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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 09:21:45 UTC

Update Date

2021-09-26 23:03:59 UTC

HMDB ID

HMDB0251767

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Embelin

Description

embelin, also known as embelic acid or embelate, belongs to the class of organic compounds known as p-benzoquinones. These are benzoquinones where the two C=O groups are attached at the 1- and 4-positions, respectively. embelin is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on embelin. This compound has been identified in human blood as reported by (PMID: 31557052 ). Embelin is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Embelin is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

HMDB0251767
     RDKit          3D
Embelin
 47 47  0  0  0  0  0  0  0  0999 V2000
    6.3404    0.7284   -0.0722 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1364    1.1571   -0.8804 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1961   -0.0016   -1.1540 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6960   -0.5870    0.1274 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9372    0.4015    0.9805 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7362    0.9558    0.3000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7816   -0.1311   -0.0867 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2981   -0.8842    1.1104 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6675   -1.9694    0.7109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9006   -1.4852    0.0041 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6363   -0.5348    0.9031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8842   -0.0119    0.2886 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0608   -0.2211    0.8601 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1152   -0.9452    2.0574 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2895    0.2899    0.2613 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4242    0.1082    0.7795 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2565    1.0485   -0.9885 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0909    1.2700   -1.5780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0438    1.9903   -2.7678 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8814    0.7472   -0.9561 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7823    0.9557   -1.5114 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4118   -0.3666   -0.0849 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2837    1.1891   -0.4889 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2048    1.0763    0.9715 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5127    1.5988   -1.8243 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5670    1.9569   -0.3574 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4043    0.3730   -1.8107 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7526   -0.7717   -1.6951 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1437   -1.5169   -0.0229 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6093   -0.8676    0.7299 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6455   -0.0975    1.9151 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6431    1.2294    1.3161 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0199    1.5067   -0.6247 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2659    1.7031    0.9713 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2834   -0.8962   -0.7500 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0538    0.2678   -0.7041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2068   -0.2263    1.8646 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1604   -1.3361    1.6842 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1625   -2.6903    0.0058 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9074   -2.5875    1.6041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5451   -2.3546   -0.2913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5809   -0.9581   -0.9138 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8845   -0.9497    1.8909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9567    0.3413    1.0842 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2684   -1.9373    1.9913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1535    1.4377   -1.4521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2774    1.9955   -3.3975 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 13 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  2  0
 18 19  1  0
 18 20  1  0
 20 21  2  0
 20 12  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  2 26  1  0
  3 27  1  0
  3 28  1  0
  4 29  1  0
  4 30  1  0
  5 31  1  0
  5 32  1  0
  6 33  1  0
  6 34  1  0
  7 35  1  0
  7 36  1  0
  8 37  1  0
  8 38  1  0
  9 39  1  0
  9 40  1  0
 10 41  1  0
 10 42  1  0
 11 43  1  0
 11 44  1  0
 14 45  1  0
 17 46  1  0
 19 47  1  0
M  END


  Mrv0541 05041403262D          

 21 21  0  0  0  0            999 V2000
    3.5724    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8605    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8605    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5749    6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460    7.0125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  9  1  0  0  0  0
 11 10  1  0  0  0  0
 13 11  1  0  0  0  0
 14 12  2  0  0  0  0
 15 12  1  0  0  0  0
 16 13  1  0  0  0  0
 16 14  1  0  0  0  0
 17 13  2  0  0  0  0
 17 15  1  0  0  0  0
 18 14  1  0  0  0  0
 19 15  2  0  0  0  0
 20 16  2  0  0  0  0
 21 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0251767

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCCCCCCCC1=C(O)C(=O)C=C(O)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C17H26O4/c1-2-3-4-5-6-7-8-9-10-11-13-16(20)14(18)12-15(19)17(13)21/h12,18,21H,2-11H2,1H3

> <INCHI_KEY>
IRSFLDGTOHBADP-UHFFFAOYSA-N

> <FORMULA>
C17H26O4

> <MOLECULAR_WEIGHT>
294.3859

> <EXACT_MASS>
294.18310932

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
34.360065153816976

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2,5-dihydroxy-3-undecylcyclohexa-2,5-diene-1,4-dione

> <ALOGPS_LOGP>
4.15

> <JCHEM_LOGP>
4.8280355880000005

> <ALOGPS_LOGS>
-4.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.17146051642547

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.863080437337704

> <JCHEM_PKA_STRONGEST_BASIC>
-4.150606641108564

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
85.33069999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.27e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
embelin

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0251767
     RDKit          3D
Embelin
 47 47  0  0  0  0  0  0  0  0999 V2000
    6.3404    0.7284   -0.0722 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1364    1.1571   -0.8804 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1961   -0.0016   -1.1540 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6960   -0.5870    0.1274 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9372    0.4015    0.9805 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7362    0.9558    0.3000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7816   -0.1311   -0.0867 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2981   -0.8842    1.1104 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6675   -1.9694    0.7109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9006   -1.4852    0.0041 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6363   -0.5348    0.9031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8842   -0.0119    0.2886 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0608   -0.2211    0.8601 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1152   -0.9452    2.0574 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2895    0.2899    0.2613 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4242    0.1082    0.7795 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2565    1.0485   -0.9885 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0909    1.2700   -1.5780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0438    1.9903   -2.7678 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8814    0.7472   -0.9561 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7823    0.9557   -1.5114 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4118   -0.3666   -0.0849 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2837    1.1891   -0.4889 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2048    1.0763    0.9715 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5127    1.5988   -1.8243 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5670    1.9569   -0.3574 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4043    0.3730   -1.8107 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7526   -0.7717   -1.6951 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1437   -1.5169   -0.0229 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6093   -0.8676    0.7299 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6455   -0.0975    1.9151 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6431    1.2294    1.3161 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0199    1.5067   -0.6247 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2659    1.7031    0.9713 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2834   -0.8962   -0.7500 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0538    0.2678   -0.7041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2068   -0.2263    1.8646 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1604   -1.3361    1.6842 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1625   -2.6903    0.0058 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9074   -2.5875    1.6041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5451   -2.3546   -0.2913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5809   -0.9581   -0.9138 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8845   -0.9497    1.8909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9567    0.3413    1.0842 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2684   -1.9373    1.9913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1535    1.4377   -1.4521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2774    1.9955   -3.3975 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 13 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  2  0
 18 19  1  0
 18 20  1  0
 20 21  2  0
 20 12  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  2 26  1  0
  3 27  1  0
  3 28  1  0
  4 29  1  0
  4 30  1  0
  5 31  1  0
  5 32  1  0
  6 33  1  0
  6 34  1  0
  7 35  1  0
  7 36  1  0
  8 37  1  0
  8 38  1  0
  9 39  1  0
  9 40  1  0
 10 41  1  0
 10 42  1  0
 11 43  1  0
 11 44  1  0
 14 45  1  0
 17 46  1  0
 19 47  1  0
M  END

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   13                                                       
CONECT   12   14   15                                                       
CONECT   13   11   16   17                                                  
CONECT   14   12   16   18                                                  
CONECT   15   12   17   19                                                  
CONECT   16   13   14   20                                                  
CONECT   17   13   15   21                                                  
CONECT   18   14                                                            
CONECT   19   15                                                            
CONECT   20   16                                                            
CONECT   21   17                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

COMPND    HMDB0251767
HETATM    1  C1  UNL     1       6.340   0.728  -0.072  1.00  0.00           C  
HETATM    2  C2  UNL     1       5.136   1.157  -0.880  1.00  0.00           C  
HETATM    3  C3  UNL     1       4.196  -0.002  -1.154  1.00  0.00           C  
HETATM    4  C4  UNL     1       3.696  -0.587   0.127  1.00  0.00           C  
HETATM    5  C5  UNL     1       2.937   0.401   0.981  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.736   0.956   0.300  1.00  0.00           C  
HETATM    7  C7  UNL     1       0.782  -0.131  -0.087  1.00  0.00           C  
HETATM    8  C8  UNL     1       0.298  -0.884   1.110  1.00  0.00           C  
HETATM    9  C9  UNL     1      -0.668  -1.969   0.711  1.00  0.00           C  
HETATM   10  C10 UNL     1      -1.901  -1.485   0.004  1.00  0.00           C  
HETATM   11  C11 UNL     1      -2.636  -0.535   0.903  1.00  0.00           C  
HETATM   12  C12 UNL     1      -3.884  -0.012   0.289  1.00  0.00           C  
HETATM   13  C13 UNL     1      -5.061  -0.221   0.860  1.00  0.00           C  
HETATM   14  O1  UNL     1      -5.115  -0.945   2.057  1.00  0.00           O  
HETATM   15  C14 UNL     1      -6.289   0.290   0.261  1.00  0.00           C  
HETATM   16  O2  UNL     1      -7.424   0.108   0.779  1.00  0.00           O  
HETATM   17  C15 UNL     1      -6.257   1.049  -0.989  1.00  0.00           C  
HETATM   18  C16 UNL     1      -5.091   1.270  -1.578  1.00  0.00           C  
HETATM   19  O3  UNL     1      -5.044   1.990  -2.768  1.00  0.00           O  
HETATM   20  C17 UNL     1      -3.881   0.747  -0.956  1.00  0.00           C  
HETATM   21  O4  UNL     1      -2.782   0.956  -1.511  1.00  0.00           O  
HETATM   22  H1  UNL     1       6.412  -0.367  -0.085  1.00  0.00           H  
HETATM   23  H2  UNL     1       7.284   1.189  -0.489  1.00  0.00           H  
HETATM   24  H3  UNL     1       6.205   1.076   0.972  1.00  0.00           H  
HETATM   25  H4  UNL     1       5.513   1.599  -1.824  1.00  0.00           H  
HETATM   26  H5  UNL     1       4.567   1.957  -0.357  1.00  0.00           H  
HETATM   27  H6  UNL     1       3.404   0.373  -1.811  1.00  0.00           H  
HETATM   28  H7  UNL     1       4.753  -0.772  -1.695  1.00  0.00           H  
HETATM   29  H8  UNL     1       3.144  -1.517  -0.023  1.00  0.00           H  
HETATM   30  H9  UNL     1       4.609  -0.868   0.730  1.00  0.00           H  
HETATM   31  H10 UNL     1       2.645  -0.097   1.915  1.00  0.00           H  
HETATM   32  H11 UNL     1       3.643   1.229   1.316  1.00  0.00           H  
HETATM   33  H12 UNL     1       2.020   1.507  -0.625  1.00  0.00           H  
HETATM   34  H13 UNL     1       1.266   1.703   0.971  1.00  0.00           H  
HETATM   35  H14 UNL     1       1.283  -0.896  -0.750  1.00  0.00           H  
HETATM   36  H15 UNL     1      -0.054   0.268  -0.704  1.00  0.00           H  
HETATM   37  H16 UNL     1      -0.207  -0.226   1.865  1.00  0.00           H  
HETATM   38  H17 UNL     1       1.160  -1.336   1.684  1.00  0.00           H  
HETATM   39  H18 UNL     1      -0.162  -2.690   0.006  1.00  0.00           H  
HETATM   40  H19 UNL     1      -0.907  -2.588   1.604  1.00  0.00           H  
HETATM   41  H20 UNL     1      -2.545  -2.355  -0.291  1.00  0.00           H  
HETATM   42  H21 UNL     1      -1.581  -0.958  -0.914  1.00  0.00           H  
HETATM   43  H22 UNL     1      -2.885  -0.950   1.891  1.00  0.00           H  
HETATM   44  H23 UNL     1      -1.957   0.341   1.084  1.00  0.00           H  
HETATM   45  H24 UNL     1      -5.268  -1.937   1.991  1.00  0.00           H  
HETATM   46  H25 UNL     1      -7.154   1.438  -1.452  1.00  0.00           H  
HETATM   47  H26 UNL     1      -4.277   1.995  -3.397  1.00  0.00           H  
CONECT    1    2   22   23   24
CONECT    2    3   25   26
CONECT    3    4   27   28
CONECT    4    5   29   30
CONECT    5    6   31   32
CONECT    6    7   33   34
CONECT    7    8   35   36
CONECT    8    9   37   38
CONECT    9   10   39   40
CONECT   10   11   41   42
CONECT   11   12   43   44
CONECT   12   13   13   20
CONECT   13   14   15
CONECT   14   45
CONECT   15   16   16   17
CONECT   17   18   18   46
CONECT   18   19   20
CONECT   19   47
CONECT   20   21   21
END

HMDB0251767
     RDKit          3D
Embelin
 47 47  0  0  0  0  0  0  0  0999 V2000
    6.3404    0.7284   -0.0722 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1364    1.1571   -0.8804 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1961   -0.0016   -1.1540 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6960   -0.5870    0.1274 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9372    0.4015    0.9805 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7362    0.9558    0.3000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7816   -0.1311   -0.0867 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2981   -0.8842    1.1104 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6675   -1.9694    0.7109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9006   -1.4852    0.0041 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6363   -0.5348    0.9031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8842   -0.0119    0.2886 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0608   -0.2211    0.8601 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1152   -0.9452    2.0574 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2895    0.2899    0.2613 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4242    0.1082    0.7795 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2565    1.0485   -0.9885 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0909    1.2700   -1.5780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0438    1.9903   -2.7678 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8814    0.7472   -0.9561 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7823    0.9557   -1.5114 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4118   -0.3666   -0.0849 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2837    1.1891   -0.4889 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2048    1.0763    0.9715 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5127    1.5988   -1.8243 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5670    1.9569   -0.3574 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4043    0.3730   -1.8107 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7526   -0.7717   -1.6951 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1437   -1.5169   -0.0229 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6093   -0.8676    0.7299 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6455   -0.0975    1.9151 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6431    1.2294    1.3161 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0199    1.5067   -0.6247 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2659    1.7031    0.9713 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2834   -0.8962   -0.7500 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0538    0.2678   -0.7041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2068   -0.2263    1.8646 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1604   -1.3361    1.6842 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1625   -2.6903    0.0058 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9074   -2.5875    1.6041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5451   -2.3546   -0.2913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5809   -0.9581   -0.9138 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8845   -0.9497    1.8909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9567    0.3413    1.0842 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2684   -1.9373    1.9913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1535    1.4377   -1.4521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2774    1.9955   -3.3975 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 13 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  2  0
 18 19  1  0
 18 20  1  0
 20 21  2  0
 20 12  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  2 26  1  0
  3 27  1  0
  3 28  1  0
  4 29  1  0
  4 30  1  0
  5 31  1  0
  5 32  1  0
  6 33  1  0
  6 34  1  0
  7 35  1  0
  7 36  1  0
  8 37  1  0
  8 38  1  0
  9 39  1  0
  9 40  1  0
 10 41  1  0
 10 42  1  0
 11 43  1  0
 11 44  1  0
 14 45  1  0
 17 46  1  0
 19 47  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
2,5-Dihydroxy-3-undecyl-1,4-benzoquinone	ChEBI
Embelic acid	ChEBI
Emberine	ChEBI
Embelate	Generator
Potassium embelate	MeSH

Chemical Formula

C₁₇H₂₆O₄

Average Molecular Weight

294.3859

Monoisotopic Molecular Weight

294.18310932

IUPAC Name

2,5-dihydroxy-3-undecylcyclohexa-2,5-diene-1,4-dione

Traditional Name

embelin

CAS Registry Number

Not Available

SMILES

CCCCCCCCCCCC1=C(O)C(=O)C=C(O)C1=O

InChI Identifier

InChI=1S/C17H26O4/c1-2-3-4-5-6-7-8-9-10-11-13-16(20)14(18)12-15(19)17(13)21/h12,18,21H,2-11H2,1H3

InChI Key

IRSFLDGTOHBADP-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as p-benzoquinones. These are benzoquinones where the two C=O groups are attached at the 1- and 4-positions, respectively.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

P-benzoquinones

Alternative Parents

Substituents

P-benzoquinone
Vinylogous acid
Enol
Organic oxide
Hydrocarbon derivative
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

hydroxybenzoquinone (CHEBI:4778 )

Ontology

Not Available

Non-excretory biofluid

Blood (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	4.15	ALOGPS
logP	4.83	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	7.86	ChemAxon
pKa (Strongest Basic)	-4.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	74.6 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	85.33 m³·mol⁻¹	ChemAxon
Polarizability	34.36 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	178.976	30932474
DeepCCS	[M-H]-	176.426	30932474
DeepCCS	[M-2H]-	209.797	30932474
DeepCCS	[M+Na]+	186.422	30932474
AllCCS	[M+H]+	175.5	32859911
AllCCS	[M+H-H2O]+	172.3	32859911
AllCCS	[M+NH4]+	178.5	32859911
AllCCS	[M+Na]+	179.4	32859911
AllCCS	[M-H]-	176.6	32859911
AllCCS	[M+Na-2H]-	177.2	32859911
AllCCS	[M+HCOO]-	177.9	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Embelin	CCCCCCCCCCCC1=C(O)C(=O)C=C(O)C1=O	3553.9	Standard polar	33892256
Embelin	CCCCCCCCCCCC1=C(O)C(=O)C=C(O)C1=O	2098.9	Standard non polar	33892256
Embelin	CCCCCCCCCCCC1=C(O)C(=O)C=C(O)C1=O	2122.7	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 - Embelin GC-MS (Non-derivatized) - 70eV, Positive	splash10-0007-9640000000-98236f099b36aef40111	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Embelin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Embelin GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Embelin GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Embelin GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Embelin GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Embelin GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Embelin GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-04	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 - Embelin 10V, Positive-QTOF	splash10-0002-0190000000-38305f4c2686a873f852	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Embelin 20V, Positive-QTOF	splash10-0ku2-7950000000-1303ed01303544b38171	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Embelin 40V, Positive-QTOF	splash10-0kam-9300000000-26ea50fcce46c80e621e	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Embelin 10V, Negative-QTOF	splash10-0006-0090000000-e197a5daaa2e8a467436	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Embelin 20V, Negative-QTOF	splash10-0006-1590000000-288acd409ad5d51f1650	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Embelin 40V, Negative-QTOF	splash10-006w-3950000000-28db96f109e4153d41dc	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

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

C00002822

Chemspider ID

3105

KEGG Compound ID

C10342

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Embelin

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

4778

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1064301

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for Embelin (HMDB0251767)

MOL for HMDB0251767 (Embelin)

3D MOL for HMDB0251767 (Embelin)

3D SDF for HMDB0251767 (Embelin)

3D-SDF for HMDB0251767 (Embelin)

PDB for HMDB0251767 (Embelin)

3D PDB for HMDB0251767 (Embelin)

SMILES for HMDB0251767 (Embelin)

INCHI for HMDB0251767 (Embelin)

Structure for HMDB0251767 (Embelin)

3D Structure for HMDB0251767 (Embelin)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra