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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2012-09-11 21:33:02 UTC

Update Date

2022-03-07 02:54:55 UTC

HMDB ID

HMDB0036413

Secondary Accession Numbers

HMDB36413

Metabolite Identification

Common Name

alpha-Cubebene

Description

alpha-Cubebene, also known as α-cubebene, belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. Based on a literature review a significant number of articles have been published on alpha-Cubebene.

Structure

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

HMDB0036413
     RDKit          3D
alpha-Cubebene
 39 41  0  0  0  0  0  0  0  0999 V2000
   -2.1169    3.1027    1.2822 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9437    1.8982    0.4392 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5017    1.7468   -0.7462 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1498    0.4399   -1.3556 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1530   -0.1921   -0.4099 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1366    0.6686    0.7520 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0828    0.5132   -0.1746 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2146   -0.2216    0.4378 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5248    0.5111    0.2459 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6822   -0.2140    0.8571 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7989    0.7737   -1.2238 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2635   -1.6178   -0.1400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0168   -2.2977    0.3597 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1418   -1.6722   -0.4068 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4834   -2.2634    0.0476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5251    2.9515    2.2196 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7925    4.0339    0.7709 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1757    3.2642    1.5868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1431    2.4663   -1.2443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7119    0.5228   -2.3562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0768   -0.1536   -1.4262 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0442    0.3559    1.7942 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3615    1.3703   -0.8103 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0886   -0.3459    1.5409 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4422    1.4971    0.7315 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3959   -0.8443    1.7260 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4285    0.5059    1.2224 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1411   -0.9068    0.1165 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9187    0.8147   -1.3233 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3483    0.0322   -1.8881 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4414    1.7994   -1.5157 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1587   -2.1749    0.1237 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1573   -1.5002   -1.2552 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0543   -3.3682    0.0848 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0559   -2.1476    1.4390 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0324   -2.0143   -1.4721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2811   -3.3506    0.2285 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2165   -2.1600   -0.7651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8043   -1.8233    1.0051 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  5  4  1  6
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
  8 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
  6  2  1  0
  7  5  1  0
 14  5  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  6 22  1  1
  7 23  1  6
  8 24  1  1
  9 25  1  0
 10 26  1  0
 10 27  1  0
 10 28  1  0
 11 29  1  0
 11 30  1  0
 11 31  1  0
 12 32  1  0
 12 33  1  0
 13 34  1  0
 13 35  1  0
 14 36  1  6
 15 37  1  0
 15 38  1  0
 15 39  1  0
M  END


  Mrv1652309272007402D          

 17 19  0  0  0  0            999 V2000
 9998.906510001.8771    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.757510000.2250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.7427 9999.5073    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9065 9998.5661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.1924 9998.1528    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.6205 9998.1528    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.0312 9999.0919    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
 9998.906510001.0466    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9998.192010000.6341    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.1920 9999.8090    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9065 9999.3966    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9999.6210 9999.8090    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10000.330610000.2252    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9999.616210000.6377    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9999.616210001.4626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.045110001.4626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.045110000.6377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  8  1  1  1  0  0  0
 12  7  1  6  0  0  0
 11  4  1  6  0  0  0
 13 14  1  0  0  0  0
 13 17  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 14 15  1  6  0  0  0
 13  3  1  1  0  0  0
 17  2  1  0  0  0  0
  8 14  1  0  0  0  0
 12 14  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0036413

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@]12[C@@H](CC[C@@H](C)[C@]11CC=C(C)[C@]21[H])C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C15H24/c1-9(2)12-6-5-11(4)15-8-7-10(3)13(15)14(12)15/h7,9,11-14H,5-6,8H2,1-4H3/t11-,12+,13-,14-,15+/m1/s1

> <INCHI_KEY>
XUEHVOLRMXNRKQ-KHMAMNHCSA-N

> <FORMULA>
C15H24

> <MOLECULAR_WEIGHT>
204.357

> <EXACT_MASS>
204.187800773

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
26.162179830268414

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,5S,6R,7S,10R)-4,10-dimethyl-7-(propan-2-yl)tricyclo[4.4.0.0^{1,5}]dec-3-ene

> <ALOGPS_LOGP>
3.88

> <JCHEM_LOGP>
4.0881301626666655

> <ALOGPS_LOGS>
-5.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
65.76790000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.84e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,5S,6R,7S,10R)-7-isopropyl-4,10-dimethyltricyclo[4.4.0.0^{1,5}]dec-3-ene

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0036413
     RDKit          3D
alpha-Cubebene
 39 41  0  0  0  0  0  0  0  0999 V2000
   -2.1169    3.1027    1.2822 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9437    1.8982    0.4392 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5017    1.7468   -0.7462 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1498    0.4399   -1.3556 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1530   -0.1921   -0.4099 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1366    0.6686    0.7520 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0828    0.5132   -0.1746 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2146   -0.2216    0.4378 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5248    0.5111    0.2459 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6822   -0.2140    0.8571 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7989    0.7737   -1.2238 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2635   -1.6178   -0.1400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0168   -2.2977    0.3597 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1418   -1.6722   -0.4068 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4834   -2.2634    0.0476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5251    2.9515    2.2196 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7925    4.0339    0.7709 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1757    3.2642    1.5868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1431    2.4663   -1.2443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7119    0.5228   -2.3562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0768   -0.1536   -1.4262 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0442    0.3559    1.7942 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3615    1.3703   -0.8103 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0886   -0.3459    1.5409 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4422    1.4971    0.7315 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3959   -0.8443    1.7260 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4285    0.5059    1.2224 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1411   -0.9068    0.1165 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9187    0.8147   -1.3233 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3483    0.0322   -1.8881 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4414    1.7994   -1.5157 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1587   -2.1749    0.1237 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1573   -1.5002   -1.2552 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0543   -3.3682    0.0848 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0559   -2.1476    1.4390 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0324   -2.0143   -1.4721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2811   -3.3506    0.2285 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2165   -2.1600   -0.7651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8043   -1.8233    1.0051 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  5  4  1  6
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
  8 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
  6  2  1  0
  7  5  1  0
 14  5  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  6 22  1  1
  7 23  1  6
  8 24  1  1
  9 25  1  0
 10 26  1  0
 10 27  1  0
 10 28  1  0
 11 29  1  0
 11 30  1  0
 11 31  1  0
 12 32  1  0
 12 33  1  0
 13 34  1  0
 13 35  1  0
 14 36  1  6
 15 37  1  0
 15 38  1  0
 15 39  1  0
M  END

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    8664.6258670.171   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8669.9478667.087   0.000  0.00  0.00           C+0
HETATM    3  H   UNK     0    8668.0538665.747   0.000  0.00  0.00           H+0
HETATM    4  C   UNK     0    8664.6258663.990   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8663.2928663.219   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8665.9588663.219   0.000  0.00  0.00           C+0
HETATM    7  H   UNK     0    8666.7258664.972   0.000  0.00  0.00           H+0
HETATM    8  C   UNK     0    8664.6258668.620   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8663.2928667.850   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8663.2928666.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8664.6258665.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8665.9598666.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8667.2848667.087   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8665.9508667.857   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8665.9508669.397   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8668.6188669.397   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8668.6188667.857   0.000  0.00  0.00           C+0
CONECT    1    8                                                            
CONECT    2   17                                                            
CONECT    3   13                                                            
CONECT    4    5    6   11                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7   12                                                            
CONECT    8    9    1   14                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12    4                                                  
CONECT   12   11    7   14   13                                             
CONECT   13   14   17    3   12                                             
CONECT   14   13   15    8   12                                             
CONECT   15   16   14                                                       
CONECT   16   15   17                                                       
CONECT   17   13   16    2                                                  
MASTER        0    0    0    0    0    0    0    0   17    0   38    0
END

COMPND    HMDB0036413
HETATM    1  C1  UNL     1      -2.117   3.103   1.282  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.944   1.898   0.439  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.502   1.747  -0.746  1.00  0.00           C  
HETATM    4  C4  UNL     1      -2.150   0.440  -1.356  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.153  -0.192  -0.410  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.137   0.669   0.752  1.00  0.00           C  
HETATM    7  C7  UNL     1       0.083   0.513  -0.175  1.00  0.00           C  
HETATM    8  C8  UNL     1       1.215  -0.222   0.438  1.00  0.00           C  
HETATM    9  C9  UNL     1       2.525   0.511   0.246  1.00  0.00           C  
HETATM   10  C10 UNL     1       3.682  -0.214   0.857  1.00  0.00           C  
HETATM   11  C11 UNL     1       2.799   0.774  -1.224  1.00  0.00           C  
HETATM   12  C12 UNL     1       1.264  -1.618  -0.140  1.00  0.00           C  
HETATM   13  C13 UNL     1      -0.017  -2.298   0.360  1.00  0.00           C  
HETATM   14  C14 UNL     1      -1.142  -1.672  -0.407  1.00  0.00           C  
HETATM   15  C15 UNL     1      -2.483  -2.263   0.048  1.00  0.00           C  
HETATM   16  H1  UNL     1      -1.525   2.951   2.220  1.00  0.00           H  
HETATM   17  H2  UNL     1      -1.793   4.034   0.771  1.00  0.00           H  
HETATM   18  H3  UNL     1      -3.176   3.264   1.587  1.00  0.00           H  
HETATM   19  H4  UNL     1      -3.143   2.466  -1.244  1.00  0.00           H  
HETATM   20  H5  UNL     1      -1.712   0.523  -2.356  1.00  0.00           H  
HETATM   21  H6  UNL     1      -3.077  -0.154  -1.426  1.00  0.00           H  
HETATM   22  H7  UNL     1      -1.044   0.356   1.794  1.00  0.00           H  
HETATM   23  H8  UNL     1       0.362   1.370  -0.810  1.00  0.00           H  
HETATM   24  H9  UNL     1       1.089  -0.346   1.541  1.00  0.00           H  
HETATM   25  H10 UNL     1       2.442   1.497   0.732  1.00  0.00           H  
HETATM   26  H11 UNL     1       3.396  -0.844   1.726  1.00  0.00           H  
HETATM   27  H12 UNL     1       4.428   0.506   1.222  1.00  0.00           H  
HETATM   28  H13 UNL     1       4.141  -0.907   0.117  1.00  0.00           H  
HETATM   29  H14 UNL     1       3.919   0.815  -1.323  1.00  0.00           H  
HETATM   30  H15 UNL     1       2.348   0.032  -1.888  1.00  0.00           H  
HETATM   31  H16 UNL     1       2.441   1.799  -1.516  1.00  0.00           H  
HETATM   32  H17 UNL     1       2.159  -2.175   0.124  1.00  0.00           H  
HETATM   33  H18 UNL     1       1.157  -1.500  -1.255  1.00  0.00           H  
HETATM   34  H19 UNL     1       0.054  -3.368   0.085  1.00  0.00           H  
HETATM   35  H20 UNL     1      -0.056  -2.148   1.439  1.00  0.00           H  
HETATM   36  H21 UNL     1      -1.032  -2.014  -1.472  1.00  0.00           H  
HETATM   37  H22 UNL     1      -2.281  -3.351   0.228  1.00  0.00           H  
HETATM   38  H23 UNL     1      -3.217  -2.160  -0.765  1.00  0.00           H  
HETATM   39  H24 UNL     1      -2.804  -1.823   1.005  1.00  0.00           H  
CONECT    1    2   16   17   18
CONECT    2    3    3    6
CONECT    3    4   19
CONECT    4    5   20   21
CONECT    5    6    7   14
CONECT    6    7   22
CONECT    7    8   23
CONECT    8    9   12   24
CONECT    9   10   11   25
CONECT   10   26   27   28
CONECT   11   29   30   31
CONECT   12   13   32   33
CONECT   13   14   34   35
CONECT   14   15   36
CONECT   15   37   38   39
END

HMDB0036413
     RDKit          3D
alpha-Cubebene
 39 41  0  0  0  0  0  0  0  0999 V2000
   -2.1169    3.1027    1.2822 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9437    1.8982    0.4392 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5017    1.7468   -0.7462 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1498    0.4399   -1.3556 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1530   -0.1921   -0.4099 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1366    0.6686    0.7520 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0828    0.5132   -0.1746 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2146   -0.2216    0.4378 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5248    0.5111    0.2459 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6822   -0.2140    0.8571 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7989    0.7737   -1.2238 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2635   -1.6178   -0.1400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0168   -2.2977    0.3597 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1418   -1.6722   -0.4068 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4834   -2.2634    0.0476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5251    2.9515    2.2196 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7925    4.0339    0.7709 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1757    3.2642    1.5868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1431    2.4663   -1.2443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7119    0.5228   -2.3562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0768   -0.1536   -1.4262 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0442    0.3559    1.7942 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3615    1.3703   -0.8103 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0886   -0.3459    1.5409 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4422    1.4971    0.7315 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3959   -0.8443    1.7260 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4285    0.5059    1.2224 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1411   -0.9068    0.1165 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9187    0.8147   -1.3233 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3483    0.0322   -1.8881 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4414    1.7994   -1.5157 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1587   -2.1749    0.1237 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1573   -1.5002   -1.2552 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0543   -3.3682    0.0848 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0559   -2.1476    1.4390 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0324   -2.0143   -1.4721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2811   -3.3506    0.2285 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2165   -2.1600   -0.7651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8043   -1.8233    1.0051 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  5  4  1  6
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
  8 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
  6  2  1  0
  7  5  1  0
 14  5  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  6 22  1  1
  7 23  1  6
  8 24  1  1
  9 25  1  0
 10 26  1  0
 10 27  1  0
 10 28  1  0
 11 29  1  0
 11 30  1  0
 11 31  1  0
 12 32  1  0
 12 33  1  0
 13 34  1  0
 13 35  1  0
 14 36  1  6
 15 37  1  0
 15 38  1  0
 15 39  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(-)-alpha-Cubebene	ChEBI
(1R,5S,6R,7S,10R)-4,10-Dimethyl-7-(propan-2-yl)tricyclo[4.4.0.0(1,5)]dec-3-ene	ChEBI
(-)-a-Cubebene	Generator
(-)-Α-cubebene	Generator
a-Cubebene	Generator
Α-cubebene	Generator
alpha-Cubenene	HMDB
Α-cubenene	HMDB
alpha-Cubebene	PhytoBank

Chemical Formula

C₁₅H₂₄

Average Molecular Weight

204.357

Monoisotopic Molecular Weight

204.187800773

IUPAC Name

(1R,5S,6R,7S,10R)-4,10-dimethyl-7-(propan-2-yl)tricyclo[4.4.0.0^{1,5}]dec-3-ene

Traditional Name

(1R,5S,6R,7S,10R)-7-isopropyl-4,10-dimethyltricyclo[4.4.0.0^{1,5}]dec-3-ene

CAS Registry Number

17699-14-8

SMILES

[H][C@]12[C@@H](CC[C@@H](C)[C@]11CC=C(C)[C@]21[H])C(C)C

InChI Identifier

InChI=1S/C15H24/c1-9(2)12-6-5-11(4)15-8-7-10(3)13(15)14(12)15/h7,9,11-14H,5-6,8H2,1-4H3/t11-,12+,13-,14-,15+/m1/s1

InChI Key

XUEHVOLRMXNRKQ-KHMAMNHCSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Sesquiterpenoids

Alternative Parents

Substituents

Cubebane sesquiterpenoid
Sesquiterpenoid
Branched unsaturated hydrocarbon
Polycyclic hydrocarbon
Cyclic olefin
Unsaturated aliphatic hydrocarbon
Unsaturated hydrocarbon
Olefin
Hydrocarbon
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

sesquiterpenoid (CHEBI:10224 )
Cubebane and ivaxillarane sesquiterpenoids (C09647 )
Sesquiterpenoids (C15) (C09647 )

Ontology

Cellular substructure

Non-excretory biofluid

Biofluid or Excreta

Saliva (PMID: 24421258)

Excreta

Biofluid or Excreta

Feces (PMID: 23454028)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0036413)

Source

Endogenous

Endogenous (HMDB: HMDB0036413)

Plant

Plant (HMDB: HMDB0036413)

Animal

Animal (HMDB: HMDB0036413)

Exogenous

Food

Food (HMDB: HMDB0036413)

Herb and spice

Herb

Spice

Herbs and Spices (FooDB: FOOD00866)

Fruit

Citrus

Lemon (FooDB: FOOD00054)
Sweet orange (FooDB: FOOD00057)
Mandarin orange (Clementine, Tangerine) (FooDB: FOOD00056)

Berry

Evergreen blackberry (FooDB: FOOD00901)
Blackberry (FooDB: FOOD00906)

Exogenous (HMDB: HMDB0036413)

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid Peroxidation (HMDB: HMDB0036413)

Biochemical pathway

Metabolic pathway

Fatty Acid Metabolism (HMDB: HMDB0036413)

Lipid metabolism pathway (HMDB: HMDB0036413)

Cellular process

Cell signaling (HMDB: HMDB0036413)

Biochemical process

Lipid transport (HMDB: HMDB0036413)

Role

Biological role

Energy source (HMDB: HMDB0036413)

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0036413)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	245.00 to 246.00 °C. @ 760.00 mm Hg	The Good Scents Company Information System
Water Solubility	0.021 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	6.263 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.0018 g/L	ALOGPS
logP	3.88	ALOGPS
logP	4.09	ChemAxon
logS	-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	65.77 m³·mol⁻¹	ChemAxon
Polarizability	26.16 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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
DeepCCS	[M-2H]-	192.665	30932474
DeepCCS	[M+Na]+	167.338	30932474
AllCCS	[M+H]+	147.1	32859911
AllCCS	[M+H-H2O]+	143.2	32859911
AllCCS	[M+NH4]+	150.7	32859911
AllCCS	[M+Na]+	151.8	32859911
AllCCS	[M-H]-	158.4	32859911
AllCCS	[M+Na-2H]-	158.7	32859911
AllCCS	[M+HCOO]-	159.2	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.	5.47 minutes	32390414
Predicted by Siyang on May 30, 2022	19.3959 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.07 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	27.0 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2625.1 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	678.7 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	243.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	368.5 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	419.3 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	805.6 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	860.2 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	106.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1523.9 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	558.9 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	1552.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	518.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	465.2 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	460.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	604.6 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	8.5 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
alpha-Cubebene	[H][C@]12[C@@H](CC[C@@H](C)[C@]11CC=C(C)[C@]21[H])C(C)C	1591.5	Standard polar	33892256
alpha-Cubebene	[H][C@]12[C@@H](CC[C@@H](C)[C@]11CC=C(C)[C@]21[H])C(C)C	1368.5	Standard non polar	33892256
alpha-Cubebene	[H][C@]12[C@@H](CC[C@@H](C)[C@]11CC=C(C)[C@]21[H])C(C)C	1364.3	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - alpha-Cubebene GC-MS (Non-derivatized) - 70eV, Positive	splash10-004v-2900000000-cb9dd96728d976cfde1a	2017-07-27	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - alpha-Cubebene GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
MS	Mass Spectrum (Electron Ionization)	splash10-0cdl-6900000000-fc2c2b48c3130ca12608	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 - alpha-Cubebene 10V, Positive-QTOF	splash10-0a4i-1390000000-5797472d9e7fa529c8bf	2017-06-28	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Cubebene 20V, Positive-QTOF	splash10-0a4i-4930000000-0826dbd6d1b12cad2c7c	2017-06-28	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Cubebene 40V, Positive-QTOF	splash10-0pxr-9500000000-5bf76df99a765e29264d	2017-06-28	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Cubebene 10V, Negative-QTOF	splash10-0udi-0090000000-90633cf8013739481342	2017-06-28	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Cubebene 20V, Negative-QTOF	splash10-0udi-0190000000-551c8a4137523d4a0891	2017-06-28	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Cubebene 40V, Negative-QTOF	splash10-0fe1-1910000000-fb0a47d8a0a09504ee1b	2017-06-28	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Cubebene 10V, Positive-QTOF	splash10-0avi-5950000000-2ef16aa9e7547e808fac	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Cubebene 20V, Positive-QTOF	splash10-052f-9410000000-bd5a53349560ca7edaac	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Cubebene 40V, Positive-QTOF	splash10-052f-9200000000-164aa0685a62957c4679	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Cubebene 10V, Negative-QTOF	splash10-0udi-0090000000-7ccf03fa1149a1e9f55f	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Cubebene 20V, Negative-QTOF	splash10-0udi-0090000000-7ccf03fa1149a1e9f55f	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Cubebene 40V, Negative-QTOF	splash10-0udi-0090000000-1bdf848163c08abe4e84	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular
Membrane

Biospecimen Locations

Feces
Saliva

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
Feces	Detected and Quantified	0-5578.634 nmol/g wet feces	Children (1-13 years old)	Not Specified	Normal	21970810	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	26806034	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Not Specified	Normal	24421258	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
Feces	Detected and Quantified	0-41203.595 nmol/g wet feces	Children (1-13 years old)	Not Specified	Treated celiac disease	21970810	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Crohns disease	26806034	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Ulcerative colitis	26806034	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 ]
Celiac disease
Di Cagno R, De Angelis M, De Pasquale I, Ndagijimana M, Vernocchi P, Ricciuti P, Gagliardi F, Laghi L, Crecchio C, Guerzoni ME, Gobbetti M, Francavilla R: Duodenal and faecal microbiota of celiac children: molecular, phenotype and metabolome characterization. BMC Microbiol. 2011 Oct 4;11:219. doi: 10.1186/1471-2180-11-219. [PubMed:21970810 ]
Crohn's disease
Ahmed I, Greenwood R, Costello B, Ratcliffe N, Probert CS: Investigation of faecal volatile organic metabolites as novel diagnostic biomarkers in inflammatory bowel disease. Aliment Pharmacol Ther. 2016 Mar;43(5):596-611. doi: 10.1111/apt.13522. Epub 2016 Jan 25. [PubMed:26806034 ]
Ulcerative colitis
Ahmed I, Greenwood R, Costello B, Ratcliffe N, Probert CS: Investigation of faecal volatile organic metabolites as novel diagnostic biomarkers in inflammatory bowel disease. Aliment Pharmacol Ther. 2016 Mar;43(5):596-611. doi: 10.1111/apt.13522. Epub 2016 Jan 25. [PubMed:26806034 ]

Associated OMIM IDs

212750 (Celiac disease)
266600 (Crohn's disease)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Cubebene

METLIN ID

Not Available

PubChem Compound

442359

PDB ID

Not Available

ChEBI ID

10224

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1054531

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Showing metabocard for alpha-Cubebene (HMDB0036413)

MOL for HMDB0036413 (alpha-Cubebene)

3D MOL for HMDB0036413 (alpha-Cubebene)

3D SDF for HMDB0036413 (alpha-Cubebene)

3D-SDF for HMDB0036413 (alpha-Cubebene)

PDB for HMDB0036413 (alpha-Cubebene)

3D PDB for HMDB0036413 (alpha-Cubebene)

SMILES for HMDB0036413 (alpha-Cubebene)

INCHI for HMDB0036413 (alpha-Cubebene)

Structure for HMDB0036413 (alpha-Cubebene)

3D Structure for HMDB0036413 (alpha-Cubebene)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra