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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 01:12:27 UTC

Update Date

2023-02-21 17:27:06 UTC

HMDB ID

HMDB0039680

Secondary Accession Numbers

HMDB39680

Metabolite Identification

Common Name

3,5,5-Trimethyl-1,2-cyclopentanedione

Description

3,5,5-Trimethyl-1,2-cyclopentanedione belongs to the class of organic compounds known as cyclic ketones. These are organic compounds containing a ketone that is conjugated to a cyclic moiety. 3,5,5-Trimethyl-1,2-cyclopentanedione has been detected, but not quantified in, a few different foods, such as arabica coffees (Coffea arabica), coffee and coffee products, and robusta coffees (Coffea canephora). This could make 3,5,5-trimethyl-1,2-cyclopentanedione a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 3,5,5-Trimethyl-1,2-cyclopentanedione.

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-Hydroxy-3,5,5-trimethyl-2-cyclo-pentenone	HMDB
2-Hydroxy-3,5,5-trimethyl-2-cyclopenten-1-one, 9ci	HMDB

Chemical Formula

C₈H₁₂O₂

Average Molecular Weight

140.1797

Monoisotopic Molecular Weight

140.083729628

IUPAC Name

3,3,5-trimethylcyclopentane-1,2-dione

Traditional Name

3,3,5-trimethylcyclopentane-1,2-dione

CAS Registry Number

53263-56-2

SMILES

CC1CC(C)(C)C(=O)C1=O

InChI Identifier

InChI=1S/C8H12O2/c1-5-4-8(2,3)7(10)6(5)9/h5H,4H2,1-3H3

InChI Key

GGXVKCBZJYLSCZ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclic ketones. These are organic compounds containing a ketone that is conjugated to a cyclic moiety.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Cyclic ketones

Alternative Parents

Substituents

Cyclic ketone
Organic oxide
Hydrocarbon derivative
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0039680)
Cell membrane (HMDB: HMDB0039680)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0039680)

Source

Exogenous

Exogenous (HMDB: HMDB0039680)

Food

Food (HMDB: HMDB0039680)

Coffee and coffee product

Coffee

Arabica coffee (FooDB: FOOD00059)
Robusta coffee (FooDB: FOOD00060)

Coffee and coffee products (FooDB: FOOD00861)

Endogenous

Plant

Coffea (HMDB: HMDB0039680)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0039680)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	87 - 88 °C	Not Available
Boiling Point	242.39 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	1198 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	0.486 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	6.03 g/L	ALOGPS
logP	1.38	ALOGPS
logP	2.53	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	16.57	ChemAxon
pKa (Strongest Basic)	-8.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	34.14 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	38.04 m³·mol⁻¹	ChemAxon
Polarizability	15.05 Å³	ChemAxon
Number of Rings	1	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]+	130.946	31661259
DarkChem	[M-H]-	127.778	31661259
DeepCCS	[M+H]+	131.654	30932474
DeepCCS	[M-H]-	127.823	30932474
DeepCCS	[M-2H]-	165.158	30932474
DeepCCS	[M+Na]+	140.52	30932474
AllCCS	[M+H]+	128.1	32859911
AllCCS	[M+H-H2O]+	123.6	32859911
AllCCS	[M+NH4]+	132.2	32859911
AllCCS	[M+Na]+	133.4	32859911
AllCCS	[M-H]-	129.5	32859911
AllCCS	[M+Na-2H]-	131.3	32859911
AllCCS	[M+HCOO]-	133.5	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3,5,5-Trimethyl-1,2-cyclopentanedione	CC1CC(C)(C)C(=O)C1=O	1682.1	Standard polar	33892256
3,5,5-Trimethyl-1,2-cyclopentanedione	CC1CC(C)(C)C(=O)C1=O	1051.0	Standard non polar	33892256
3,5,5-Trimethyl-1,2-cyclopentanedione	CC1CC(C)(C)C(=O)C1=O	1050.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3,5,5-Trimethyl-1,2-cyclopentanedione,1TMS,isomer #1	CC1=C(O[Si](C)(C)C)C(=O)C(C)(C)C1	1249.3	Semi standard non polar	33892256
3,5,5-Trimethyl-1,2-cyclopentanedione,1TMS,isomer #1	CC1=C(O[Si](C)(C)C)C(=O)C(C)(C)C1	1177.8	Standard non polar	33892256
3,5,5-Trimethyl-1,2-cyclopentanedione,1TBDMS,isomer #1	CC1=C(O[Si](C)(C)C(C)(C)C)C(=O)C(C)(C)C1	1476.8	Semi standard non polar	33892256
3,5,5-Trimethyl-1,2-cyclopentanedione,1TBDMS,isomer #1	CC1=C(O[Si](C)(C)C(C)(C)C)C(=O)C(C)(C)C1	1393.2	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 3,5,5-Trimethyl-1,2-cyclopentanedione GC-MS (Non-derivatized) - 70eV, Positive	splash10-056u-9200000000-61635fdee10363b297e0	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3,5,5-Trimethyl-1,2-cyclopentanedione 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 - 3,5,5-Trimethyl-1,2-cyclopentanedione 10V, Positive-QTOF	splash10-0006-1900000000-6511d8d19bd8f1310571	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5,5-Trimethyl-1,2-cyclopentanedione 20V, Positive-QTOF	splash10-0006-9800000000-ace3258466b43558aa93	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5,5-Trimethyl-1,2-cyclopentanedione 40V, Positive-QTOF	splash10-05nf-9000000000-25009ac65af98f674bec	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5,5-Trimethyl-1,2-cyclopentanedione 10V, Negative-QTOF	splash10-000i-0900000000-c1316bcee802636f3445	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5,5-Trimethyl-1,2-cyclopentanedione 20V, Negative-QTOF	splash10-000i-1900000000-c30c1eb9d37514ce185b	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5,5-Trimethyl-1,2-cyclopentanedione 40V, Negative-QTOF	splash10-0awi-9400000000-7cd824e2e620c0cb32ae	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5,5-Trimethyl-1,2-cyclopentanedione 10V, Positive-QTOF	splash10-000x-4900000000-84629fdaa73819ce9f3e	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5,5-Trimethyl-1,2-cyclopentanedione 20V, Positive-QTOF	splash10-059x-9200000000-9042624330b82b7869ea	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5,5-Trimethyl-1,2-cyclopentanedione 40V, Positive-QTOF	splash10-0006-9000000000-733fa84191f55d58bb16	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5,5-Trimethyl-1,2-cyclopentanedione 10V, Negative-QTOF	splash10-000i-0900000000-a5734f49b62679635a5a	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5,5-Trimethyl-1,2-cyclopentanedione 20V, Negative-QTOF	splash10-01q0-5900000000-7dd1842f6987a542fadb	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5,5-Trimethyl-1,2-cyclopentanedione 40V, Negative-QTOF	splash10-059i-9800000000-e509b13d0833f90607dc	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)	2021-09-24	Wishart Lab	View Spectrum
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, 1000 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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 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, 900 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

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+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Membrane (predicted from logP)

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

FDB019309

KNApSAcK ID

Not Available

Chemspider ID

35014854

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

69698813

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1619151

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 3,5,5-Trimethyl-1,2-cyclopentanedione (HMDB0039680)

MOL for HMDB0039680 (3,5,5-Trimethyl-1,2-cyclopentanedione)

3D MOL for HMDB0039680 (3,5,5-Trimethyl-1,2-cyclopentanedione)

3D SDF for HMDB0039680 (3,5,5-Trimethyl-1,2-cyclopentanedione)

3D-SDF for HMDB0039680 (3,5,5-Trimethyl-1,2-cyclopentanedione)

PDB for HMDB0039680 (3,5,5-Trimethyl-1,2-cyclopentanedione)

3D PDB for HMDB0039680 (3,5,5-Trimethyl-1,2-cyclopentanedione)

SMILES for HMDB0039680 (3,5,5-Trimethyl-1,2-cyclopentanedione)

INCHI for HMDB0039680 (3,5,5-Trimethyl-1,2-cyclopentanedione)

Structure for HMDB0039680 (3,5,5-Trimethyl-1,2-cyclopentanedione)

3D Structure for HMDB0039680 (3,5,5-Trimethyl-1,2-cyclopentanedione)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra