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Showing metabocard for (-)-Limonene (HMDB0004321)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2006-08-13 16:44:29 UTC
Update Date2022-03-07 02:49:20 UTC
HMDB IDHMDB0004321
Secondary Accession Numbers
  • HMDB04321
Metabolite Identification
Common Name(-)-Limonene
DescriptionLimonene 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
Data?1582752306
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0004321 ((-)-Limonene)

  Mrv1652303202019022D          

 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   -0.5346    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   -0.5346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1782   -0.1223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1782    0.7027    0.0000 C   0  0  1  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  6  0  0  0
M  END
Download

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

HMDB0004321
     RDKit          3D
(-)-Limonene
 26 26  0  0  0  0  0  0  0  0999 V2000
   -2.5269    0.8014   -0.9069 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0720   -0.1283   -0.0819 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9557   -1.2827    0.2816 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7132   -0.0070    0.4560 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1242    1.3143    0.0255 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2339    1.4227    0.6369 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0540    0.3995    0.3939 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4314    0.3822    0.9426 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5223   -0.7093   -0.4469 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1928   -1.1652    0.1024 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5387    0.7189   -1.3137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9633    1.6568   -1.2169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0018   -1.0559    0.0384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8545   -1.4287    1.3708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6763   -2.1915   -0.2970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7903    0.0391    1.5673 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7756    2.1303    0.3710 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0311    1.3100   -1.0869 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5806    2.2312    1.2321 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5665   -0.5545    1.5556 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1712    0.4284    0.1281 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5667    1.2659    1.5951 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2042   -1.5642   -0.4337 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3539   -0.3681   -1.4946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2946   -1.8438   -0.6545 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3785   -1.8012    0.9924 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 HMDB0004321 ((-)-Limonene)

  Mrv1652303202019022D          

 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   -0.5346    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   -0.5346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1782   -0.1223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1782    0.7027    0.0000 C   0  0  1  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  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0004321

> <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-/m1/s1

> <INCHI_KEY>
XMGQYMWWDOXHJM-SNVBAGLBSA-N

> <FORMULA>
C10H16

> <MOLECULAR_WEIGHT>
136.234

> <EXACT_MASS>
136.125200512

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
17.226676344955674

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S)-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>
(-)-limonene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

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

HMDB0004321
     RDKit          3D
(-)-Limonene
 26 26  0  0  0  0  0  0  0  0999 V2000
   -2.5269    0.8014   -0.9069 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0720   -0.1283   -0.0819 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9557   -1.2827    0.2816 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7132   -0.0070    0.4560 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1242    1.3143    0.0255 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2339    1.4227    0.6369 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0540    0.3995    0.3939 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4314    0.3822    0.9426 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5223   -0.7093   -0.4469 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1928   -1.1652    0.1024 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5387    0.7189   -1.3137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9633    1.6568   -1.2169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0018   -1.0559    0.0384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8545   -1.4287    1.3708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6763   -2.1915   -0.2970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7903    0.0391    1.5673 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7756    2.1303    0.3710 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0311    1.3100   -1.0869 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5806    2.2312    1.2321 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5665   -0.5545    1.5556 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1712    0.4284    0.1281 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5667    1.2659    1.5951 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2042   -1.5642   -0.4337 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3539   -0.3681   -1.4946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2946   -1.8438   -0.6545 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3785   -1.8012    0.9924 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 HMDB0004321 ((-)-Limonene)

HEADER    PROTEIN                                 20-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-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 HMDB0004321 ((-)-Limonene)

COMPND    HMDB0004321
HETATM    1  C1  UNL     1      -2.527   0.801  -0.907  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.072  -0.128  -0.082  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.956  -1.283   0.282  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.713  -0.007   0.456  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.124   1.314   0.025  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.234   1.423   0.637  1.00  0.00           C  
HETATM    7  C7  UNL     1       2.054   0.399   0.394  1.00  0.00           C  
HETATM    8  C8  UNL     1       3.431   0.382   0.943  1.00  0.00           C  
HETATM    9  C9  UNL     1       1.522  -0.709  -0.447  1.00  0.00           C  
HETATM   10  C10 UNL     1       0.193  -1.165   0.102  1.00  0.00           C  
HETATM   11  H1  UNL     1      -3.539   0.719  -1.314  1.00  0.00           H  
HETATM   12  H2  UNL     1      -1.963   1.657  -1.217  1.00  0.00           H  
HETATM   13  H3  UNL     1      -4.002  -1.056   0.038  1.00  0.00           H  
HETATM   14  H4  UNL     1      -2.854  -1.429   1.371  1.00  0.00           H  
HETATM   15  H5  UNL     1      -2.676  -2.191  -0.297  1.00  0.00           H  
HETATM   16  H6  UNL     1      -0.790   0.039   1.567  1.00  0.00           H  
HETATM   17  H7  UNL     1      -0.776   2.130   0.371  1.00  0.00           H  
HETATM   18  H8  UNL     1       0.031   1.310  -1.087  1.00  0.00           H  
HETATM   19  H9  UNL     1       1.581   2.231   1.232  1.00  0.00           H  
HETATM   20  H10 UNL     1       3.566  -0.555   1.556  1.00  0.00           H  
HETATM   21  H11 UNL     1       4.171   0.428   0.128  1.00  0.00           H  
HETATM   22  H12 UNL     1       3.567   1.266   1.595  1.00  0.00           H  
HETATM   23  H13 UNL     1       2.204  -1.564  -0.434  1.00  0.00           H  
HETATM   24  H14 UNL     1       1.354  -0.368  -1.495  1.00  0.00           H  
HETATM   25  H15 UNL     1      -0.295  -1.844  -0.655  1.00  0.00           H  
HETATM   26  H16 UNL     1       0.378  -1.801   0.992  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 HMDB0004321 ((-)-Limonene)

CC(=C)[C@H]1CCC(C)=CC1
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INCHI for HMDB0004321 ((-)-Limonene)

InChI=1S/C10H16/c1-8(2)10-6-4-9(3)5-7-10/h4,10H,1,5-7H2,2-3H3/t10-/m1/s1
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View in JSmolView Stereo Labels
Synonyms
Chemical FormulaC10H16
Average Molecular Weight136.234
Monoisotopic Molecular Weight136.125200512
IUPAC Name(4S)-1-methyl-4-(prop-1-en-2-yl)cyclohex-1-ene
Traditional Name(-)-limonene
CAS Registry Number5989-54-8
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 KeyXMGQYMWWDOXHJM-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.
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 locationSource
ProcessNot Available
Role
Biological roleIndustrial application
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-74.3 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.014 mg/mL at 25 °CNot Available
LogP4.57LI,J & PURDUE,EM (1995)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane (predicted from logP)
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB006329
KNApSAcK IDC00000803
Chemspider ID388386
KEGG Compound IDC00521
BioCyc IDNot Available
BiGG ID47361
Wikipedia LinkLimonene
METLIN ID6911
PubChem Compound439250
PDB IDNot Available
ChEBI ID15383
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceSakane, 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
  1. 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 ]
  2. 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 ]
  3. 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 ]
  4. 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