Showing NP-Card for (-)-Limonene (NP0000505)

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Record Information
Version2.0
Created at2006-08-13 16:44:29 UTC
Updated at2025-02-11 15:47:16 UTC
NP-MRD IDNP0000505
Natural Product DOIhttps://doi.org/10.57994/2605
Secondary Accession NumbersNone
Natural Product 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000505 ((-)-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 NP0000505 ((-)-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 NP0000505 ((-)-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>
NP0000505

> <DATABASE_NAME>
NP-MRD

> <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 NP0000505 ((-)-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

PDB for NP0000505 ((-)-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
Download

3D PDB for NP0000505 ((-)-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 NP0000505 ((-)-Limonene)

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

INCHI for NP0000505 ((-)-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 NMR Assignments
Synonyms
Chemical FormulaC10H16
Average Mass136.2340 Da
Monoisotopic Mass136.12520 Da
IUPAC Name(4S)-1-methyl-4-(prop-1-en-2-yl)cyclohex-1-ene
Traditional Name(-)-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-/m1/s1
InChI KeyXMGQYMWWDOXHJM-SNVBAGLBSA-N
Experimental Spectra
Predicted Spectra
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600.133705802, CDCl3, simulated)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-05-16View Spectrum
Species
Species of Origin
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
Physical Properties
StateLiquid
Experimental Properties
PropertyValueReference
Melting Point-74.3 °CNot Available
Boiling Point176.00 to 177.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility0.014 mg/mL at 25 °CNot Available
LogP4.57Li, J., Perdue, E.M. (1995) Physicochemical properties of selected monoterpenes. Pre-print Extended Abstract, Presented Before The Division of Environmental Chemistry, Amer Chem Soc, Anaheim, Ca: April 2-7
Predicted 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
Polarizability17.23 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0004321
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB006329
KNApSAcK IDC00000803
Chemspider ID388386
KEGG Compound IDC00521
BioCyc IDNot Available
BiGG ID47361
Wikipedia LinkLimonene
METLIN ID6911
PubChem Compound439250
PDB IDNot Available
ChEBI ID15383
Good Scents IDrw1007831
References
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 ]
  5. Liu Y, Ma X, Liang H, Stephanopoulos G, Zhou K: Monoterpenoid biosynthesis by engineered microbes. J Ind Microbiol Biotechnol. 2021 Oct 2. pii: 6380491. doi: 10.1093/jimb/kuab065. [PubMed:34601590 ]