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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:40:03 UTC

Update Date

2023-02-21 17:19:48 UTC

HMDB ID

HMDB0030959

Secondary Accession Numbers

HMDB30959

Metabolite Identification

Common Name

(Z)-3-Nonen-1-ol

Description

(Z)-3-Nonen-1-ol 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, (Z)-3-nonen-1-ol is considered to be a fatty alcohol. Based on a literature review a small amount of articles have been published on (Z)-3-Nonen-1-ol.

Structure

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

COMPND    HMDB0030959
HETATM    1  C1  UNL     1       3.940   0.870  -0.651  1.00  0.00           C  
HETATM    2  C2  UNL     1       3.364  -0.498  -0.406  1.00  0.00           C  
HETATM    3  C3  UNL     1       2.079  -0.443   0.391  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.097   0.380  -0.410  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.245   0.492   0.324  1.00  0.00           C  
HETATM    6  C6  UNL     1      -0.855  -0.806   0.556  1.00  0.00           C  
HETATM    7  C7  UNL     1      -2.022  -1.163   0.095  1.00  0.00           C  
HETATM    8  C8  UNL     1      -2.859  -0.287  -0.720  1.00  0.00           C  
HETATM    9  C9  UNL     1      -4.212  -0.011  -0.065  1.00  0.00           C  
HETATM   10  O1  UNL     1      -4.079   0.599   1.163  1.00  0.00           O  
HETATM   11  H1  UNL     1       3.535   1.634   0.075  1.00  0.00           H  
HETATM   12  H2  UNL     1       5.061   0.873  -0.636  1.00  0.00           H  
HETATM   13  H3  UNL     1       3.663   1.268  -1.659  1.00  0.00           H  
HETATM   14  H4  UNL     1       4.142  -1.103   0.102  1.00  0.00           H  
HETATM   15  H5  UNL     1       3.210  -0.973  -1.402  1.00  0.00           H  
HETATM   16  H6  UNL     1       1.730  -1.501   0.496  1.00  0.00           H  
HETATM   17  H7  UNL     1       2.326   0.019   1.367  1.00  0.00           H  
HETATM   18  H8  UNL     1       1.528   1.398  -0.500  1.00  0.00           H  
HETATM   19  H9  UNL     1       0.931  -0.124  -1.366  1.00  0.00           H  
HETATM   20  H10 UNL     1       0.003   0.924   1.344  1.00  0.00           H  
HETATM   21  H11 UNL     1      -0.816   1.260  -0.173  1.00  0.00           H  
HETATM   22  H12 UNL     1      -0.263  -1.520   1.171  1.00  0.00           H  
HETATM   23  H13 UNL     1      -2.375  -2.163   0.335  1.00  0.00           H  
HETATM   24  H14 UNL     1      -3.138  -0.919  -1.626  1.00  0.00           H  
HETATM   25  H15 UNL     1      -2.406   0.591  -1.162  1.00  0.00           H  
HETATM   26  H16 UNL     1      -4.837   0.646  -0.701  1.00  0.00           H  
HETATM   27  H17 UNL     1      -4.769  -0.957   0.057  1.00  0.00           H  
HETATM   28  H18 UNL     1      -3.733   1.518   1.107  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3   14   15
CONECT    3    4   16   17
CONECT    4    5   18   19
CONECT    5    6   20   21
CONECT    6    7    7   22
CONECT    7    8   23
CONECT    8    9   24   25
CONECT    9   10   26   27
CONECT   10   28
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(3Z)-3-Nonen-1-ol	HMDB
(Z)-Non-3-en-1-ol	HMDB
cis-3-Nonen-1-ol	HMDB

Chemical Formula

C₉H₁₈O

Average Molecular Weight

142.2386

Monoisotopic Molecular Weight

142.135765198

IUPAC Name

(3Z)-non-3-en-1-ol

Traditional Name

(3Z)-non-3-en-1-ol

CAS Registry Number

10340-23-5

SMILES

CCCCC\C=C/CCO

InChI Identifier

InChI=1S/C9H18O/c1-2-3-4-5-6-7-8-9-10/h6-7,10H,2-5,8-9H2,1H3/b7-6-

InChI Key

IFTBJDZSLBRRMC-SREVYHEPSA-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
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Fatty alcohols (LMFA05000134 )

Ontology

Cellular substructure

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0030959)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0030959)

Source

Endogenous

Endogenous (HMDB: HMDB0030959)

Plant

Plant (HMDB: HMDB0030959)
Cucurbitaceae (HMDB: HMDB0030959)

Animal

Animal (HMDB: HMDB0030959)

Exogenous

Food

Food (HMDB: HMDB0030959)

Gourd

Cucumber (FooDB: FOOD00065)
Muskmelon (FooDB: FOOD00064)

Fruit

Fruits (FooDB: FOOD00871)

Vegetable

Leaf vegetable

Green vegetables (FooDB: FOOD00872)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Fatty Acid Metabolism (HMDB: HMDB0030959)

Chemical reaction

Lipid Peroxidation (HMDB: HMDB0030959)

Cellular process

Cell signaling (HMDB: HMDB0030959)

Biochemical process

Lipid transport (HMDB: HMDB0030959)

Role

Biological role

Energy storage (HMDB: HMDB0030959)

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0030959)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	107.00 to 109.00 °C. @ 20.00 mm Hg	The Good Scents Company Information System
Water Solubility	619.3 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	3.226 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.45 g/L	ALOGPS
logP	3.46	ALOGPS
logP	2.67	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	16.79	ChemAxon
pKa (Strongest Basic)	-2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	20.23 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	46.26 m³·mol⁻¹	ChemAxon
Polarizability	18.33 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]+	136.79	31661259
DarkChem	[M-H]-	132.837	31661259
DeepCCS	[M+H]+	135.611	30932474
DeepCCS	[M-H]-	132.595	30932474
DeepCCS	[M-2H]-	169.413	30932474
DeepCCS	[M+Na]+	144.457	30932474
AllCCS	[M+H]+	135.7	32859911
AllCCS	[M+H-H2O]+	131.6	32859911
AllCCS	[M+NH4]+	139.5	32859911
AllCCS	[M+Na]+	140.6	32859911
AllCCS	[M-H]-	139.8	32859911
AllCCS	[M+Na-2H]-	142.2	32859911
AllCCS	[M+HCOO]-	144.8	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(Z)-3-Nonen-1-ol	CCCCC\C=C/CCO	1652.6	Standard polar	33892256
(Z)-3-Nonen-1-ol	CCCCC\C=C/CCO	1140.3	Standard non polar	33892256
(Z)-3-Nonen-1-ol	CCCCC\C=C/CCO	1161.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
(Z)-3-Nonen-1-ol,1TMS,isomer #1	CCCCC/C=C\CCO[Si](C)(C)C	1271.3	Semi standard non polar	33892256
(Z)-3-Nonen-1-ol,1TBDMS,isomer #1	CCCCC/C=C\CCO[Si](C)(C)C(C)(C)C	1481.3	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 - (Z)-3-Nonen-1-ol GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a6r-9200000000-8afe0738d79eade28d4d	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (Z)-3-Nonen-1-ol GC-MS (1 TMS) - 70eV, Positive	splash10-00di-9400000000-fc2a12782f7f7db48977	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (Z)-3-Nonen-1-ol GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (Z)-3-Nonen-1-ol 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 - (Z)-3-Nonen-1-ol 10V, Positive-QTOF	splash10-004l-1900000000-7b31cbb24cae889e5d59	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-3-Nonen-1-ol 20V, Positive-QTOF	splash10-004i-7900000000-8972da2708b4f8c3a330	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-3-Nonen-1-ol 40V, Positive-QTOF	splash10-052f-9000000000-d46e9234d6318796e675	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-3-Nonen-1-ol 10V, Negative-QTOF	splash10-0006-0900000000-1656c25a3b3d19ded296	2016-08-04	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-3-Nonen-1-ol 20V, Negative-QTOF	splash10-0006-1900000000-d6e2ca5f780ec853f578	2016-08-04	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-3-Nonen-1-ol 40V, Negative-QTOF	splash10-006y-9300000000-919d34d25cd21eb4a501	2016-08-04	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-3-Nonen-1-ol 10V, Negative-QTOF	splash10-0006-0900000000-31a4c0b614cfbc7c3156	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-3-Nonen-1-ol 20V, Negative-QTOF	splash10-0006-0900000000-022d6bb66536ee87da98	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-3-Nonen-1-ol 40V, Negative-QTOF	splash10-014l-9000000000-ee7c7a380d0e8febf40d	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-3-Nonen-1-ol 10V, Positive-QTOF	splash10-0apl-9000000000-2618f7daecbdac8682d0	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-3-Nonen-1-ol 20V, Positive-QTOF	splash10-0a4l-9000000000-19edfd51d0a8c739b12b	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-3-Nonen-1-ol 40V, Positive-QTOF	splash10-0a4l-9000000000-741dc8004f618063a6d8	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]-)	2023-02-03	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

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

FDB002938

KNApSAcK ID

Not Available

Chemspider ID

4516777

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5364631

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1001811

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 (Z)-3-Nonen-1-ol (HMDB0030959)

MOL for HMDB0030959 ((Z)-3-Nonen-1-ol)

3D MOL for HMDB0030959 ((Z)-3-Nonen-1-ol)

3D SDF for HMDB0030959 ((Z)-3-Nonen-1-ol)

3D-SDF for HMDB0030959 ((Z)-3-Nonen-1-ol)

PDB for HMDB0030959 ((Z)-3-Nonen-1-ol)

3D PDB for HMDB0030959 ((Z)-3-Nonen-1-ol)

SMILES for HMDB0030959 ((Z)-3-Nonen-1-ol)

INCHI for HMDB0030959 ((Z)-3-Nonen-1-ol)

Structure for HMDB0030959 ((Z)-3-Nonen-1-ol)

3D Structure for HMDB0030959 ((Z)-3-Nonen-1-ol)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra