Hmdb loader

Showing metabocard for Cembrene (HMDB0036845)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 22:01:28 UTC
Update Date2022-03-07 02:55:05 UTC
HMDB IDHMDB0036845
Secondary Accession Numbers
  • HMDB36845
Metabolite Identification
Common NameCembrene
DescriptionCembrene, 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0036845 (Cembrene)


  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
Download

3D MOL for HMDB0036845 (Cembrene)

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
Download

3D SDF for HMDB0036845 (Cembrene)


  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

$$$$
Download

3D-SDF for HMDB0036845 (Cembrene)

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
Download

PDB for HMDB0036845 (Cembrene)

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
Download

3D PDB for HMDB0036845 (Cembrene)

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
Download

SMILES for HMDB0036845 (Cembrene)

CC(C)[C@@H]1CC\C(C)=C\CC\C(C)=C\C\C=C(\C)/C=C/1
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INCHI for HMDB0036845 (Cembrene)

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
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View in JSmolView Stereo Labels
Synonyms
ValueSource
ThunbergeneHMDB
(1E,3Z,6E,10E,14S)-3,7,11-Trimethyl-14-(1-methylethyl)-1,3,6,10-cyclotetradecatetraeneHMDB
(+)-CembreneHMDB
(+)-ThunbergeneHMDB
(S)-(+)-CembreneHMDB
1(S)-CembreneHMDB
ThunbergenHMDB
Chemical FormulaC20H32
Average Molecular Weight272.4681
Monoisotopic Molecular Weight272.250401024
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 Number1898-13-1
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 KeyDMHADBQKVWXPPM-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.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassDiterpenoids
Direct ParentCembrane diterpenoids
Alternative Parents
Substituents
  • Cembrane diterpenoid
  • Branched unsaturated hydrocarbon
  • Cyclic olefin
  • Unsaturated aliphatic hydrocarbon
  • Unsaturated hydrocarbon
  • Olefin
  • Hydrocarbon
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point58 - 59 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility7.0e-05 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.002 g/LALOGPS
logP6.9ALOGPS
logP6.52ChemAxon
logS-5.1ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity95.42 m³·mol⁻¹ChemAxon
Polarizability34.93 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+176.0530932474
DeepCCS[M-H]-173.69230932474
DeepCCS[M-2H]-207.90530932474
DeepCCS[M+Na]+183.10630932474
AllCCS[M+H]+168.032859911
AllCCS[M+H-H2O]+164.432859911
AllCCS[M+NH4]+171.432859911
AllCCS[M+Na]+172.332859911
AllCCS[M-H]-179.032859911
AllCCS[M+Na-2H]-179.632859911
AllCCS[M+HCOO]-180.432859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
CembreneCC(C)[C@@H]1CC\C(C)=C\CC\C(C)=C\C\C=C(\C)/C=C/12250.7Standard polar33892256
CembreneCC(C)[C@@H]1CC\C(C)=C\CC\C(C)=C\C\C=C(\C)/C=C/11950.4Standard non polar33892256
CembreneCC(C)[C@@H]1CC\C(C)=C\CC\C(C)=C\C\C=C(\C)/C=C/11959.3Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - Cembrene GC-MS (Non-derivatized)splash10-054o-9800000000-eeae686283d72746a9582014-06-16HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cembrene GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cembrene 10V, Positive-QTOFsplash10-00di-0090000000-d10590d89514cc99f1e22021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cembrene 20V, Positive-QTOFsplash10-00e9-0090000000-3609ade1f226129e72f22021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cembrene 40V, Positive-QTOFsplash10-0006-9000000000-1721daf5b5a2632b9ef72021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cembrene 10V, Negative-QTOFsplash10-00di-0090000000-4c81b77566a3712a29802021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cembrene 20V, Negative-QTOFsplash10-00di-0090000000-4c81b77566a3712a29802021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cembrene 40V, Negative-QTOFsplash10-0abi-0090000000-07fe9437e59eee3293a02021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
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 IDNot Available
KNApSAcK IDC00053024
Chemspider ID24534211
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkCembrene A
METLIN IDNot Available
PubChem Compound11747713
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1568331
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]
  2. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  3. 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 ]
  4. 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 ]
  5. 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 ]
  6. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
  7. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.