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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:36:23 UTC

Update Date

2023-02-21 17:19:33 UTC

HMDB ID

HMDB0030368

Secondary Accession Numbers

HMDB30368

Metabolite Identification

Common Name

(3R,5Z)-5-Octene-1,3-diol

Description

(3R,5Z)-5-Octene-1,3-diol belongs to the class of organic compounds known as fatty alcohols. These are aliphatic alcohols consisting of a chain of a least six carbon atoms. Thus, (3R,5Z)-5-octene-1,3-diol is considered to be a fatty alcohol. Based on a literature review a small amount of articles have been published on (3R,5Z)-5-Octene-1,3-diol.

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

C₈H₁₆O₂

Average Molecular Weight

144.2114

Monoisotopic Molecular Weight

144.115029756

IUPAC Name

(5Z)-oct-5-ene-1,3-diol

Traditional Name

(5Z)-oct-5-ene-1,3-diol

CAS Registry Number

130272-38-7

SMILES

CC\C=C/CC(O)CCO

InChI Identifier

InChI=1S/C8H16O2/c1-2-3-4-5-8(10)6-7-9/h3-4,8-10H,2,5-7H2,1H3/b4-3-

InChI Key

QTHIKVMVWXLPKQ-ARJAWSKDSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as fatty alcohols. These are aliphatic alcohols consisting of a chain of a least six carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty alcohols

Direct Parent

Fatty alcohols

Alternative Parents

Substituents

Fatty alcohol
Secondary alcohol
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0030368)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0030368)

Source

Endogenous

Endogenous (HMDB: HMDB0030368)

Plant

Plant (HMDB: HMDB0030368)

Animal

Animal (HMDB: HMDB0030368)

Exogenous

Food

Food (HMDB: HMDB0030368)

Fruit

Pome

Pomes (FooDB: FOOD00856)

Exogenous (HMDB: HMDB0030368)

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid Peroxidation (HMDB: HMDB0030368)

Biochemical pathway

Metabolic pathway

Fatty Acid Metabolism (HMDB: HMDB0030368)

Lipid metabolism pathway (HMDB: HMDB0030368)

Cellular process

Cell signaling (HMDB: HMDB0030368)

Biochemical process

Lipid transport (HMDB: HMDB0030368)

Role

Biological role

Energy source (HMDB: HMDB0030368)

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0030368)

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	26.2 g/L	ALOGPS
logP	1.35	ALOGPS
logP	0.76	ChemAxon
logS	-0.74	ALOGPS
pKa (Strongest Acidic)	15.06	ChemAxon
pKa (Strongest Basic)	-2.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	40.46 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	43.28 m³·mol⁻¹	ChemAxon
Polarizability	17 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	133.047	31661259
DarkChem	[M-H]-	131.088	31661259
DeepCCS	[M+H]+	133.246	30932474
DeepCCS	[M-H]-	129.637	30932474
DeepCCS	[M-2H]-	166.938	30932474
DeepCCS	[M+Na]+	142.157	30932474
AllCCS	[M+H]+	136.3	32859911
AllCCS	[M+H-H2O]+	132.2	32859911
AllCCS	[M+NH4]+	140.1	32859911
AllCCS	[M+Na]+	141.2	32859911
AllCCS	[M-H]-	136.7	32859911
AllCCS	[M+Na-2H]-	139.0	32859911
AllCCS	[M+HCOO]-	141.6	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.	3.19 minutes	32390414
Predicted by Siyang on May 30, 2022	9.958 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	5.49 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	61.1 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1425.5 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	279.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	110.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	184.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	93.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	349.5 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	328.5 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	108.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	770.4 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	305.1 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	1020.6 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	240.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	263.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	469.7 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	241.5 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	43.0 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(3R,5Z)-5-Octene-1,3-diol	CC\C=C/CC(O)CCO	2048.8	Standard polar	33892256
(3R,5Z)-5-Octene-1,3-diol	CC\C=C/CC(O)CCO	1204.7	Standard non polar	33892256
(3R,5Z)-5-Octene-1,3-diol	CC\C=C/CC(O)CCO	1246.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
(3R,5Z)-5-Octene-1,3-diol,1TMS,isomer #1	CC/C=C\CC(CCO)O[Si](C)(C)C	1320.3	Semi standard non polar	33892256
(3R,5Z)-5-Octene-1,3-diol,1TMS,isomer #2	CC/C=C\CC(O)CCO[Si](C)(C)C	1332.6	Semi standard non polar	33892256
(3R,5Z)-5-Octene-1,3-diol,2TMS,isomer #1	CC/C=C\CC(CCO[Si](C)(C)C)O[Si](C)(C)C	1396.0	Semi standard non polar	33892256
(3R,5Z)-5-Octene-1,3-diol,1TBDMS,isomer #1	CC/C=C\CC(CCO)O[Si](C)(C)C(C)(C)C	1547.3	Semi standard non polar	33892256
(3R,5Z)-5-Octene-1,3-diol,1TBDMS,isomer #2	CC/C=C\CC(O)CCO[Si](C)(C)C(C)(C)C	1546.8	Semi standard non polar	33892256
(3R,5Z)-5-Octene-1,3-diol,2TBDMS,isomer #1	CC/C=C\CC(CCO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	1819.2	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 - (3R,5Z)-5-Octene-1,3-diol GC-MS (Non-derivatized) - 70eV, Positive	splash10-004j-9100000000-2d532e3fe817748ae54b	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,5Z)-5-Octene-1,3-diol GC-MS (2 TMS) - 70eV, Positive	splash10-00di-9450000000-e07545e8d9ac7509a6b6	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,5Z)-5-Octene-1,3-diol GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,5Z)-5-Octene-1,3-diol 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 - (3R,5Z)-5-Octene-1,3-diol 10V, Positive-QTOF	splash10-004j-1900000000-c296329eb5f60ef481f4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3R,5Z)-5-Octene-1,3-diol 20V, Positive-QTOF	splash10-056s-8900000000-593f6d8b67e9e77fa2f4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3R,5Z)-5-Octene-1,3-diol 40V, Positive-QTOF	splash10-0a4l-9100000000-ea6c12f655dc268009ec	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3R,5Z)-5-Octene-1,3-diol 10V, Negative-QTOF	splash10-0006-1900000000-3ce43739c3345dc56ef4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3R,5Z)-5-Octene-1,3-diol 20V, Negative-QTOF	splash10-01r5-7900000000-60b49232bf60bccb3118	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3R,5Z)-5-Octene-1,3-diol 40V, Negative-QTOF	splash10-0005-9100000000-e543c552d5bf2431870d	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3R,5Z)-5-Octene-1,3-diol 10V, Negative-QTOF	splash10-0006-1900000000-b8aa69135abd192adb80	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3R,5Z)-5-Octene-1,3-diol 20V, Negative-QTOF	splash10-0006-9400000000-712763a188f4f666c5f4	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3R,5Z)-5-Octene-1,3-diol 40V, Negative-QTOF	splash10-0a4l-9000000000-4edd2757ce4cf9131500	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3R,5Z)-5-Octene-1,3-diol 10V, Positive-QTOF	splash10-0aos-9000000000-11363aacd4741fb5d928	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3R,5Z)-5-Octene-1,3-diol 20V, Positive-QTOF	splash10-014l-9000000000-83944e442ba2c59128e5	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3R,5Z)-5-Octene-1,3-diol 40V, Positive-QTOF	splash10-052o-9000000000-1d752e01e248bac60b28	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)	2021-09-16	Wishart Lab	View Spectrum
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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 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, 900 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, 1000 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

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	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

FDB002214

KNApSAcK ID

Not Available

Chemspider ID

20120943

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21159437

PDB ID

Not Available

ChEBI ID

Not Available

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 ]
(). 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 (3R,5Z)-5-Octene-1,3-diol (HMDB0030368)

MOL for HMDB0030368 ((3R,5Z)-5-Octene-1,3-diol)

3D MOL for HMDB0030368 ((3R,5Z)-5-Octene-1,3-diol)

3D SDF for HMDB0030368 ((3R,5Z)-5-Octene-1,3-diol)

3D-SDF for HMDB0030368 ((3R,5Z)-5-Octene-1,3-diol)

PDB for HMDB0030368 ((3R,5Z)-5-Octene-1,3-diol)

3D PDB for HMDB0030368 ((3R,5Z)-5-Octene-1,3-diol)

SMILES for HMDB0030368 ((3R,5Z)-5-Octene-1,3-diol)

INCHI for HMDB0030368 ((3R,5Z)-5-Octene-1,3-diol)

Structure for HMDB0030368 ((3R,5Z)-5-Octene-1,3-diol)

3D Structure for HMDB0030368 ((3R,5Z)-5-Octene-1,3-diol)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra