Jump To Section:

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

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-06-18 18:49:51 UTC

Update Date

2023-02-21 17:30:10 UTC

HMDB ID

HMDB0060682

Secondary Accession Numbers

HMDB60682

Metabolite Identification

Common Name

2-Propyl-2,4-pentadienoic acid

Description

2-Propyl-2,4-pentadienoic acid is a metabolite of valproic acid. Valproic acid (VPA) is a chemical compound and an acid that has found clinical use as an anticonvulsant and mood-stabilizing drug, primarily in the treatment of epilepsy, bipolar disorder, and, less commonly, major depression. It is also used to treat migraine headaches and schizophrenia. VPA is a liquid at room temperature, but it can be reacted with a base such as sodium hydroxide to form the salt sodium valproate, which is a solid. (Wikipedia)

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2,4-Diene-vpa	Kegg
2-Propyl-2,4-pentadienoate	Generator
2-Propyl-2,4-pentadienoic acid, (e)-isomer	HMDB
2-PPDA	HMDB
2-Propyl-2,4-pentadienoic acid, (Z)-isomer	HMDB

Chemical Formula

C₈H₁₂O₂

Average Molecular Weight

140.1797

Monoisotopic Molecular Weight

140.083729628

IUPAC Name

(2E)-2-propylpenta-2,4-dienoic acid

Traditional Name

2,4-Diene-VPA

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C8H12O2/c1-3-5-7(6-4-2)8(9)10/h3,5H,1,4,6H2,2H3,(H,9,10)/b7-5+

InChI Key

UUILWXIBBZVJDU-FNORWQNLSA-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

methyl-branched fatty acid (CHEBI:80642 )
Branched fatty acids (C16656 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (HMDB: HMDB0060682)

Organ

Liver (HMDB: HMDB0060682)
Kidney (HMDB: HMDB0060682)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0060682)

Cellular substructure

Membrane (HMDB: HMDB0060682)

Source

Endogenous

Endogenous (HMDB: HMDB0060682)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Valproic Acid Metabolism Pathway (PathBank: SMP0000635)

Role

Not Available

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	5.49 g/L	ALOGPS
logP	2.28	ALOGPS
logP	2.34	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	5.09	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	4	ChemAxon
Refractivity	41.17 m³·mol⁻¹	ChemAxon
Polarizability	15.5 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]+	135.273	31661259
DarkChem	[M-H]-	130.444	31661259
DeepCCS	[M+H]+	132.645	30932474
DeepCCS	[M-H]-	129.092	30932474
DeepCCS	[M-2H]-	166.044	30932474
DeepCCS	[M+Na]+	141.309	30932474
AllCCS	[M+H]+	134.3	32859911
AllCCS	[M+H-H2O]+	130.1	32859911
AllCCS	[M+NH4]+	138.3	32859911
AllCCS	[M+Na]+	139.4	32859911
AllCCS	[M-H]-	131.4	32859911
AllCCS	[M+Na-2H]-	133.6	32859911
AllCCS	[M+HCOO]-	136.2	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 √ó 2.1 mm; 1.7 Œºmparticle diameter). Predicted by Afia on May 17, 2022.	5.38 minutes	32390414
Predicted by Siyang on May 30, 2022	15.3136 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.51 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1992.2 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	485.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	179.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	344.2 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	261.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	569.7 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	627.5 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	224.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1286.5 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	439.2 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	1345.0 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	440.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	402.5 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	513.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	476.5 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	34.9 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-Propyl-2,4-pentadienoic acid	CCC\C(=C/C=C)C(O)=O	2010.9	Standard polar	33892256
2-Propyl-2,4-pentadienoic acid	CCC\C(=C/C=C)C(O)=O	1097.1	Standard non polar	33892256
2-Propyl-2,4-pentadienoic acid	CCC\C(=C/C=C)C(O)=O	1150.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2-Propyl-2,4-pentadienoic acid,1TMS,isomer #1	C=C/C=C(\CCC)C(=O)O[Si](C)(C)C	1225.5	Semi standard non polar	33892256
2-Propyl-2,4-pentadienoic acid,1TBDMS,isomer #1	C=C/C=C(\CCC)C(=O)O[Si](C)(C)C(C)(C)C	1454.2	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-Propyl-2,4-pentadienoic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-00ou-9200000000-ba4b7f259ad38315a5a9	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Propyl-2,4-pentadienoic acid GC-MS (1 TMS) - 70eV, Positive	splash10-00dj-9400000000-403c0fc9bd59b1f80fde	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Propyl-2,4-pentadienoic 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-Propyl-2,4-pentadienoic acid 10V, Positive-QTOF	splash10-0006-3900000000-6b67a18198af2bba243a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Propyl-2,4-pentadienoic acid 20V, Positive-QTOF	splash10-0005-9400000000-29e2cfdc9d5d9eb17649	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Propyl-2,4-pentadienoic acid 40V, Positive-QTOF	splash10-0006-9000000000-ca5450d8710a12cb33d5	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Propyl-2,4-pentadienoic acid 10V, Negative-QTOF	splash10-000i-4900000000-cc2ed0a2469c54811a58	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Propyl-2,4-pentadienoic acid 20V, Negative-QTOF	splash10-000b-9400000000-1d0218608b5da33ce925	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Propyl-2,4-pentadienoic acid 40V, Negative-QTOF	splash10-000e-9100000000-eab2077c8aa959ce7bcb	2016-08-03	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

Membrane (predicted from logP)

Biospecimen Locations

Blood
Urine

Tissue Locations

Kidney
Liver

Pathways

Name	SMPDB/PathBank	KEGG
Valproic Acid Metabolism Pathway		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details

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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C16656

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6441809

PDB ID

Not Available

ChEBI ID

80642

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

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 ]
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Showing metabocard for 2-Propyl-2,4-pentadienoic acid (HMDB0060682)

MOL for HMDB0060682 (2-Propyl-2,4-pentadienoic acid)

3D MOL for HMDB0060682 (2-Propyl-2,4-pentadienoic acid)

3D SDF for HMDB0060682 (2-Propyl-2,4-pentadienoic acid)

3D-SDF for HMDB0060682 (2-Propyl-2,4-pentadienoic acid)

PDB for HMDB0060682 (2-Propyl-2,4-pentadienoic acid)

3D PDB for HMDB0060682 (2-Propyl-2,4-pentadienoic acid)

SMILES for HMDB0060682 (2-Propyl-2,4-pentadienoic acid)

INCHI for HMDB0060682 (2-Propyl-2,4-pentadienoic acid)

Structure for HMDB0060682 (2-Propyl-2,4-pentadienoic acid)

3D Structure for HMDB0060682 (2-Propyl-2,4-pentadienoic 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