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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (2) Show 2 proteins XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2006-08-13 16:44:29 UTC

Update Date

2022-03-07 02:49:20 UTC

HMDB ID

HMDB0004321

Secondary Accession Numbers

HMDB04321

Metabolite Identification

Common Name

(-)-Limonene

Description

Limonene is a monoterpene with a clear colourless liquid at room temperature, a naturally occurring chemical which is the major component in oil of oranges. Limonene is widely used as a flavour and fragrance and is listed to be generally recognized as safe in food by the Food and Drug Administration (21 CFR 182.60 in the Code of Federal Regulations, U.S.A.). Limonene is a botanical (plant-derived) solvent of low toxicity. Mild skin irritation may occur from exposure to limonene and oxidation products of limonene may produce dermal sensitization, and may have irritative and bronchoconstrictive airway effects; however, data are scant and more studies are required. Limonene has been shown to cause a male rat-specific kidney toxicity referred to as hyaline droplet nephropathy. Furthermore, chronic exposure to limonene causes a significant incidence of renal tubular tumours exclusively in male rats. Limonene is one of the active components of dietary phytochemicals that appears to be protective against cancer (PMID:16563357 , 15499193 , 15325315 , 2024047 ).

Structure

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

View in JSmol View Stereo Labels

Synonyms

Value	Source
(-)-(S)-Limonene	ChEBI
(-)-(4S)-Limonene	ChEBI
(4S)-1-Methyl-4-isopropenylcyclohex-1-ene	ChEBI
(4S)-4-Isopropenyl-1-methylcyclohexene	ChEBI
(S)-(-)-p-Mentha-1,8-diene	ChEBI
(S)-1-Methyl-4-(1-methylethenyl)cyclohexene	ChEBI
(S)-p-Mentha-1,8-diene	ChEBI
4AlphaH-p-mentha-1,8-diene	ChEBI
L-Limonen	ChEBI
L-Limonene	ChEBI
4-Isopropenyl-1-methyl-1-cyclohexene	HMDB
Limonene	HMDB
(+)-Limonene	HMDB
AISA 5203-L (+)limonene	HMDB
Dipentene	HMDB
1-Methyl-4-(1-methylethenyl)cyclohexene	HMDB
Limonene, (+-)-isomer	HMDB
(D)-Limonene	HMDB
4-Mentha-1,8-diene	HMDB
Limonene, (S)-isomer	HMDB
Limonene, (R)-isomer	HMDB
(R)-(+)-Limonene	HMDB
(R)-4-Isopropenyl-1-methylcyclohexene	HMDB
(+)-(R)-4-Isopropenyl-1-methylcyclohexene	HMDB
(4R)-1-Methyl-4-(1-methylethenyl)cyclohexene	HMDB
D-Limonene	HMDB
4 Mentha 1,8 diene	HMDB
D Limonene	HMDB
(-)-alpha-Limonene	HMDB
(-)-Α-limonene	HMDB
(4S)-1-Methyl-4-(1-methylethenyl)cyclohexene	HMDB
(4S)-Limonene	HMDB
(S)-(-)-Limonene	HMDB
(S)-1-Methyl-4-(prop-1-en-2-yl)cyclohex-1-ene	HMDB
(S)-4-Isopropenyl-1-methyl-1-cyclohexene	HMDB
(S)-Limonene	HMDB
beta-Limonene	HMDB
L-Carvene	HMDB
Β-limonene	HMDB
(-)-Limonene	ChEBI

Chemical Formula

C₁₀H₁₆

Average Molecular Weight

136.234

Monoisotopic Molecular Weight

136.125200512

IUPAC Name

(4S)-1-methyl-4-(prop-1-en-2-yl)cyclohex-1-ene

Traditional Name

(-)-limonene

CAS Registry Number

5989-54-8

SMILES

CC(=C)[C@H]1CCC(C)=CC1

InChI Identifier

InChI=1S/C10H16/c1-8(2)10-6-4-9(3)5-7-10/h4,10H,1,5-7H2,2-3H3/t10-/m1/s1

InChI Key

XMGQYMWWDOXHJM-SNVBAGLBSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as menthane monoterpenoids. These are monoterpenoids with a structure based on the o-, m-, or p-menthane backbone. P-menthane consists of the cyclohexane ring with a methyl group and a (2-methyl)-propyl group at the 1 and 4 ring position, respectively. The o- and m- menthanes are much rarer, and presumably arise by alkyl migration of p-menthanes.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Menthane monoterpenoids

Alternative Parents

Substituents

P-menthane monoterpenoid
Monocyclic monoterpenoid
Branched unsaturated hydrocarbon
Cycloalkene
Cyclic olefin
Unsaturated aliphatic hydrocarbon
Unsaturated hydrocarbon
Olefin
Hydrocarbon
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

limonene (CHEBI:15383 )
Menthane monoterpenoids (C00521 )
Cyclic monoterpenes (C00521 )
Menthane monoterpenoids (LMPR0102090002 )

Ontology

Sweet

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0004321)
Extracellular (HMDB: HMDB0004321)

Source

Exogenous

Exogenous (HMDB: HMDB0004321)

Food

Vegetable

Root vegetable

Carrot (FooDB: FOOD00245)

Cabbage

Cauliflower (FooDB: FOOD00031)

Stalk vegetable

Celery stalks (FooDB: FOOD00215)

Herb and spice

Spice

Herb

Dill (FooDB: FOOD00013)
Fennel (FooDB: FOOD00082)
Parsley (FooDB: FOOD00131)
Sweet bay (FooDB: FOOD00097)
Rosemary (FooDB: FOOD00159)
Peppermint (FooDB: FOOD00113)
Hyssop (FooDB: FOOD00089)

Herbs and Spices (FooDB: FOOD00866)

Fruit

Tropical fruit

Guava (FooDB: FOOD00150)

Not Available

EC 3.1.1.7 (acetylcholinesterase) inhibitor (HMDB: HMDB0004321)
P450 inhibitor (HMDB: HMDB0004321)

Apoptotic (HMDB: HMDB0004321)

Industrial application

Pharmaceutical industry

Antineoplastic agent

Antineoplastic agent (HMDB: HMDB0004321)

Food and nutrition

Food additive

Flavoring agent

Flavor (HMDB: HMDB0004321)

Agriculture

Pesticide

Insecticide (HMDB: HMDB0004321)

Pesticide (HMDB: HMDB0004321)

Physical Properties

State

Liquid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	-74.3 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	0.014 mg/mL at 25 °C	Not Available
LogP	4.57	LI,J & PURDUE,EM (1995)

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.46 g/L	ALOGPS
logP	4.5	ALOGPS
logP	3.22	ChemAxon
logS	-2.5	ALOGPS
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	0 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	46.48 m³·mol⁻¹	ChemAxon
Polarizability	17.23 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]+	134.754	31661259
DarkChem	[M-H]-	129.433	31661259
DeepCCS	[M+H]+	133.925	30932474
DeepCCS	[M-H]-	131.262	30932474
DeepCCS	[M-2H]-	167.051	30932474
DeepCCS	[M+Na]+	142.189	30932474
AllCCS	[M+H]+	127.7	32859911
AllCCS	[M+H-H2O]+	123.0	32859911
AllCCS	[M+NH4]+	132.0	32859911
AllCCS	[M+Na]+	133.3	32859911
AllCCS	[M-H]-	132.7	32859911
AllCCS	[M+Na-2H]-	134.5	32859911
AllCCS	[M+HCOO]-	136.6	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.	6.15 minutes	32390414
Predicted by Siyang on May 30, 2022	17.4234 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.1 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2237.0 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	651.2 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	242.5 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	412.8 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	248.6 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	623.6 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	763.2 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	162.3 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1412.8 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	494.3 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	1312.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	490.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	433.2 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	544.9 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	644.2 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	22.0 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(-)-Limonene	CC(=C)[C@H]1CCC(C)=CC1	1204.7	Standard polar	33892256
(-)-Limonene	CC(=C)[C@H]1CCC(C)=CC1	1015.2	Standard non polar	33892256
(-)-Limonene	CC(=C)[C@H]1CCC(C)=CC1	1017.5	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - (-)-Limonene EI-B (Non-derivatized)	splash10-0173-9100000000-239928f205c8242a700a	2018-05-25	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - (-)-Limonene EI-B (Non-derivatized)	splash10-014l-9100000000-507f7afbc17b7c2556e2	2018-05-25	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - (-)-Limonene EI-B (Non-derivatized)	splash10-014l-9100000000-1a0c62c6971532ab6782	2018-05-25	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - (-)-Limonene EI-B (Non-derivatized)	splash10-0173-9100000000-239928f205c8242a700a	2018-05-25	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - (-)-Limonene EI-B (Non-derivatized)	splash10-014l-9100000000-507f7afbc17b7c2556e2	2018-05-25	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - (-)-Limonene EI-B (Non-derivatized)	splash10-014l-9100000000-1a0c62c6971532ab6782	2018-05-25	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (-)-Limonene GC-MS (Non-derivatized) - 70eV, Positive	splash10-0fgo-9200000000-a79c6ccef83c7113ab9f	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (-)-Limonene GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
MS	Mass Spectrum (Electron Ionization)	splash10-014l-9100000000-7e8881e736cecb723a2b	2015-03-01	Not Available	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - (-)-Limonene Quattro_QQQ 10V, Positive-QTOF (Annotated)	splash10-001c-8900000000-dfd6c14e6a4e49bfc6dc	2012-07-25	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - (-)-Limonene Quattro_QQQ 25V, Positive-QTOF (Annotated)	splash10-002f-9000000000-06c43b864c090aaae8ae	2012-07-25	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - (-)-Limonene Quattro_QQQ 40V, Positive-QTOF (Annotated)	splash10-01t9-9000000000-e5ee54500bc5feda4631	2012-07-25	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (-)-Limonene 10V, Positive-QTOF	splash10-000i-1900000000-5567709cc9ec1c9909db	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (-)-Limonene 20V, Positive-QTOF	splash10-000i-9600000000-4570df18c5140586d0bf	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (-)-Limonene 40V, Positive-QTOF	splash10-1000-9100000000-61312f12f069cd9de75c	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (-)-Limonene 10V, Negative-QTOF	splash10-000i-0900000000-88ada45edfe65d9e7f3a	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (-)-Limonene 20V, Negative-QTOF	splash10-000i-0900000000-1192305465e6c746cfa9	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (-)-Limonene 40V, Negative-QTOF	splash10-00kr-4900000000-199ee0c6ed49a35bcff4	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (-)-Limonene 10V, Positive-QTOF	splash10-001a-9400000000-fb09a1cdd4bc09480281	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (-)-Limonene 20V, Positive-QTOF	splash10-0564-9000000000-dc5effa7f00987fc8567	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (-)-Limonene 40V, Positive-QTOF	splash10-00mo-9000000000-40d99aa482e2ce5a66f1	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (-)-Limonene 10V, Negative-QTOF	splash10-000i-0900000000-a013b4ae27f975ab5621	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (-)-Limonene 20V, Negative-QTOF	splash10-000i-0900000000-a013b4ae27f975ab5621	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (-)-Limonene 40V, Negative-QTOF	splash10-014i-8900000000-d835e92fba2c2a238797	2021-09-23	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, CDCl₃, experimental)	2012-12-05	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular
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

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

15383

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Sakane, Soichi; Fujiwara, Junya; Maruoka, Keiji; Yamamoto, Hisashi. Chiral leaving group: asymmetric synthesis of limonene and bisabolene. Tetrahedron (1986), 42(8), 2193-2201.

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Flamm WG, Lehman-McKeeman LD: The human relevance of the renal tumor-inducing potential of d-limonene in male rats: implications for risk assessment. Regul Toxicol Pharmacol. 1991 Feb;13(1):70-86. [PubMed:2024047 ]
Aggarwal BB, Shishodia S: Molecular targets of dietary agents for prevention and therapy of cancer. Biochem Pharmacol. 2006 May 14;71(10):1397-421. Epub 2006 Feb 23. [PubMed:16563357 ]
Tsuda H, Ohshima Y, Nomoto H, Fujita K, Matsuda E, Iigo M, Takasuka N, Moore MA: Cancer prevention by natural compounds. Drug Metab Pharmacokinet. 2004 Aug;19(4):245-63. [PubMed:15499193 ]
DeWitt C, Bebarta V: Botanical solvents. Clin Occup Environ Med. 2004 Aug;4(3):445-54, v-vi. [PubMed:15325315 ]

Enzymes

Enzyme Details

1. Cytochrome P450 2C9

General function:: Involved in monooxygenase activity
Specific function:: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. This enzyme contributes to the wide pharmacokinetics variability of the metabolism of drugs such as S-warfarin, diclofenac, phenytoin, tolbutamide and losartan.
Gene Name:: CYP2C9
Uniprot ID:: P11712
Molecular weight:: 55627.365

Enzyme Details

2. Cytochrome P450 2C19

General function:: Involved in monooxygenase activity
Specific function:: Responsible for the metabolism of a number of therapeutic agents such as the anticonvulsant drug S-mephenytoin, omeprazole, proguanil, certain barbiturates, diazepam, propranolol, citalopram and imipramine.
Gene Name:: CYP2C19
Uniprot ID:: P33261
Molecular weight:: 55944.565

Showing metabocard for (-)-Limonene (HMDB0004321)

MOL for HMDB0004321 ((-)-Limonene)

3D MOL for HMDB0004321 ((-)-Limonene)

3D SDF for HMDB0004321 ((-)-Limonene)

3D-SDF for HMDB0004321 ((-)-Limonene)

PDB for HMDB0004321 ((-)-Limonene)

3D PDB for HMDB0004321 ((-)-Limonene)

SMILES for HMDB0004321 ((-)-Limonene)

INCHI for HMDB0004321 ((-)-Limonene)

Structure for HMDB0004321 ((-)-Limonene)

3D Structure for HMDB0004321 ((-)-Limonene)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes