Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 22:01:28 UTC

Update Date

2022-03-07 02:55:05 UTC

HMDB ID

HMDB0036845

Secondary Accession Numbers

HMDB36845

Metabolite Identification

Common Name

Cembrene

Description

Cembrene, also known as thunbergene or 1(S)-cembrene, belongs to the class of organic compounds known as cembrane diterpenoids. These are diterpenoids with a structure based a cembrane skeleton, which is characterized by the presence of an isopropyl group at C-1 and by three symmetrically disposed methyl groups a the t C-4, -8 and -12 positions. Based on a literature review a small amount of articles have been published on Cembrene.

Structure

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

HMDB0036845
     RDKit          3D
Cembrene
 52 52  0  0  0  0  0  0  0  0999 V2000
    0.0439   -4.2866    0.5095 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3275   -2.8327    0.2868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0823   -2.6160   -0.7714 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5355   -1.2602   -1.1345 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9800   -1.0006   -0.8578 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3936    0.0482   -0.1513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8283    0.3273    0.1352 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4352    1.0570    0.4457 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0594    2.0390   -0.6257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1244    3.0927   -0.2554 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0452    3.1037    0.3137 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7328    4.4626    0.5375 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8605    1.9627    0.8124 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3947    1.1135   -0.2794 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7108   -0.3054    0.0234 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2156   -0.5349    0.1964 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9498   -0.1657   -1.0499 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3947   -2.0372    0.4279 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9637   -0.8666    1.1673 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1610   -1.8697    1.2500 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9899   -4.5081    0.0188 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0922   -4.5561    1.5621 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7503   -4.9574    0.0685 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3682   -3.4888   -1.3910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4159   -1.2033   -2.2647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8976   -0.4731   -0.7581 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6917   -1.7056   -1.2574 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9920    0.8091    1.1078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1481    1.0783   -0.6446 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4536   -0.5839    0.0952 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5356    0.5517    0.8150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8918    1.5503    1.3325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0775    2.4799   -0.9334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7896    1.4817   -1.5428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5095    4.1198   -0.5291 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4728    4.6031   -0.2711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0229    5.2589    0.5843 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2560    4.4503    1.5154 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7955    2.3612    1.3493 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3719    1.4408    1.6597 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7587    1.1495   -1.2050 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3652    1.5699   -0.6690 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4451   -0.9200   -0.8627 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6144    0.0023    1.0693 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9053   -0.7602   -1.0708 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2422    0.8996   -1.1044 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3891   -0.5019   -1.9507 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8728   -2.6177   -0.3605 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8762   -2.3033    1.3883 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4603   -2.3170    0.4494 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1630   -0.2960    2.1158 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2330   -2.0452    2.3086 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
  4  5  1  0
  5  6  2  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 15 19  1  0
 19 20  2  0
 20  2  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  3 24  1  0
  4 25  1  0
  4 26  1  0
  5 27  1  0
  7 28  1  0
  7 29  1  0
  7 30  1  0
  8 31  1  0
  8 32  1  0
  9 33  1  0
  9 34  1  0
 10 35  1  0
 12 36  1  0
 12 37  1  0
 12 38  1  0
 13 39  1  0
 13 40  1  0
 14 41  1  0
 14 42  1  0
 15 43  1  6
 16 44  1  0
 17 45  1  0
 17 46  1  0
 17 47  1  0
 18 48  1  0
 18 49  1  0
 18 50  1  0
 19 51  1  0
 20 52  1  0
M  END

  Mrv1652309272007282D          

 20 20  0  0  0  0            999 V2000
   28.0347  -21.1608    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   27.8390  -20.3639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.3374  -21.6005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.0179  -20.3089    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.7053  -21.0715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.6846  -19.5463    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.9463  -21.3978    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.9152  -19.2372    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.2618  -18.9555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.1767  -21.0955    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.9599  -22.2222    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.1115  -19.5876    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.5550  -21.6383    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.8538  -20.3364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.8474  -21.2158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.0294  -20.4085    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.4867  -19.7868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.8246  -21.3725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.4057  -20.7872    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.8204  -22.1944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  4  2  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  2  0  0  0  0
  6  9  1  0  0  0  0
  7 10  2  0  0  0  0
  7 11  1  0  0  0  0
  8 12  1  0  0  0  0
 10 13  1  0  0  0  0
 12 14  1  0  0  0  0
 13 15  1  0  0  0  0
 14 16  2  0  0  0  0
 16 17  1  0  0  0  0
 15 16  1  0  0  0  0
  1 18  1  6  0  0  0
  1  2  1  0  0  0  0
 18 19  1  0  0  0  0
  1  3  1  0  0  0  0
 18 20  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0036845

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)[C@@H]1CC\C(C)=C\CC\C(C)=C\C\C=C(\C)/C=C/1

> <INCHI_IDENTIFIER>
InChI=1S/C20H32/c1-16(2)20-14-12-18(4)10-6-8-17(3)9-7-11-19(5)13-15-20/h8,10-12,14,16,20H,6-7,9,13,15H2,1-5H3/b14-12+,17-8+,18-10-,19-11+/t20-/m0/s1

> <INCHI_KEY>
DMHADBQKVWXPPM-QXIQWJTQSA-N

> <FORMULA>
C20H32

> <MOLECULAR_WEIGHT>
272.4681

> <EXACT_MASS>
272.250401024

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
52

> <JCHEM_AVERAGE_POLARIZABILITY>
34.92727791371369

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1E,3Z,6E,10E,14S)-3,7,11-trimethyl-14-(propan-2-yl)cyclotetradeca-1,3,6,10-tetraene

> <ALOGPS_LOGP>
6.90

> <JCHEM_LOGP>
6.524965355999999

> <ALOGPS_LOGS>
-5.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
95.4246

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.01e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1E,3Z,6E,10E,14S)-14-isopropyl-3,7,11-trimethylcyclotetradeca-1,3,6,10-tetraene

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0036845
     RDKit          3D
Cembrene
 52 52  0  0  0  0  0  0  0  0999 V2000
    0.0439   -4.2866    0.5095 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3275   -2.8327    0.2868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0823   -2.6160   -0.7714 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5355   -1.2602   -1.1345 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9800   -1.0006   -0.8578 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3936    0.0482   -0.1513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8283    0.3273    0.1352 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4352    1.0570    0.4457 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0594    2.0390   -0.6257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1244    3.0927   -0.2554 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0452    3.1037    0.3137 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7328    4.4626    0.5375 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8605    1.9627    0.8124 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3947    1.1135   -0.2794 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7108   -0.3054    0.0234 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2156   -0.5349    0.1964 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9498   -0.1657   -1.0499 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3947   -2.0372    0.4279 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9637   -0.8666    1.1673 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1610   -1.8697    1.2500 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9899   -4.5081    0.0188 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0922   -4.5561    1.5621 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7503   -4.9574    0.0685 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3682   -3.4888   -1.3910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4159   -1.2033   -2.2647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8976   -0.4731   -0.7581 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6917   -1.7056   -1.2574 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9920    0.8091    1.1078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1481    1.0783   -0.6446 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4536   -0.5839    0.0952 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5356    0.5517    0.8150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8918    1.5503    1.3325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0775    2.4799   -0.9334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7896    1.4817   -1.5428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5095    4.1198   -0.5291 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4728    4.6031   -0.2711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0229    5.2589    0.5843 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2560    4.4503    1.5154 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7955    2.3612    1.3493 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3719    1.4408    1.6597 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7587    1.1495   -1.2050 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3652    1.5699   -0.6690 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4451   -0.9200   -0.8627 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6144    0.0023    1.0693 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9053   -0.7602   -1.0708 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2422    0.8996   -1.1044 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3891   -0.5019   -1.9507 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8728   -2.6177   -0.3605 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8762   -2.3033    1.3883 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4603   -2.3170    0.4494 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1630   -0.2960    2.1158 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2330   -2.0452    2.3086 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
  4  5  1  0
  5  6  2  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 15 19  1  0
 19 20  2  0
 20  2  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  3 24  1  0
  4 25  1  0
  4 26  1  0
  5 27  1  0
  7 28  1  0
  7 29  1  0
  7 30  1  0
  8 31  1  0
  8 32  1  0
  9 33  1  0
  9 34  1  0
 10 35  1  0
 12 36  1  0
 12 37  1  0
 12 38  1  0
 13 39  1  0
 13 40  1  0
 14 41  1  0
 14 42  1  0
 15 43  1  6
 16 44  1  0
 17 45  1  0
 17 46  1  0
 17 47  1  0
 18 48  1  0
 18 49  1  0
 18 50  1  0
 19 51  1  0
 20 52  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      52.332 -39.500   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      51.966 -38.013   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      51.030 -40.321   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      50.433 -37.910   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      49.850 -39.333   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      49.811 -36.486   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      48.433 -39.943   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      48.375 -35.909   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      50.889 -35.384   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      46.997 -39.378   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      48.459 -41.481   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      46.875 -36.564   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      45.836 -40.391   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      46.394 -37.961   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      44.515 -39.603   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      44.855 -38.096   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      43.842 -36.935   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      53.806 -39.895   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      54.891 -38.803   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      53.798 -41.429   0.000  0.00  0.00           C+0
CONECT    1   18    2    3                                                  
CONECT    2    4    1                                                       
CONECT    3    5    1                                                       
CONECT    4    2    6                                                       
CONECT    5    3    7                                                       
CONECT    6    4    8    9                                                  
CONECT    7    5   10   11                                                  
CONECT    8    6   12                                                       
CONECT    9    6                                                            
CONECT   10    7   13                                                       
CONECT   11    7                                                            
CONECT   12    8   14                                                       
CONECT   13   10   15                                                       
CONECT   14   12   16                                                       
CONECT   15   13   16                                                       
CONECT   16   14   17   15                                                  
CONECT   17   16                                                            
CONECT   18    1   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   40    0
END

