDB: HMDB0031562)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0031562)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0031562)

Source

Endogenous

Endogenous (HMDB: HMDB0031562)

Animal

Animal (HMDB: HMDB0031562)

Exogenous

Food

Food (HMDB: HMDB0031562)

Exogenous (HMDB: HMDB0031562)

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid Peroxidation (HMDB: HMDB0031562)

Biochemical pathway

Metabolic pathway

Fatty Acid Metabolism (HMDB: HMDB0031562)

Lipid metabolism pathway (HMDB: HMDB0031562)

Cellular process

Cell signaling (HMDB: HMDB0031562)

Biochemical process

Lipid transport (HMDB: HMDB0031562)

Role

Biological role

Energy source (HMDB: HMDB0031562)

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0031562)

Food and nutrition

Food additive

Flavoring agent

Flavoring Agent (HMDB: HMDB0031562)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	199.00 to 200.00 °C. @ 760.00 mm Hg	The Good Scents Company Information System
Water Solubility	0 slightly	The Good Scents Company Information System
LogP	1.413 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	21.2 g/L	ALOGPS
logP	1.56	ALOGPS
logP	1.55	ChemAxon
logS	-0.73	ALOGPS
pKa (Strongest Acidic)	4.88	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	2	ChemAxon
Refractivity	32.16 m³·mol⁻¹	ChemAxon
Polarizability	12.13 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]+	123.429	31661259
DarkChem	[M-H]-	120.566	31661259
DeepCCS	[M+H]+	126.623	30932474
DeepCCS	[M-H]-	123.709	30932474
DeepCCS	[M-2H]-	160.283	30932474
DeepCCS	[M+Na]+	135.21	30932474
AllCCS	[M+H]+	127.4	32859911
AllCCS	[M+H-H2O]+	123.1	32859911
AllCCS	[M+NH4]+	131.5	32859911
AllCCS	[M+Na]+	132.7	32859911
AllCCS	[M-H]-	126.1	32859911
AllCCS	[M+Na-2H]-	129.4	32859911
AllCCS	[M+HCOO]-	133.0	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.	3.01 minutes	32390414
Predicted by Siyang on May 30, 2022	10.5074 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.87 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	53.1 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1432.5 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	350.1 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	103.0 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	218.9 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	69.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	320.1 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	308.7 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	87.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	799.6 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	322.8 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	844.0 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	247.2 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	303.0 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	424.8 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	294.9 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	61.9 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-Methyl-3-pentenoic acid	C\C=C/C(C)C(O)=O	1894.3	Standard polar	33892256
2-Methyl-3-pentenoic acid	C\C=C/C(C)C(O)=O	910.6	Standard non polar	33892256
2-Methyl-3-pentenoic acid	C\C=C/C(C)C(O)=O	947.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2-Methyl-3-pentenoic acid,1TMS,isomer #1	C/C=C\C(C)C(=O)O[Si](C)(C)C	995.6	Semi standard non polar	33892256
2-Methyl-3-pentenoic acid,1TBDMS,isomer #1	C/C=C\C(C)C(=O)O[Si](C)(C)C(C)(C)C	1218.2	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 - 2-Methyl-3-pentenoic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-016u-9000000000-65851551fc2426ee31ac	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Methyl-3-pentenoic acid GC-MS (1 TMS) - 70eV, Positive	splash10-00y0-9200000000-c8d6e7250a7e2beb9023	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Methyl-3-pentenoic 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 - 2-Methyl-3-pentenoic acid 10V, Positive-QTOF	splash10-014j-9500000000-c560eda9c571cd6346d9	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-3-pentenoic acid 20V, Positive-QTOF	splash10-014j-9100000000-c0b6a64b6dab9b8a8f64	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-3-pentenoic acid 40V, Positive-QTOF	splash10-014l-9000000000-bd7929da38c876d23cff	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-3-pentenoic acid 10V, Negative-QTOF	splash10-03di-2900000000-d23e301e012476a3357c	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-3-pentenoic acid 20V, Negative-QTOF	splash10-02t9-9500000000-fa0da667c55699f34c11	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-3-pentenoic acid 40V, Negative-QTOF	splash10-014i-9000000000-fbe108f8c659c1278d41	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-3-pentenoic acid 10V, Positive-QTOF	splash10-014i-9000000000-e93be4a020face81d9dd	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-3-pentenoic acid 20V, Positive-QTOF	splash10-014l-9000000000-ac9d52bee47f03b1c373	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-3-pentenoic acid 40V, Positive-QTOF	splash10-00kf-9000000000-73a15f95b901ac2c2bc5	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-3-pentenoic acid 10V, Negative-QTOF	splash10-03di-1900000000-d014aeabef634afa5715	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-3-pentenoic acid 20V, Negative-QTOF	splash10-01ot-9300000000-71b8fcc3cf64deeb5510	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-3-pentenoic acid 40V, Negative-QTOF	splash10-0006-9000000000-f829d771e8d9bbf0c14f	2021-09-25	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
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

FDB008177

KNApSAcK ID

Not Available

Chemspider ID

32700710

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

71587183

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1036341

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 2-Methyl-3-pentenoic acid (HMDB0031562)

MOL for HMDB0031562 (2-Methyl-3-pentenoic acid)

3D MOL for HMDB0031562 (2-Methyl-3-pentenoic acid)

3D SDF for HMDB0031562 (2-Methyl-3-pentenoic acid)

3D-SDF for HMDB0031562 (2-Methyl-3-pentenoic acid)

PDB for HMDB0031562 (2-Methyl-3-pentenoic acid)

3D PDB for HMDB0031562 (2-Methyl-3-pentenoic acid)

SMILES for HMDB0031562 (2-Methyl-3-pentenoic acid)

INCHI for HMDB0031562 (2-Methyl-3-pentenoic acid)

Structure for HMDB0031562 (2-Methyl-3-pentenoic acid)

3D Structure for HMDB0031562 (2-Methyl-3-pentenoic 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