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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:42:00 UTC

Update Date

2023-02-21 17:20:14 UTC

HMDB ID

HMDB0031267

Secondary Accession Numbers

HMDB31267

Metabolite Identification

Common Name

3-Nonanone

Description

3-Nonanone belongs to the class of organic compounds known as ketones. These are organic compounds in which a carbonyl group is bonded to two carbon atoms R2C=O (neither R may be a hydrogen atom). Ketones that have one or more alpha-hydrogen atoms undergo keto-enol tautomerization, the tautomer being an enol. Thus, 3-nonanone is considered to be an oxygenated hydrocarbon. 3-Nonanone is a sweet, fresh, and fruity tasting compound. 3-Nonanone has been detected, but not quantified in, several different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), domestic pigs (Sus scrofa domestica), fruits, and milk (cow). This could make 3-nonanone a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 3-Nonanone.

Structure

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

COMPND    HMDB0031267
HETATM    1  C1  UNL     1       3.120  -0.745  -0.205  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.910   0.568  -0.878  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.542   1.118  -0.958  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.815   1.394   0.302  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.462   0.251   1.175  1.00  0.00           C  
HETATM    6  C6  UNL     1      -0.480  -0.761   0.585  1.00  0.00           C  
HETATM    7  C7  UNL     1      -1.809  -0.213   0.252  1.00  0.00           C  
HETATM    8  O1  UNL     1      -2.089   0.920   0.496  1.00  0.00           O  
HETATM    9  C8  UNL     1      -2.826  -1.094  -0.404  1.00  0.00           C  
HETATM   10  C9  UNL     1      -4.105  -0.322  -0.647  1.00  0.00           C  
HETATM   11  H1  UNL     1       3.495  -0.624   0.855  1.00  0.00           H  
HETATM   12  H2  UNL     1       2.261  -1.418  -0.228  1.00  0.00           H  
HETATM   13  H3  UNL     1       3.956  -1.332  -0.692  1.00  0.00           H  
HETATM   14  H4  UNL     1       3.637   1.326  -0.432  1.00  0.00           H  
HETATM   15  H5  UNL     1       3.330   0.439  -1.929  1.00  0.00           H  
HETATM   16  H6  UNL     1       0.924   0.417  -1.599  1.00  0.00           H  
HETATM   17  H7  UNL     1       1.603   2.109  -1.512  1.00  0.00           H  
HETATM   18  H8  UNL     1      -0.131   1.940   0.005  1.00  0.00           H  
HETATM   19  H9  UNL     1       1.447   2.118   0.888  1.00  0.00           H  
HETATM   20  H10 UNL     1      -0.103   0.684   2.071  1.00  0.00           H  
HETATM   21  H11 UNL     1       1.307  -0.280   1.636  1.00  0.00           H  
HETATM   22  H12 UNL     1      -0.584  -1.567   1.374  1.00  0.00           H  
HETATM   23  H13 UNL     1      -0.019  -1.271  -0.274  1.00  0.00           H  
HETATM   24  H14 UNL     1      -3.011  -2.012   0.158  1.00  0.00           H  
HETATM   25  H15 UNL     1      -2.410  -1.335  -1.424  1.00  0.00           H  
HETATM   26  H16 UNL     1      -4.063   0.611  -0.040  1.00  0.00           H  
HETATM   27  H17 UNL     1      -4.203   0.003  -1.699  1.00  0.00           H  
HETATM   28  H18 UNL     1      -4.975  -0.925  -0.319  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   22   23
CONECT    7    8    8    9
CONECT    9   10   24   25
CONECT   10   26   27   28
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Ethyl hexyl ketone	HMDB
Ethyl N-hexyl ketone	HMDB
FEMA 3440	HMDB
N-Hexyl ethyl ketone	HMDB
Nonan-3-one	HMDB

Chemical Formula

C₉H₁₈O

Average Molecular Weight

142.2386

Monoisotopic Molecular Weight

142.135765198

IUPAC Name

nonan-3-one

Traditional Name

3-nonanone

CAS Registry Number

925-78-0

SMILES

CCCCCCC(=O)CC

InChI Identifier

InChI=1S/C9H18O/c1-3-5-6-7-8-9(10)4-2/h3-8H2,1-2H3

InChI Key

IYTXKIXETAELAV-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as ketones. These are organic compounds in which a carbonyl group is bonded to two carbon atoms R2C=O (neither R may be a hydrogen atom). Ketones that have one or more alpha-hydrogen atoms undergo keto-enol tautomerization, the tautomer being an enol.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Ketones

Alternative Parents

Substituents

Ketone
Organic oxide
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Oxygenated hydrocarbons (LMFA12000053 )

Ontology

Sweet

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0031267)
Cell membrane (HMDB: HMDB0031267)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0031267)

Source

Endogenous

Endogenous (HMDB: HMDB0031267)

Plant

Plant (HMDB: HMDB0031267)

Exogenous

Food

Food (HMDB: HMDB0031267)

Animal origin

Poultry

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Milk and milk product

Unfermented milk

Milk (Cow) (FooDB: FOOD00618)

Fruit

Fruits (FooDB: FOOD00871)

Exogenous (HMDB: HMDB0031267)

Process

Not Available

Role

Industrial application

Food and nutrition

Food additive

Flavoring agent

Flavoring Agent (HMDB: HMDB0031267)

Physical Properties

State

Liquid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	-8 °C	Not Available
Boiling Point	187.00 to 188.00 °C. @ 760.00 mm Hg	The Good Scents Company Information System
Water Solubility	0 slightly	The Good Scents Company Information System
LogP	3.015 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.42 g/L	ALOGPS
logP	3.14	ALOGPS
logP	3.29	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Basic)	-7.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	17.07 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	43.85 m³·mol⁻¹	ChemAxon
Polarizability	18.41 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]+	134.348	31661259
DarkChem	[M-H]-	131.913	31661259
DeepCCS	[M+H]+	139.066	30932474
DeepCCS	[M-H]-	136.138	30932474
DeepCCS	[M-2H]-	173.173	30932474
DeepCCS	[M+Na]+	148.13	30932474
AllCCS	[M+H]+	137.4	32859911
AllCCS	[M+H-H2O]+	133.3	32859911
AllCCS	[M+NH4]+	141.2	32859911
AllCCS	[M+Na]+	142.3	32859911
AllCCS	[M-H]-	139.7	32859911
AllCCS	[M+Na-2H]-	142.0	32859911
AllCCS	[M+HCOO]-	144.7	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.	6.47 minutes	32390414
Predicted by Siyang on May 30, 2022	17.0964 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	4.73 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2175.8 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	587.6 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	218.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	379.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	372.9 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	714.5 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	697.8 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	105.2 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1505.0 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	467.7 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	1459.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	477.7 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	430.4 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	523.9 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	13.2 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3-Nonanone	CCCCCCC(=O)CC	1359.3	Standard polar	33892256
3-Nonanone	CCCCCCC(=O)CC	1056.1	Standard non polar	33892256
3-Nonanone	CCCCCCC(=O)CC	1078.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3-Nonanone,1TMS,isomer #1	CC=C(CCCCCC)O[Si](C)(C)C	1261.4	Semi standard non polar	33892256
3-Nonanone,1TMS,isomer #1	CC=C(CCCCCC)O[Si](C)(C)C	1254.1	Standard non polar	33892256
3-Nonanone,1TMS,isomer #2	CCCCCC=C(CC)O[Si](C)(C)C	1258.2	Semi standard non polar	33892256
3-Nonanone,1TMS,isomer #2	CCCCCC=C(CC)O[Si](C)(C)C	1242.2	Standard non polar	33892256
3-Nonanone,1TBDMS,isomer #1	CC=C(CCCCCC)O[Si](C)(C)C(C)(C)C	1477.5	Semi standard non polar	33892256
3-Nonanone,1TBDMS,isomer #1	CC=C(CCCCCC)O[Si](C)(C)C(C)(C)C	1443.8	Standard non polar	33892256
3-Nonanone,1TBDMS,isomer #2	CCCCCC=C(CC)O[Si](C)(C)C(C)(C)C	1471.5	Semi standard non polar	33892256
3-Nonanone,1TBDMS,isomer #2	CCCCCC=C(CC)O[Si](C)(C)C(C)(C)C	1426.0	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - 3-Nonanone EI-B (Non-derivatized)	splash10-054o-9000000000-576b2a3e3912b972f8c1	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 3-Nonanone EI-B (Non-derivatized)	splash10-054o-9000000000-576b2a3e3912b972f8c1	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Nonanone GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4i-9100000000-715ee89f8599c8415339	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Nonanone 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 - 3-Nonanone 10V, Positive-QTOF	splash10-0006-1900000000-28883ed659f247270daa	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Nonanone 20V, Positive-QTOF	splash10-052f-9400000000-c53d4c2f93c8985a5b7a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Nonanone 40V, Positive-QTOF	splash10-052f-9000000000-e88913da86061a44a36b	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Nonanone 10V, Negative-QTOF	splash10-0006-0900000000-36844d21bfd5cef7dd4a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Nonanone 20V, Negative-QTOF	splash10-0006-4900000000-99ecbe8f706163a5bfbe	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Nonanone 40V, Negative-QTOF	splash10-0avi-9100000000-7e2f9ee135f806e68d81	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Nonanone 10V, Negative-QTOF	splash10-0006-0900000000-31a4c0b614cfbc7c3156	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Nonanone 20V, Negative-QTOF	splash10-06r6-8900000000-7496fcaec08b61b3a1c6	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Nonanone 40V, Negative-QTOF	splash10-0a4i-9000000000-0abf00616b4aa3e1385d	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Nonanone 10V, Positive-QTOF	splash10-052f-9000000000-d9ac35d11c229890377d	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Nonanone 20V, Positive-QTOF	splash10-0a4l-9000000000-88e194e384597211c316	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Nonanone 40V, Positive-QTOF	splash10-0a4l-9000000000-8227f4fcf71ffe496a48	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]+)	2023-02-03	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

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

FDB003309

KNApSAcK ID

C00055664

Chemspider ID

55177

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Nonanone

METLIN ID

Not Available

PubChem Compound

61235

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1032891

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for 3-Nonanone (HMDB0031267)

MOL for HMDB0031267 (3-Nonanone)

3D MOL for HMDB0031267 (3-Nonanone)

3D SDF for HMDB0031267 (3-Nonanone)

3D-SDF for HMDB0031267 (3-Nonanone)

PDB for HMDB0031267 (3-Nonanone)

3D PDB for HMDB0031267 (3-Nonanone)

SMILES for HMDB0031267 (3-Nonanone)

INCHI for HMDB0031267 (3-Nonanone)

Structure for HMDB0031267 (3-Nonanone)

3D Structure for HMDB0031267 (3-Nonanone)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra