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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:31:28 UTC

Update Date

2022-03-07 02:52:13 UTC

HMDB ID

HMDB0029613

Secondary Accession Numbers

HMDB29613

Metabolite Identification

Common Name

9-Azabicyclo[3.3.1]nonan-3-one

Description

9-Azabicyclo[3.3.1]nonan-3-one belongs to the class of organic compounds known as piperidinones. Piperidinones are compounds containing a piperidine ring which bears a ketone. 9-Azabicyclo[3.3.1]nonan-3-one has been detected, but not quantified in, fruits and pomegranates (Punica granatum). This could make 9-azabicyclo[3.3.1]nonan-3-one a potential biomarker for the consumption of these foods. Based on a literature review a small amount of articles have been published on 9-Azabicyclo[3.3.1]nonan-3-one.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
9-azabicyclo(3.3.1)Nonan-3-one	HMDB
alpha-Phosphinylbenzyl alcohol	HMDB
Granatonine	HMDB
Norgranatan-3-one	HMDB
Norpseudopelletierine	HMDB

Chemical Formula

C₈H₁₃NO

Average Molecular Weight

139.1949

Monoisotopic Molecular Weight

139.099714043

IUPAC Name

9-azabicyclo[3.3.1]nonan-3-one

Traditional Name

9-azabicyclo[3.3.1]nonan-3-one

CAS Registry Number

4390-39-0

SMILES

O=C1CC2CCCC(C1)N2

InChI Identifier

InChI=1S/C8H13NO/c10-8-4-6-2-1-3-7(5-8)9-6/h6-7,9H,1-5H2

InChI Key

JIYPUEZSSJAXBO-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as piperidinones. Piperidinones are compounds containing a piperidine ring which bears a ketone.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Piperidines

Sub Class

Piperidinones

Direct Parent

Piperidinones

Alternative Parents

Substituents

Piperidinone
Ketone
Cyclic ketone
Secondary aliphatic amine
Secondary amine
Azacycle
Organopnictogen compound
Amine
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Carbonyl group
Hydrocarbon derivative
Organic oxide
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0029613)
Cytoplasm (HMDB: HMDB0029613)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0029613)

Source

Endogenous

Endogenous (HMDB: HMDB0029613)

Plant

Plant (HMDB: HMDB0029613)

Exogenous

Food

Food (HMDB: HMDB0029613)

Fruit

Tropical fruit

Pomegranate (FooDB: FOOD00151)

Fruits (FooDB: FOOD00871)

Exogenous (HMDB: HMDB0029613)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	123 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	210800 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	25.6 g/L	ALOGPS
logP	0.47	ALOGPS
logP	0.76	ChemAxon
logS	-0.74	ALOGPS
pKa (Strongest Acidic)	18.09	ChemAxon
pKa (Strongest Basic)	8.19	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	29.1 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	38.65 m³·mol⁻¹	ChemAxon
Polarizability	15.19 Å³	ChemAxon
Number of Rings	2	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]+	129.225	31661259
DarkChem	[M-H]-	123.916	31661259
DeepCCS	[M+H]+	135.8	30932474
DeepCCS	[M-H]-	132.754	30932474
DeepCCS	[M-2H]-	169.591	30932474
DeepCCS	[M+Na]+	144.626	30932474
AllCCS	[M+H]+	132.5	32859911
AllCCS	[M+H-H2O]+	127.9	32859911
AllCCS	[M+NH4]+	136.8	32859911
AllCCS	[M+Na]+	138.0	32859911
AllCCS	[M-H]-	130.3	32859911
AllCCS	[M+Na-2H]-	131.6	32859911
AllCCS	[M+HCOO]-	133.1	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.	1.71 minutes	32390414
Predicted by Siyang on May 30, 2022	8.8171 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	5.22 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	950.0 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	274.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	106.4 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	168.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	74.6 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	247.7 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	269.4 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	546.0 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	671.8 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	223.6 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	752.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	169.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	199.7 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	722.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	363.6 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	214.1 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
9-Azabicyclo[3.3.1]nonan-3-one	O=C1CC2CCCC(C1)N2	2047.8	Standard polar	33892256
9-Azabicyclo[3.3.1]nonan-3-one	O=C1CC2CCCC(C1)N2	1225.7	Standard non polar	33892256
9-Azabicyclo[3.3.1]nonan-3-one	O=C1CC2CCCC(C1)N2	1302.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
9-Azabicyclo[3.3.1]nonan-3-one,1TMS,isomer #1	C[Si](C)(C)OC1=CC2CCCC(C1)N2	1453.1	Semi standard non polar	33892256
9-Azabicyclo[3.3.1]nonan-3-one,1TMS,isomer #1	C[Si](C)(C)OC1=CC2CCCC(C1)N2	1348.0	Standard non polar	33892256
9-Azabicyclo[3.3.1]nonan-3-one,1TMS,isomer #2	C[Si](C)(C)N1C2CCCC1CC(=O)C2	1474.2	Semi standard non polar	33892256
9-Azabicyclo[3.3.1]nonan-3-one,1TMS,isomer #2	C[Si](C)(C)N1C2CCCC1CC(=O)C2	1538.0	Standard non polar	33892256
9-Azabicyclo[3.3.1]nonan-3-one,2TMS,isomer #1	C[Si](C)(C)OC1=CC2CCCC(C1)N2[Si](C)(C)C	1539.2	Semi standard non polar	33892256
9-Azabicyclo[3.3.1]nonan-3-one,2TMS,isomer #1	C[Si](C)(C)OC1=CC2CCCC(C1)N2[Si](C)(C)C	1505.1	Standard non polar	33892256
9-Azabicyclo[3.3.1]nonan-3-one,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CC2CCCC(C1)N2	1678.0	Semi standard non polar	33892256
9-Azabicyclo[3.3.1]nonan-3-one,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CC2CCCC(C1)N2	1597.4	Standard non polar	33892256
9-Azabicyclo[3.3.1]nonan-3-one,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C2CCCC1CC(=O)C2	1742.5	Semi standard non polar	33892256
9-Azabicyclo[3.3.1]nonan-3-one,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C2CCCC1CC(=O)C2	1822.0	Standard non polar	33892256
9-Azabicyclo[3.3.1]nonan-3-one,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CC2CCCC(C1)N2[Si](C)(C)C(C)(C)C	1997.4	Semi standard non polar	33892256
9-Azabicyclo[3.3.1]nonan-3-one,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CC2CCCC(C1)N2[Si](C)(C)C(C)(C)C	1966.3	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 9-Azabicyclo[3.3.1]nonan-3-one GC-MS (Non-derivatized) - 70eV, Positive	splash10-03ys-9500000000-8dd03faec664db2970c2	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 9-Azabicyclo[3.3.1]nonan-3-one GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 9-Azabicyclo[3.3.1]nonan-3-one 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 - 9-Azabicyclo[3.3.1]nonan-3-one 10V, Positive-QTOF	splash10-0006-0900000000-2e076e7899cff5ce3a5b	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-Azabicyclo[3.3.1]nonan-3-one 20V, Positive-QTOF	splash10-0006-1900000000-3d4d8d2f92b3853e808c	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-Azabicyclo[3.3.1]nonan-3-one 40V, Positive-QTOF	splash10-000x-9200000000-68389711b522184e168e	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-Azabicyclo[3.3.1]nonan-3-one 10V, Negative-QTOF	splash10-000i-0900000000-7793fcaeffdb42b831de	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-Azabicyclo[3.3.1]nonan-3-one 20V, Negative-QTOF	splash10-000i-0900000000-34d82c0effb6305951bf	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-Azabicyclo[3.3.1]nonan-3-one 40V, Negative-QTOF	splash10-05g3-6900000000-742031da3504786396ca	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-Azabicyclo[3.3.1]nonan-3-one 10V, Positive-QTOF	splash10-0006-0900000000-8391859fd0a834ff9018	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-Azabicyclo[3.3.1]nonan-3-one 20V, Positive-QTOF	splash10-00di-1900000000-50b1dbb161b8f96ca582	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-Azabicyclo[3.3.1]nonan-3-one 40V, Positive-QTOF	splash10-059y-9200000000-3fd5c2e93bcf9915f36e	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-Azabicyclo[3.3.1]nonan-3-one 10V, Negative-QTOF	splash10-000i-0900000000-46122e7c9ba4f80060de	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-Azabicyclo[3.3.1]nonan-3-one 20V, Negative-QTOF	splash10-000i-1900000000-122cce62f9a3259be226	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-Azabicyclo[3.3.1]nonan-3-one 40V, Negative-QTOF	splash10-0006-9200000000-4af34625949602cd775a	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

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

FDB000781

KNApSAcK ID

C00055082

Chemspider ID

128569

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

145745

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1810611

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 9-Azabicyclo[3.3.1]nonan-3-one (HMDB0029613)

MOL for HMDB0029613 (9-Azabicyclo[3.3.1]nonan-3-one)

3D MOL for HMDB0029613 (9-Azabicyclo[3.3.1]nonan-3-one)

3D SDF for HMDB0029613 (9-Azabicyclo[3.3.1]nonan-3-one)

3D-SDF for HMDB0029613 (9-Azabicyclo[3.3.1]nonan-3-one)

PDB for HMDB0029613 (9-Azabicyclo[3.3.1]nonan-3-one)

3D PDB for HMDB0029613 (9-Azabicyclo[3.3.1]nonan-3-one)

SMILES for HMDB0029613 (9-Azabicyclo[3.3.1]nonan-3-one)

INCHI for HMDB0029613 (9-Azabicyclo[3.3.1]nonan-3-one)

Structure for HMDB0029613 (9-Azabicyclo[3.3.1]nonan-3-one)

3D Structure for HMDB0029613 (9-Azabicyclo[3.3.1]nonan-3-one)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra