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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2012-09-12 02:38:34 UTC

Update Date

2023-02-21 17:28:32 UTC

HMDB ID

HMDB0041011

Secondary Accession Numbers

HMDB41011

Metabolite Identification

Common Name

beta-Cyclocitral

Description

beta-Cyclocitral, also known as β-cyclocitral, belongs to the class of organic compounds known as organic oxides. These are organic compounds containing an oxide group. beta-Cyclocitral is a sweet, clean, and damascone tasting compound. beta-Cyclocitral is found, on average, in the highest concentration within orange mints (Mentha aquatica) and safflowers (Carthamus tinctorius). beta-Cyclocitral has also been detected, but not quantified in, several different foods, such as garden tomatoes (Solanum lycopersicum), garden tomato (var.), teas (Camellia sinensis), black tea, and cauliflowers (Brassica oleracea var. botrytis). This could make beta-cyclocitral a potential biomarker for the consumption of these foods. beta-Cyclocitral is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a small amount of articles have been published on beta-Cyclocitral.

Structure

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

COMPND    HMDB0041011
HETATM    1  C1  UNL     1       2.662   0.837   0.533  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.435   0.058   0.244  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.272   0.690   0.248  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.254   2.141   0.540  1.00  0.00           C  
HETATM    5  O1  UNL     1      -0.838   2.731   0.543  1.00  0.00           O  
HETATM    6  C5  UNL     1      -1.030   0.035  -0.024  1.00  0.00           C  
HETATM    7  C6  UNL     1      -2.064   0.466   0.995  1.00  0.00           C  
HETATM    8  C7  UNL     1      -1.580   0.450  -1.392  1.00  0.00           C  
HETATM    9  C8  UNL     1      -0.953  -1.474  -0.017  1.00  0.00           C  
HETATM   10  C9  UNL     1       0.321  -1.882  -0.723  1.00  0.00           C  
HETATM   11  C10 UNL     1       1.546  -1.385  -0.035  1.00  0.00           C  
HETATM   12  H1  UNL     1       3.553   0.189   0.657  1.00  0.00           H  
HETATM   13  H2  UNL     1       2.839   1.552  -0.293  1.00  0.00           H  
HETATM   14  H3  UNL     1       2.580   1.424   1.473  1.00  0.00           H  
HETATM   15  H4  UNL     1       1.151   2.686   0.746  1.00  0.00           H  
HETATM   16  H5  UNL     1      -2.756  -0.400   1.188  1.00  0.00           H  
HETATM   17  H6  UNL     1      -1.629   0.743   1.957  1.00  0.00           H  
HETATM   18  H7  UNL     1      -2.687   1.305   0.642  1.00  0.00           H  
HETATM   19  H8  UNL     1      -0.749   0.550  -2.134  1.00  0.00           H  
HETATM   20  H9  UNL     1      -2.179   1.389  -1.308  1.00  0.00           H  
HETATM   21  H10 UNL     1      -2.240  -0.357  -1.787  1.00  0.00           H  
HETATM   22  H11 UNL     1      -1.784  -1.931  -0.591  1.00  0.00           H  
HETATM   23  H12 UNL     1      -0.986  -1.882   1.016  1.00  0.00           H  
HETATM   24  H13 UNL     1       0.281  -1.414  -1.733  1.00  0.00           H  
HETATM   25  H14 UNL     1       0.371  -2.973  -0.880  1.00  0.00           H  
HETATM   26  H15 UNL     1       1.802  -1.975   0.874  1.00  0.00           H  
HETATM   27  H16 UNL     1       2.410  -1.575  -0.739  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3    3   11
CONECT    3    4    6
CONECT    4    5    5   15
CONECT    6    7    8    9
CONECT    7   16   17   18
CONECT    8   19   20   21
CONECT    9   10   22   23
CONECT   10   11   24   25
CONECT   11   26   27
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
2,6,6-Trimethyl-1-cyclohexene-1-carboxaldehyde	ChEBI
2,6,6-Trimethyl-1-cyclohexene-1-carbaldehyde	Kegg
b-Cyclocitral	Generator
Β-cyclocitral	Generator
1-Formyl-2,6,6-trimethyl-1-cyclohexene	HMDB
2,6,6-Trimethyl-1-cyclohexen-1-carboxaldehyde	HMDB
2,6,6-Trimethyl-cyclohexene-1-carboxaldehyde	HMDB
2,6,6-Trimethyl-cyclohexenecarboxaldehyde	HMDB
2,6,6-Trimethylcyclohex-1-ene-1-carbaldehyde	HMDB
2,6,6-Trimethylcyclohexene-1-carbaldehyde	HMDB
2,6,6-Trimethylcyclohexenecarbaldehyde	HMDB
alpha(beta)-Cyclocitral	HMDB
beta -Cyclocitral	HMDB
beta-Cyclocitrol	HMDB

Chemical Formula

C₁₀H₁₆O

Average Molecular Weight

152.2334

Monoisotopic Molecular Weight

152.120115134

IUPAC Name

2,6,6-trimethylcyclohex-1-ene-1-carbaldehyde

Traditional Name

β-cyclocitral

CAS Registry Number

432-25-7

SMILES

CC1=C(C=O)C(C)(C)CCC1

InChI Identifier

InChI=1S/C10H16O/c1-8-5-4-6-10(2,3)9(8)7-11/h7H,4-6H2,1-3H3

InChI Key

MOQGCGNUWBPGTQ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as organic oxides. These are organic compounds containing an oxide group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organic oxides

Sub Class

Not Available

Direct Parent

Organic oxides

Alternative Parents

Substituents

Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aldehyde
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

monoterpenoid (CHEBI:53177 )

Ontology

Sweet

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0041011)
Cell membrane (HMDB: HMDB0041011)

Excreta

Biofluid or Excreta

Urine (PMID: 24023812)
Feces (PMID: 23454028)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0041011)

Source

Exogenous

Exogenous (HMDB: HMDB0041011)

Food

Food (HMDB: HMDB0041011)

Vegetable

Cabbage

Cauliflower (FooDB: FOOD00031)

Fruit vegetable

Fruit

Other fruit

Fig (FooDB: FOOD00081)

Cereal and cereal product

Cereal

Oat (FooDB: FOOD00022)

Herb and spice

Oilseed crop

Safflower (FooDB: FOOD00042)

Herb

Orange mint (FooDB: FOOD00110)

Herbs and Spices (FooDB: FOOD00866)

Tea

Endogenous

Plant

Plant (HMDB: HMDB0041011)
Poaceae (HMDB: HMDB0041011)

Process

Not Available

Role

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Emulsifier (HMDB: HMDB0041011)

Food and nutrition

Food additive

Flavoring agent

Flavoring Agent (HMDB: HMDB0041011)

Biological role

Nutrient (HMDB: HMDB0041011)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	62.00 to 63.00 °C. @ 3.00 mm Hg	The Good Scents Company Information System
Water Solubility	86.14 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	3.100 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	1.26 g/L	ALOGPS
logP	2.96	ALOGPS
logP	2.41	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Basic)	-4.3	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	1	ChemAxon
Refractivity	47.1 m³·mol⁻¹	ChemAxon
Polarizability	18.03 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]+	134.208	31661259
DarkChem	[M-H]-	129.394	31661259
DeepCCS	[M+H]+	138.729	30932474
DeepCCS	[M-H]-	135.84	30932474
DeepCCS	[M-2H]-	172.305	30932474
DeepCCS	[M+Na]+	147.843	30932474
AllCCS	[M+H]+	132.5	32859911
AllCCS	[M+H-H2O]+	128.1	32859911
AllCCS	[M+NH4]+	136.5	32859911
AllCCS	[M+Na]+	137.7	32859911
AllCCS	[M-H]-	136.1	32859911
AllCCS	[M+Na-2H]-	137.7	32859911
AllCCS	[M+HCOO]-	139.6	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. Predicted by Afia on May 17, 2022.	5.71 minutes	32390414
Predicted by Siyang on May 30, 2022	17.1712 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.76 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2165.8 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	604.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	224.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	385.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	253.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	706.7 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	813.8 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	154.9 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1352.6 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	479.0 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	1519.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	509.6 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	430.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	568.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	646.7 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	26.7 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
beta-Cyclocitral	CC1=C(C=O)C(C)(C)CCC1	1568.5	Standard polar	33892256
beta-Cyclocitral	CC1=C(C=O)C(C)(C)CCC1	1136.2	Standard non polar	33892256
beta-Cyclocitral	CC1=C(C=O)C(C)(C)CCC1	1146.5	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - beta-Cyclocitral EI-B (Non-derivatized)	splash10-0l0i-4900000000-f6c4a4fe93d19741cab0	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - beta-Cyclocitral EI-B (Non-derivatized)	splash10-0l0i-4900000000-f6c4a4fe93d19741cab0	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - beta-Cyclocitral GC-MS (Non-derivatized) - 70eV, Positive	splash10-052r-3900000000-6391af660fd4d8a21547	2016-09-22	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - beta-Cyclocitral GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
MS	Mass Spectrum (Electron Ionization)	splash10-052o-9300000000-be54b6f8155405712fdf	2015-03-01	Not Available	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - beta-Cyclocitral 10V, Positive-QTOF	splash10-0udi-1900000000-a06d949d55e95a72b6b7	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - beta-Cyclocitral 20V, Positive-QTOF	splash10-0udi-9800000000-19d87f66741a50d0e677	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - beta-Cyclocitral 40V, Positive-QTOF	splash10-0gb9-9100000000-9690930ec35bca459333	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - beta-Cyclocitral 10V, Negative-QTOF	splash10-0udi-0900000000-dcfa64ac0ff4ae18463b	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - beta-Cyclocitral 20V, Negative-QTOF	splash10-0udi-0900000000-6237aac949530326cbf1	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - beta-Cyclocitral 40V, Negative-QTOF	splash10-0kmr-3900000000-5d5d6b808dcc3a96c3e3	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - beta-Cyclocitral 10V, Positive-QTOF	splash10-0udi-6900000000-10632e4d0107c6bea634	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - beta-Cyclocitral 20V, Positive-QTOF	splash10-0arr-9200000000-06e9f20fa2dfd319b3ba	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - beta-Cyclocitral 40V, Positive-QTOF	splash10-067i-9100000000-eec8f7754558ce99427a	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - beta-Cyclocitral 10V, Negative-QTOF	splash10-0uk9-0900000000-242103d291e18a765c21	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - beta-Cyclocitral 20V, Negative-QTOF	splash10-0fk9-0900000000-64f4832ef5436e56e9ff	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - beta-Cyclocitral 40V, Negative-QTOF	splash10-0a4i-0900000000-a4b505d5001ef400c380	2021-09-23	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

Biospecimen Locations

Feces
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	23454028	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	24023812	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Nonalcoholic fatty liver disease (NAFLD)	23454028	details

Associated Disorders and Diseases

Disease References

Nonalcoholic fatty liver disease
Raman M, Ahmed I, Gillevet PM, Probert CS, Ratcliffe NM, Smith S, Greenwood R, Sikaroodi M, Lam V, Crotty P, Bailey J, Myers RP, Rioux KP: Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease. Clin Gastroenterol Hepatol. 2013 Jul;11(7):868-75.e1-3. doi: 10.1016/j.cgh.2013.02.015. Epub 2013 Feb 27. [PubMed:23454028 ]

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9895

PDB ID

Not Available

ChEBI ID

53177

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1037211

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 beta-Cyclocitral (HMDB0041011)

MOL for HMDB0041011 (beta-Cyclocitral)

3D MOL for HMDB0041011 (beta-Cyclocitral)

3D SDF for HMDB0041011 (beta-Cyclocitral)

3D-SDF for HMDB0041011 (beta-Cyclocitral)

PDB for HMDB0041011 (beta-Cyclocitral)

3D PDB for HMDB0041011 (beta-Cyclocitral)

SMILES for HMDB0041011 (beta-Cyclocitral)

INCHI for HMDB0041011 (beta-Cyclocitral)

Structure for HMDB0041011 (beta-Cyclocitral)

3D Structure for HMDB0041011 (beta-Cyclocitral)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra