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Showing metabocard for (+)-Limonene (HMDB0003375)

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enzymes (2) Show 2 proteins
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-08-12 19:51:01 UTC
Update Date2022-03-07 02:49:18 UTC
HMDB IDHMDB0003375
Secondary Accession Numbers
  • HMDB03375
Metabolite Identification
Common Name(+)-Limonene
Description(+)-Limonene, also known as d-limonene, is a naturally occurring monoterpene which is the major component in orange oil. Currently, (+)-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.). Recently, however, (+)-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. Although (+)-limonene is not carcinogenic in female rats or male and female mice given much higher dosages, the male rat-specific nephrocarcinogenicity of (+)-limonene may raise some concern regarding the safety of (+)-limonene for human consumption. A considerable body of scientific data has indicated that the renal toxicity of (+)-limonene results from the accumulation of a protein, alpha 2u-globulin, in male rat kidney proximal tubule lysosomes. This protein is synthesized exclusively by adult male rats. Other species, including humans, synthesize proteins that share significant homology with alpha 2u-globulin. However, none of these proteins, including the mouse equivalent of alpha 2u-globulin, can produce this toxicity, indicating a unique specificity for alpha 2u-globulin. With chronic exposure to (+)-limonene, the hyaline droplet nephropathy progresses and the kidney shows tubular cell necrosis, granular cast formation at the corticomedullary junction, and compensatory cell proliferation. Both (+)-limonene and cis-d-limonene-1,2-oxide (the major metabolite involved in this toxicity) are negative in vitro mutagenicity screens. Therefore, the toxicity-related renal cell proliferation is believed to be integrally involved in the carcinogenicity of (+)-limonene as persistent elevations in renal cell proliferation may increase fixation of spontaneously altered DNA or serve to promote spontaneously initiated cells. The scientific data demonstrates that the tumorigenic activity of (+)-limonene in male rats is not relevant to humans. The three major lines of evidence supporting the human safety of (+)-limonene are (1) the male rat specificity of the nephrotoxicity and carcinogenicity; (2) the pivotal role that alpha 2u-globulin plays in the toxicity, as evidenced by the complete lack of toxicity in other species despite the presence of structurally similar proteins; and (3) the lack of genotoxicity of both (+)-limonene and d-limonene-1,2-oxide, supporting the concept of a nongenotoxic mechanism, namely, sustained renal cell proliferation (PMID:2024047 ).
Structure
Data?1589308122
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0003375 ((+)-Limonene)


  Mrv1652309272007452D          

 10 10  0  0  0  0            999 V2000
    0.5360    1.1152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5360    1.9402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2505    0.7027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3218   -0.5347    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8928    1.1152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6073    0.7027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6073   -0.1223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8928   -0.5347    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1783   -0.1223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1783    0.7027    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  5  6  1  0  0  0  0
  5 10  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  7  4  1  0  0  0  0
 10  1  1  1  0  0  0
M  END
Download

3D MOL for HMDB0003375 ((+)-Limonene)

HMDB0003375
     RDKit          3D
(+)-Limonene
 26 26  0  0  0  0  0  0  0  0999 V2000
   -2.7208    0.9557   -0.3367 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0563   -0.0832    0.0951 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7607   -1.4175    0.1794 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6442   -0.1004    0.5258 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0438   -1.1544   -0.3387 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5044   -1.0564   -0.1664 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0583    0.1470   -0.3519 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4957    0.3724   -0.2103 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0690    1.2304   -0.7133 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0697    1.1984    0.4553 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3234    1.9549   -0.4391 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7652    0.8585   -0.6302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6725   -1.8362    1.2042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3341   -2.1063   -0.5698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8352   -1.2972   -0.0889 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6266   -0.5178    1.5743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3535   -2.1568   -0.0838 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2364   -0.9019   -1.3924 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1481   -1.9035    0.1012 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7633    1.2996   -0.7626 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0288   -0.4672   -0.7021 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8312    0.4134    0.8435 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5329    2.2146   -0.7456 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5742    0.9991   -1.6655 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5330    2.1017    0.4992 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7424    1.2533    1.3646 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10  4  1  0
  1 11  1  0
  1 12  1  0
  3 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  1
  5 17  1  0
  5 18  1  0
  6 19  1  0
  8 20  1  0
  8 21  1  0
  8 22  1  0
  9 23  1  0
  9 24  1  0
 10 25  1  0
 10 26  1  0
M  END
Download

3D SDF for HMDB0003375 ((+)-Limonene)


  Mrv1652309272007452D          

 10 10  0  0  0  0            999 V2000
    0.5360    1.1152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5360    1.9402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2505    0.7027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3218   -0.5347    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8928    1.1152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6073    0.7027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6073   -0.1223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8928   -0.5347    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1783   -0.1223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1783    0.7027    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  5  6  1  0  0  0  0
  5 10  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  7  4  1  0  0  0  0
 10  1  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0003375

> <DATABASE_NAME>
hmdb

> <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-/m0/s1

> <INCHI_KEY>
XMGQYMWWDOXHJM-JTQLQIEISA-N

> <FORMULA>
C10H16

> <MOLECULAR_WEIGHT>
136.234

> <EXACT_MASS>
136.125200512

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
17.54931315245657

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R)-1-methyl-4-(prop-1-en-2-yl)cyclohex-1-ene

> <ALOGPS_LOGP>
4.50

> <JCHEM_LOGP>
3.2198126516666665

> <ALOGPS_LOGS>
-2.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
46.4803

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.57e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
α-limonene

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0003375 ((+)-Limonene)

HMDB0003375
     RDKit          3D
(+)-Limonene
 26 26  0  0  0  0  0  0  0  0999 V2000
   -2.7208    0.9557   -0.3367 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0563   -0.0832    0.0951 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7607   -1.4175    0.1794 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6442   -0.1004    0.5258 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0438   -1.1544   -0.3387 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5044   -1.0564   -0.1664 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0583    0.1470   -0.3519 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4957    0.3724   -0.2103 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0690    1.2304   -0.7133 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0697    1.1984    0.4553 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3234    1.9549   -0.4391 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7652    0.8585   -0.6302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6725   -1.8362    1.2042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3341   -2.1063   -0.5698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8352   -1.2972   -0.0889 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6266   -0.5178    1.5743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3535   -2.1568   -0.0838 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2364   -0.9019   -1.3924 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1481   -1.9035    0.1012 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7633    1.2996   -0.7626 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0288   -0.4672   -0.7021 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8312    0.4134    0.8435 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5329    2.2146   -0.7456 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5742    0.9991   -1.6655 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5330    2.1017    0.4992 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7424    1.2533    1.3646 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10  4  1  0
  1 11  1  0
  1 12  1  0
  3 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  1
  5 17  1  0
  5 18  1  0
  6 19  1  0
  8 20  1  0
  8 21  1  0
  8 22  1  0
  9 23  1  0
  9 24  1  0
 10 25  1  0
 10 26  1  0
M  END
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PDB for HMDB0003375 ((+)-Limonene)

HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  C   UNK     0       1.001   2.082   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.001   3.622   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.334   1.312   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.334  -0.998   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.667   2.082   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.000   1.312   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.000  -0.228   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.667  -0.998   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.333  -0.228   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.333   1.312   0.000  0.00  0.00           C+0
CONECT    1    2    3   10                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    7                                                            
CONECT    5    6   10                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    4                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    5    9    1                                                  
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for HMDB0003375 ((+)-Limonene)

COMPND    HMDB0003375
HETATM    1  C1  UNL     1      -2.721   0.956  -0.337  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.056  -0.083   0.095  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.761  -1.418   0.179  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.644  -0.100   0.526  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.044  -1.154  -0.339  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.504  -1.056  -0.166  1.00  0.00           C  
HETATM    7  C7  UNL     1       2.058   0.147  -0.352  1.00  0.00           C  
HETATM    8  C8  UNL     1       3.496   0.372  -0.210  1.00  0.00           C  
HETATM    9  C9  UNL     1       1.069   1.230  -0.713  1.00  0.00           C  
HETATM   10  C10 UNL     1       0.070   1.198   0.455  1.00  0.00           C  
HETATM   11  H1  UNL     1      -2.323   1.955  -0.439  1.00  0.00           H  
HETATM   12  H2  UNL     1      -3.765   0.858  -0.630  1.00  0.00           H  
HETATM   13  H3  UNL     1      -2.673  -1.836   1.204  1.00  0.00           H  
HETATM   14  H4  UNL     1      -2.334  -2.106  -0.570  1.00  0.00           H  
HETATM   15  H5  UNL     1      -3.835  -1.297  -0.089  1.00  0.00           H  
HETATM   16  H6  UNL     1      -0.627  -0.518   1.574  1.00  0.00           H  
HETATM   17  H7  UNL     1      -0.353  -2.157  -0.084  1.00  0.00           H  
HETATM   18  H8  UNL     1      -0.236  -0.902  -1.392  1.00  0.00           H  
HETATM   19  H9  UNL     1       2.148  -1.903   0.101  1.00  0.00           H  
HETATM   20  H10 UNL     1       3.763   1.300  -0.763  1.00  0.00           H  
HETATM   21  H11 UNL     1       4.029  -0.467  -0.702  1.00  0.00           H  
HETATM   22  H12 UNL     1       3.831   0.413   0.843  1.00  0.00           H  
HETATM   23  H13 UNL     1       1.533   2.215  -0.746  1.00  0.00           H  
HETATM   24  H14 UNL     1       0.574   0.999  -1.666  1.00  0.00           H  
HETATM   25  H15 UNL     1      -0.533   2.102   0.499  1.00  0.00           H  
HETATM   26  H16 UNL     1       0.742   1.253   1.365  1.00  0.00           H  
CONECT    1    2    2   11   12
CONECT    2    3    4
CONECT    3   13   14   15
CONECT    4    5   10   16
CONECT    5    6   17   18
CONECT    6    7    7   19
CONECT    7    8    9
CONECT    8   20   21   22
CONECT    9   10   23   24
CONECT   10   25   26
END
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SMILES for HMDB0003375 ((+)-Limonene)

CC(=C)[C@@H]1CCC(C)=CC1
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INCHI for HMDB0003375 ((+)-Limonene)

InChI=1S/C10H16/c1-8(2)10-6-4-9(3)5-7-10/h4,10H,1,5-7H2,2-3H3/t10-/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(+)-(4R)-LimoneneChEBI
(+)-(R)-LimoneneChEBI
(+)-4-Isopropenyl-1-methylcyclohexeneChEBI
(+)-LimoneneChEBI
(4R)-1-Methyl-4-isopropenylcyclohex-1-eneChEBI
(4R)-4-Isopropenyl-1-methylcyclohexeneChEBI
(R)-(+)-LimoneneChEBI
(R)-(+)-p-Mentha-1,8-dieneChEBI
(R)-1-Methyl-4-(1-methylethenyl)cyclohexeneChEBI
(R)-4-Isopropenyl-1-methyl-1-cyclohexeneChEBI
(R)-p-Mentha-1,8-dieneChEBI
4BetaH-p-mentha-1,8-dieneChEBI
D-(+)-LimoneneChEBI
D-LimonenChEBI
AISA 5203-L (+)limoneneHMDB
DipenteneHMDB
(-)-LimoneneHMDB
1-Methyl-4-(1-methylethenyl)cyclohexeneHMDB
LimoneneHMDB
Limonene, (+-)-isomerHMDB
(D)-LimoneneHMDB
4-Mentha-1,8-dieneHMDB
Limonene, (R)-isomerHMDB
(+)-DipenteneHMDB
(+)-alpha-LimoneneHMDB
(+)-p-Mentha-1,8-dieneHMDB
(+)-Α-limoneneHMDB
(4R)-(+)-LimoneneHMDB
(4R)-1-Methyl-4-(1-methylethenyl)cyclohexeneHMDB
(4R)-LimoneneHMDB
(R)-1-Methyl-4-(prop-1-en-2-yl)cyclohex-1-eneHMDB
(R)-LimoneneHMDB
1-Methyl-4-prop-1-en-2-yl-cyclohexeneHMDB
(+)-(R)-4-Isopropenyl-1-methylcyclohexeneHMDB
D LimoneneHMDB
4 Mentha 1,8 dieneHMDB
(R)-4-Isopropenyl-1-methylcyclohexeneHMDB
D-LimoneneChEBI
d-LimoneneHMDB
(4R)-1-Methyl-4-(prop-1-en-2-yl)cyclohex-1-eneHMDB
R-LimoneneHMDB
p-Mentha-1,8-dienePhytoBank
(±)-DipentenePhytoBank
(±)-LimonenePhytoBank
(±)-alpha-LimonenePhytoBank
(±)-α-LimonenePhytoBank
1,8-p-MenthadienePhytoBank
1-Methyl-4-(prop-1-en-2-yl)cyclohex-1-enePhytoBank
1-Methyl-4-isopropenyl-1-cyclohexenePhytoBank
1-Methyl-4-isopropenylcyclohexenePhytoBank
1-Methyl-p-isopropenyl-1-cyclohexenePhytoBank
4-Isopropenyl-1-methyl-1-cyclohexenePhytoBank
4-Isopropenyl-1-methylcyclohexenePhytoBank
dl-LimonenePhytoBank
DipentenPhytoBank
LimonenPhytoBank
alpha-LimonenePhytoBank
α-LimonenePhytoBank
Chemical FormulaC10H16
Average Molecular Weight136.234
Monoisotopic Molecular Weight136.125200512
IUPAC Name(4R)-1-methyl-4-(prop-1-en-2-yl)cyclohex-1-ene
Traditional Nameα-limonene
CAS Registry Number5989-27-5
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-/m0/s1
InChI KeyXMGQYMWWDOXHJM-JTQLQIEISA-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.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassMonoterpenoids
Direct ParentMenthane 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 FrameworkAliphatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-90 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP4.38GRIFFIN,S ET AL. (1999)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.46 g/LALOGPS
logP4.5ALOGPS
logP3.22ChemAxon
logS-2.5ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity46.48 m³·mol⁻¹ChemAxon
Polarizability17.55 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+134.2831661259
DarkChem[M-H]-129.14831661259
DeepCCS[M+H]+134.48230932474
DeepCCS[M-H]-131.82330932474
DeepCCS[M-2H]-167.52130932474
DeepCCS[M+Na]+142.80230932474
AllCCS[M+H]+127.732859911
AllCCS[M+H-H2O]+123.032859911
AllCCS[M+NH4]+132.032859911
AllCCS[M+Na]+133.332859911
AllCCS[M-H]-132.732859911
AllCCS[M+Na-2H]-134.532859911
AllCCS[M+HCOO]-136.632859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
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 minutes32390414
Predicted by Siyang on May 30, 202217.4234 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.1 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid2237.0 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid651.2 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid242.5 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid412.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid248.6 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid623.6 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid763.2 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)162.3 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1412.8 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid494.3 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1312.8 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid490.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid433.2 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate544.9 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA644.2 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water22.0 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
(+)-LimoneneCC(=C)[C@@H]1CCC(C)=CC11204.7Standard polar33892256
(+)-LimoneneCC(=C)[C@@H]1CCC(C)=CC11015.2Standard non polar33892256
(+)-LimoneneCC(=C)[C@@H]1CCC(C)=CC11017.5Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - (+)-Limonene EI-B (Non-derivatized)splash10-0173-9100000000-239928f205c8242a700a2017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - (+)-Limonene EI-B (Non-derivatized)splash10-014l-9100000000-507f7afbc17b7c2556e22017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - (+)-Limonene EI-B (Non-derivatized)splash10-014l-9100000000-1a0c62c6971532ab67822017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - (+)-Limonene EI-B (Non-derivatized)splash10-0173-9100000000-239928f205c8242a700a2018-05-18HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - (+)-Limonene EI-B (Non-derivatized)splash10-014l-9100000000-507f7afbc17b7c2556e22018-05-18HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - (+)-Limonene EI-B (Non-derivatized)splash10-014l-9100000000-1a0c62c6971532ab67822018-05-18HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - (+)-Limonene GC-EI-Q (Non-derivatized)splash10-014l-9100000000-0b286d388287bcc487f22020-07-08HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - (+)-Limonene GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9200000000-df40612bbf371089d7ac2017-08-28Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - (+)-Limonene GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
MSMass Spectrum (Electron Ionization)splash10-014l-9100000000-fbf154446f93ee5019c02015-03-01Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - (+)-Limonene Quattro_QQQ 10V, Positive-QTOF (Annotated)splash10-000i-6900000000-f7ee4bad43b6ccae0ccb2012-07-25HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - (+)-Limonene Quattro_QQQ 25V, Positive-QTOF (Annotated)splash10-00ou-9000000000-51a52c25a98124e179e92012-07-25HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - (+)-Limonene Quattro_QQQ 40V, Positive-QTOF (Annotated)splash10-0006-9000000000-9655665d3d36755028cc2012-07-25HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - (+)-Limonene EI-B (HITACHI RMU-6M) , Positive-QTOFsplash10-0173-9100000000-239928f205c8242a700a2012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - (+)-Limonene EI-B (HITACHI M-80B) , Positive-QTOFsplash10-014l-9100000000-bc8708fdb2d1955dce922012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - (+)-Limonene EI-B (HITACHI M-80) , Positive-QTOFsplash10-014l-9100000000-1a0c62c6971532ab67822012-08-31HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (+)-Limonene 10V, Positive-QTOFsplash10-000i-2900000000-bce8f8616cfd3b16cac92017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (+)-Limonene 20V, Positive-QTOFsplash10-000i-9600000000-583a2621a826cedbca612017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (+)-Limonene 40V, Positive-QTOFsplash10-1000-9100000000-d78cd6fbdd7a13fe9dfa2017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (+)-Limonene 10V, Negative-QTOFsplash10-000i-0900000000-2950ad058f77d7bc9f762017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (+)-Limonene 20V, Negative-QTOFsplash10-000i-0900000000-6f48f3b0b500d4f25ec92017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (+)-Limonene 40V, Negative-QTOFsplash10-014r-5900000000-1c30c00bfa4058f5e22b2017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (+)-Limonene 10V, Negative-QTOFsplash10-000i-0900000000-a013b4ae27f975ab56212021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (+)-Limonene 20V, Negative-QTOFsplash10-000i-0900000000-a013b4ae27f975ab56212021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (+)-Limonene 40V, Negative-QTOFsplash10-014i-8900000000-d835e92fba2c2a2387972021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (+)-Limonene 10V, Positive-QTOFsplash10-001a-9400000000-fb09a1cdd4bc094802812021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (+)-Limonene 20V, Positive-QTOFsplash10-0564-9000000000-dc5effa7f00987fc85672021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (+)-Limonene 40V, Positive-QTOFsplash10-00mo-9000000000-40d99aa482e2ce5a66f12021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, CDCl3, experimental)2012-12-05Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane (predicted from logP)
Biospecimen Locations
  • Blood
  • Breath
  • Feces
  • Saliva
  • Urine
Tissue Locations
  • Epidermis
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.19 (0.02 - 2.40) uMAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedNewborn (0-30 days old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedChildren (1-13 years old)BothNormal details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Not SpecifiedNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BreathDetected but not QuantifiedNot QuantifiedChildren (1-13 years old)Not SpecifiedAsthma details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Campylobacter jejuni infection		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Clostridium difficile infection		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Ulcerative Colitis		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Nonalcoholic fatty liver disease (NAFLD)		 details
FecesDetected but not QuantifiedNot QuantifiedChildren (1-13 years old)BothAutism details
FecesDetected but not QuantifiedNot QuantifiedChildren (1-13 years old)BothPervasive Developmental Disorder Not Otherwise Specified details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothBreast cancer details
Associated Disorders and Diseases
Disease References
Asthma
  1. Gahleitner F, Guallar-Hoyas C, Beardsmore CS, Pandya HC, Thomas CP: Metabolomics pilot study to identify volatile organic compound markers of childhood asthma in exhaled breath. Bioanalysis. 2013 Sep;5(18):2239-47. doi: 10.4155/bio.13.184. [PubMed:24053239 ]
Ulcerative colitis
  1. Garner CE, Smith S, de Lacy Costello B, White P, Spencer R, Probert CS, Ratcliffe NM: Volatile organic compounds from feces and their potential for diagnosis of gastrointestinal disease. FASEB J. 2007 Jun;21(8):1675-88. Epub 2007 Feb 21. [PubMed:17314143 ]
Nonalcoholic fatty liver disease
  1. 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 ]
Autism
  1. De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI, Cristofori F, Guerzoni ME, Gobbetti M, Francavilla R: Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. PLoS One. 2013 Oct 9;8(10):e76993. doi: 10.1371/journal.pone.0076993. eCollection 2013. [PubMed:24130822 ]
Pervasive developmental disorder not otherwise specified
  1. De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI, Cristofori F, Guerzoni ME, Gobbetti M, Francavilla R: Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. PLoS One. 2013 Oct 9;8(10):e76993. doi: 10.1371/journal.pone.0076993. eCollection 2013. [PubMed:24130822 ]
Perillyl alcohol administration for cancer treatment
  1. Silva CL, Passos M, Camara JS: Solid phase microextraction, mass spectrometry and metabolomic approaches for detection of potential urinary cancer biomarkers--a powerful strategy for breast cancer diagnosis. Talanta. 2012 Jan 30;89:360-8. doi: 10.1016/j.talanta.2011.12.041. Epub 2011 Dec 22. [PubMed:22284503 ]
Associated OMIM IDs
DrugBank IDDB08921
Phenol Explorer Compound IDNot Available
FooDB IDFDB006329
KNApSAcK IDC00010868
Chemspider ID389747
KEGG Compound IDC06099
BioCyc IDCPD-4886
BiGG IDNot Available
Wikipedia LinkLimonene
METLIN IDNot Available
PubChem Compound440917
PDB IDNot Available
ChEBI ID15382
Food Biomarker OntologyNot Available
VMH IDLIMNEN
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis Referencev. Braun, Julius; Lemke, Georg. Preparation of pure d- and l-limonene. Berichte der Deutschen Chemischen Gesellschaft [Abteilung] B: Abhandlungen (1923), 56B 1562-3.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Bhatia KS, Singh J: Effect of linolenic acid/ethanol or limonene/ethanol and iontophoresis on the in vitro percutaneous absorption of LHRH and ultrastructure of human epidermis. Int J Pharm. 1999 Apr 15;180(2):235-50. [PubMed:10370194 ]
  2. Cal K, Janicki S, Sznitowska M: In vitro studies on penetration of terpenes from matrix-type transdermal systems through human skin. Int J Pharm. 2001 Aug 14;224(1-2):81-8. [PubMed:11472817 ]
  3. Matura M, Goossens A, Bordalo O, Garcia-Bravo B, Magnusson K, Wrangsjo K, Karlberg AT: Oxidized citrus oil (R-limonene): a frequent skin sensitizer in Europe. J Am Acad Dermatol. 2002 Nov;47(5):709-14. [PubMed:12399762 ]
  4. Falk A, Gullstrand E, Lof A, Wigaeus-Hjelm E: Liquid/air partition coefficients of four terpenes. Br J Ind Med. 1990 Jan;47(1):62-4. [PubMed:2310709 ]
  5. Lim PF, Liu XY, Kang L, Ho PC, Chan YW, Chan SY: Limonene GP1/PG organogel as a vehicle in transdermal delivery of haloperidol. Int J Pharm. 2006 Mar 27;311(1-2):157-64. Epub 2006 Jan 31. [PubMed:16451823 ]
  6. Yamane MA, Williams AC, Barry BW: Terpene penetration enhancers in propylene glycol/water co-solvent systems: effectiveness and mechanism of action. J Pharm Pharmacol. 1995 Dec;47(12A):978-89. [PubMed:8932680 ]
  7. Cornwell PA, Barry BW, Stoddart CP, Bouwstra JA: Wide-angle X-ray diffraction of human stratum corneum: effects of hydration and terpene enhancer treatment. J Pharm Pharmacol. 1994 Dec;46(12):938-50. [PubMed:7536240 ]
  8. 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 ]
  9. 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 ]
  10. 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 ]
  11. 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
Reactions
(+)-Limonene + NADPH + Oxygen → (+)-trans-Carveol + NADP + Waterdetails
(+)-Limonene + NADPH + Oxygen → (-)-trans-Carveol + NADP + Waterdetails
(+)-Limonene + NADPH + Oxygen → (S)-p-Mentha-1,8-dien-7-ol + NADP + Waterdetails
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
Reactions
(+)-Limonene + NADPH + Oxygen → (+)-trans-Carveol + NADP + Waterdetails
(+)-Limonene + NADPH + Oxygen → (-)-trans-Carveol + NADP + Waterdetails
(+)-Limonene + NADPH + Oxygen → (S)-p-Mentha-1,8-dien-7-ol + NADP + Waterdetails