COMPND    HMDB0036845
HETATM    1  C1  UNL     1       0.044  -4.287   0.510  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.328  -2.833   0.287  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.082  -2.616  -0.771  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.536  -1.260  -1.135  1.00  0.00           C  
HETATM    5  C5  UNL     1      -2.980  -1.001  -0.858  1.00  0.00           C  
HETATM    6  C6  UNL     1      -3.394   0.048  -0.151  1.00  0.00           C  
HETATM    7  C7  UNL     1      -4.828   0.327   0.135  1.00  0.00           C  
HETATM    8  C8  UNL     1      -2.435   1.057   0.446  1.00  0.00           C  
HETATM    9  C9  UNL     1      -2.059   2.039  -0.626  1.00  0.00           C  
HETATM   10  C10 UNL     1      -1.124   3.093  -0.255  1.00  0.00           C  
HETATM   11  C11 UNL     1       0.045   3.104   0.314  1.00  0.00           C  
HETATM   12  C12 UNL     1       0.733   4.463   0.538  1.00  0.00           C  
HETATM   13  C13 UNL     1       0.861   1.963   0.812  1.00  0.00           C  
HETATM   14  C14 UNL     1       1.395   1.114  -0.279  1.00  0.00           C  
HETATM   15  C15 UNL     1       1.711  -0.305   0.023  1.00  0.00           C  
HETATM   16  C16 UNL     1       3.216  -0.535   0.196  1.00  0.00           C  
HETATM   17  C17 UNL     1       3.950  -0.166  -1.050  1.00  0.00           C  
HETATM   18  C18 UNL     1       3.395  -2.037   0.428  1.00  0.00           C  
HETATM   19  C19 UNL     1       0.964  -0.867   1.167  1.00  0.00           C  
HETATM   20  C20 UNL     1       0.161  -1.870   1.250  1.00  0.00           C  
HETATM   21  H1  UNL     1       0.990  -4.508   0.019  1.00  0.00           H  
HETATM   22  H2  UNL     1       0.092  -4.556   1.562  1.00  0.00           H  
HETATM   23  H3  UNL     1      -0.750  -4.957   0.068  1.00  0.00           H  
HETATM   24  H4  UNL     1      -1.368  -3.489  -1.391  1.00  0.00           H  
HETATM   25  H5  UNL     1      -1.416  -1.203  -2.265  1.00  0.00           H  
HETATM   26  H6  UNL     1      -0.898  -0.473  -0.758  1.00  0.00           H  
HETATM   27  H7  UNL     1      -3.692  -1.706  -1.257  1.00  0.00           H  
HETATM   28  H8  UNL     1      -4.992   0.809   1.108  1.00  0.00           H  
HETATM   29  H9  UNL     1      -5.148   1.078  -0.645  1.00  0.00           H  
HETATM   30  H10 UNL     1      -5.454  -0.584   0.095  1.00  0.00           H  
HETATM   31  H11 UNL     1      -1.536   0.552   0.815  1.00  0.00           H  
HETATM   32  H12 UNL     1      -2.892   1.550   1.332  1.00  0.00           H  
HETATM   33  H13 UNL     1      -3.078   2.480  -0.933  1.00  0.00           H  
HETATM   34  H14 UNL     1      -1.790   1.482  -1.543  1.00  0.00           H  
HETATM   35  H15 UNL     1      -1.509   4.120  -0.529  1.00  0.00           H  
HETATM   36  H16 UNL     1       1.473   4.603  -0.271  1.00  0.00           H  
HETATM   37  H17 UNL     1      -0.023   5.259   0.584  1.00  0.00           H  
HETATM   38  H18 UNL     1       1.256   4.450   1.515  1.00  0.00           H  
HETATM   39  H19 UNL     1       1.795   2.361   1.349  1.00  0.00           H  
HETATM   40  H20 UNL     1       0.372   1.441   1.660  1.00  0.00           H  
HETATM   41  H21 UNL     1       0.759   1.149  -1.205  1.00  0.00           H  
HETATM   42  H22 UNL     1       2.365   1.570  -0.669  1.00  0.00           H  
HETATM   43  H23 UNL     1       1.445  -0.920  -0.863  1.00  0.00           H  
HETATM   44  H24 UNL     1       3.614   0.002   1.069  1.00  0.00           H  
HETATM   45  H25 UNL     1       4.905  -0.760  -1.071  1.00  0.00           H  
HETATM   46  H26 UNL     1       4.242   0.900  -1.104  1.00  0.00           H  
HETATM   47  H27 UNL     1       3.389  -0.502  -1.951  1.00  0.00           H  
HETATM   48  H28 UNL     1       2.873  -2.618  -0.361  1.00  0.00           H  
HETATM   49  H29 UNL     1       2.876  -2.303   1.388  1.00  0.00           H  
HETATM   50  H30 UNL     1       4.460  -2.317   0.449  1.00  0.00           H  
HETATM   51  H31 UNL     1       1.163  -0.296   2.116  1.00  0.00           H  
HETATM   52  H32 UNL     1      -0.233  -2.045   2.309  1.00  0.00           H  
CONECT    1    2   21   22   23
CONECT    2    3    3   20
CONECT    3    4   24
CONECT    4    5   25   26
CONECT    5    6    6   27
CONECT    6    7    8
CONECT    7   28   29   30
CONECT    8    9   31   32
CONECT    9   10   33   34
CONECT   10   11   11   35
CONECT   11   12   13
CONECT   12   36   37   38
CONECT   13   14   39   40
CONECT   14   15   41   42
CONECT   15   16   19   43
CONECT   16   17   18   44
CONECT   17   45   46   47
CONECT   18   48   49   50
CONECT   19   20   20   51
CONECT   20   52
END

HMDB0036845
     RDKit          3D
Cembrene
 52 52  0  0  0  0  0  0  0  0999 V2000
    0.0439   -4.2866    0.5095 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3275   -2.8327    0.2868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0823   -2.6160   -0.7714 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5355   -1.2602   -1.1345 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9800   -1.0006   -0.8578 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3936    0.0482   -0.1513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8283    0.3273    0.1352 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4352    1.0570    0.4457 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0594    2.0390   -0.6257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1244    3.0927   -0.2554 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0452    3.1037    0.3137 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7328    4.4626    0.5375 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8605    1.9627    0.8124 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3947    1.1135   -0.2794 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7108   -0.3054    0.0234 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2156   -0.5349    0.1964 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9498   -0.1657   -1.0499 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3947   -2.0372    0.4279 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9637   -0.8666    1.1673 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1610   -1.8697    1.2500 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9899   -4.5081    0.0188 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0922   -4.5561    1.5621 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7503   -4.9574    0.0685 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3682   -3.4888   -1.3910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4159   -1.2033   -2.2647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8976   -0.4731   -0.7581 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6917   -1.7056   -1.2574 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9920    0.8091    1.1078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1481    1.0783   -0.6446 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4536   -0.5839    0.0952 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5356    0.5517    0.8150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8918    1.5503    1.3325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0775    2.4799   -0.9334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7896    1.4817   -1.5428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5095    4.1198   -0.5291 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4728    4.6031   -0.2711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0229    5.2589    0.5843 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2560    4.4503    1.5154 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7955    2.3612    1.3493 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3719    1.4408    1.6597 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7587    1.1495   -1.2050 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3652    1.5699   -0.6690 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4451   -0.9200   -0.8627 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6144    0.0023    1.0693 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9053   -0.7602   -1.0708 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2422    0.8996   -1.1044 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3891   -0.5019   -1.9507 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8728   -2.6177   -0.3605 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8762   -2.3033    1.3883 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4603   -2.3170    0.4494 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1630   -0.2960    2.1158 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2330   -2.0452    2.3086 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
  4  5  1  0
  5  6  2  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 15 19  1  0
 19 20  2  0
 20  2  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  3 24  1  0
  4 25  1  0
  4 26  1  0
  5 27  1  0
  7 28  1  0
  7 29  1  0
  7 30  1  0
  8 31  1  0
  8 32  1  0
  9 33  1  0
  9 34  1  0
 10 35  1  0
 12 36  1  0
 12 37  1  0
 12 38  1  0
 13 39  1  0
 13 40  1  0
 14 41  1  0
 14 42  1  0
 15 43  1  6
 16 44  1  0
 17 45  1  0
 17 46  1  0
 17 47  1  0
 18 48  1  0
 18 49  1  0
 18 50  1  0
 19 51  1  0
 20 52  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Thunbergene	HMDB
(1E,3Z,6E,10E,14S)-3,7,11-Trimethyl-14-(1-methylethyl)-1,3,6,10-cyclotetradecatetraene	HMDB
(+)-Cembrene	HMDB
(+)-Thunbergene	HMDB
(S)-(+)-Cembrene	HMDB
1(S)-Cembrene	HMDB
Thunbergen	HMDB

Chemical Formula

C₂₀H₃₂

Average Molecular Weight

272.4681

Monoisotopic Molecular Weight

272.250401024

IUPAC Name

(1E,3Z,6E,10E,14S)-3,7,11-trimethyl-14-(propan-2-yl)cyclotetradeca-1,3,6,10-tetraene

Traditional Name

(1E,3Z,6E,10E,14S)-14-isopropyl-3,7,11-trimethylcyclotetradeca-1,3,6,10-tetraene

CAS Registry Number

1898-13-1

SMILES

CC(C)[C@@H]1CC\C(C)=C\CC\C(C)=C\C\C=C(\C)/C=C/1

InChI Identifier

InChI=1S/C20H32/c1-16(2)20-14-12-18(4)10-6-8-17(3)9-7-11-19(5)13-15-20/h8,10-12,14,16,20H,6-7,9,13,15H2,1-5H3/b14-12+,17-8+,18-10-,19-11+/t20-/m0/s1

InChI Key

DMHADBQKVWXPPM-QXIQWJTQSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cembrane diterpenoids. These are diterpenoids with a structure based a cembrane skeleton, which is characterized by the presence of an isopropyl group at C-1 and by three symmetrically disposed methyl groups a the t C-4, -8 and -12 positions.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Cembrane diterpenoids

Alternative Parents

Substituents

Cembrane diterpenoid
Branched unsaturated hydrocarbon
Cyclic olefin
Unsaturated aliphatic hydrocarbon
Unsaturated hydrocarbon
Olefin
Hydrocarbon
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Route of exposure

Enteral

Ingestion (HMDB: HMDB0036845)

Source

Endogenous

Endogenous (HMDB: HMDB0036845)

Plant

Plant (HMDB: HMDB0036845)

Animal

Animal (HMDB: HMDB0036845)

Exogenous

Food

Food (HMDB: HMDB0036845)

Herb and spice

Herbs and Spices (FooDB: FOOD00866)

Fat and oil

Fats and oils (FooDB: FOOD00864)

Exogenous (HMDB: HMDB0036845)

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid Peroxidation (HMDB: HMDB0036845)

Biochemical pathway

Metabolic pathway

Fatty Acid Metabolism (HMDB: HMDB0036845)

Lipid metabolism pathway (HMDB: HMDB0036845)

Cellular process

Cell signaling (HMDB: HMDB0036845)

Biochemical process

Lipid transport (HMDB: HMDB0036845)

Role

Biological role

Energy source (HMDB: HMDB0036845)

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0036845)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	58 - 59 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	7.0e-05 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.002 g/L	ALOGPS
logP	6.9	ALOGPS
logP	6.52	ChemAxon
logS	-5.1	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	95.42 m³·mol⁻¹	ChemAxon
Polarizability	34.93 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	176.05	30932474
DeepCCS	[M-H]-	173.692	30932474
DeepCCS	[M-2H]-	207.905	30932474
DeepCCS	[M+Na]+	183.106	30932474
AllCCS	[M+H]+	168.0	32859911
AllCCS	[M+H-H2O]+	164.4	32859911
AllCCS	[M+NH4]+	171.4	32859911
AllCCS	[M+Na]+	172.3	32859911
AllCCS	[M-H]-	179.0	32859911
AllCCS	[M+Na-2H]-	179.6	32859911
AllCCS	[M+HCOO]-	180.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Cembrene	CC(C)[C@@H]1CC\C(C)=C\CC\C(C)=C\C\C=C(\C)/C=C/1	2250.7	Standard polar	33892256
Cembrene	CC(C)[C@@H]1CC\C(C)=C\CC\C(C)=C\C\C=C(\C)/C=C/1	1950.4	Standard non polar	33892256
Cembrene	CC(C)[C@@H]1CC\C(C)=C\CC\C(C)=C\C\C=C(\C)/C=C/1	1959.3	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - Cembrene GC-MS (Non-derivatized)	splash10-054o-9800000000-eeae686283d72746a958	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cembrene GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cembrene 10V, Positive-QTOF	splash10-00di-0090000000-d10590d89514cc99f1e2	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cembrene 20V, Positive-QTOF	splash10-00e9-0090000000-3609ade1f226129e72f2	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cembrene 40V, Positive-QTOF	splash10-0006-9000000000-1721daf5b5a2632b9ef7	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cembrene 10V, Negative-QTOF	splash10-00di-0090000000-4c81b77566a3712a2980	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cembrene 20V, Negative-QTOF	splash10-00di-0090000000-4c81b77566a3712a2980	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cembrene 40V, Negative-QTOF	splash10-0abi-0090000000-07fe9437e59eee3293a0	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular
Membrane

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00053024

Chemspider ID

24534211

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Cembrene A

METLIN ID

Not Available

PubChem Compound

11747713

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1568331

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Sawant SS, Sylvester PW, Avery MA, Desai P, Youssef DT, El Sayed KA: Bioactive rearranged and halogenated semisynthetic derivatives of the marine natural product sarcophine. J Nat Prod. 2004 Dec;67(12):2017-23. [PubMed:15620244 ]
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 Cembrene (HMDB0036845)

MOL for HMDB0036845 (Cembrene)

3D MOL for HMDB0036845 (Cembrene)

3D SDF for HMDB0036845 (Cembrene)

3D-SDF for HMDB0036845 (Cembrene)

PDB for HMDB0036845 (Cembrene)

3D PDB for HMDB0036845 (Cembrene)

SMILES for HMDB0036845 (Cembrene)

INCHI for HMDB0036845 (Cembrene)

Structure for HMDB0036845 (Cembrene)

3D Structure for HMDB0036845 (Cembrene)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra