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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 02:12:29 UTC

Update Date

2022-03-07 02:56:40 UTC

HMDB ID

HMDB0040646

Secondary Accession Numbers

HMDB40646

Metabolite Identification

Common Name

Myrsinone

Description

Myrsinone belongs to the class of organic compounds known as ubiquinones. These are coenzyme Q derivatives containing a 5, 6-dimethoxy-3-methyl(1,4-benzoquinone) moiety to which an isoprenyl group is attached at ring position 2(or 6). Based on a literature review a small amount of articles have been published on Myrsinone.

Structure

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

HMDB0040646
     RDKit          3D
Myrsinone
 47 47  0  0  0  0  0  0  0  0999 V2000
    6.7657   -0.2612   -0.1473 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9543   -0.5027    1.1045 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7676    0.4299    1.0726 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8960    0.1856   -0.1414 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7242    1.1157   -0.1611 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8086    0.9405   -1.3318 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2037   -0.4057   -1.4300 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3694   -0.8570   -0.2978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8267   -0.0376    0.0289 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5518   -0.6459    1.2038 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7898    0.0318    1.6242 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9232   -0.0410    0.6797 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8996   -0.7457   -0.4153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0711   -0.7688   -1.3207 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0055   -1.4613   -2.3661 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2564   -0.0069   -0.9960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3636   -0.0261   -1.8476 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2886    0.7104    0.1134 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4456    1.4407    0.4092 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1589    0.7311    0.9835 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1873    1.4141    2.0415 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7208   -0.8108   -0.0270 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9649    0.8004   -0.3206 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2618   -0.7062   -1.0272 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5694   -1.5402    1.1029 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5390   -0.2586    2.0025 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2090    0.3475    2.0218 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1439    1.4832    1.0297 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5373    0.4040   -1.0355 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6531   -0.8691   -0.1749 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0890    2.1673   -0.1824 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1934    1.0047    0.8078 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0533    1.7683   -1.2327 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3514    1.1484   -2.2772 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5608   -0.4110   -2.3564 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0101   -1.1369   -1.6406 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0087   -1.8922   -0.4842 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9989   -0.9331    0.6148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4938    0.1327   -0.8048 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5637    0.9938    0.3956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8231   -1.7172    0.9494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8419   -0.7894    2.0754 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6356    1.1106    1.8971 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1519   -0.4952    2.5617 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0342   -1.3681   -0.6718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7189   -0.9277   -2.1549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3233    1.2547   -0.0922 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
 14 15  2  0
 14 16  1  0
 16 17  1  0
 16 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
 13 45  1  0
 17 46  1  0
 19 47  1  0
M  END


  Mrv0541 05061312002D          

 21 21  0  0  0  0            999 V2000
    2.1434   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -6.6000    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   -6.6000    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   -6.6000    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   -6.6000    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
   10.7171   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171   -7.8375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881   -7.8375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460   -7.8375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171   -8.6625    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
 13 12  2  0  0  0  0
 14 12  1  0  0  0  0
 15 13  1  0  0  0  0
 16 14  1  0  0  0  0
 17 15  1  0  0  0  0
 17 16  2  0  0  0  0
 18 14  2  0  0  0  0
 19 15  2  0  0  0  0
 20 16  1  0  0  0  0
 21 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0040646

> <DATABASE_NAME>
hmdb

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

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

> <INCHI_KEY>
JPFXYNDBKFIYLX-UHFFFAOYSA-N

> <FORMULA>
C17H26O4

> <MOLECULAR_WEIGHT>
294.3859

> <EXACT_MASS>
294.18310932

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
34.57723501510914

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
4.28

> <JCHEM_LOGP>
4.8280355880000005

> <ALOGPS_LOGS>
-4.88

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.31285030428159

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.009260551963592

> <JCHEM_PKA_STRONGEST_BASIC>
-4.086790698805616

> <JCHEM_POLAR_SURFACE_AREA>
74.60000000000001

> <JCHEM_REFRACTIVITY>
85.33069999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.85e-03 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0040646
     RDKit          3D
Myrsinone
 47 47  0  0  0  0  0  0  0  0999 V2000
    6.7657   -0.2612   -0.1473 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9543   -0.5027    1.1045 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7676    0.4299    1.0726 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8960    0.1856   -0.1414 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7242    1.1157   -0.1611 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8086    0.9405   -1.3318 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2037   -0.4057   -1.4300 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3694   -0.8570   -0.2978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8267   -0.0376    0.0289 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5518   -0.6459    1.2038 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7898    0.0318    1.6242 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9232   -0.0410    0.6797 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8996   -0.7457   -0.4153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0711   -0.7688   -1.3207 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0055   -1.4613   -2.3661 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2564   -0.0069   -0.9960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3636   -0.0261   -1.8476 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2886    0.7104    0.1134 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4456    1.4407    0.4092 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1589    0.7311    0.9835 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1873    1.4141    2.0415 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7208   -0.8108   -0.0270 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9649    0.8004   -0.3206 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2618   -0.7062   -1.0272 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5694   -1.5402    1.1029 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5390   -0.2586    2.0025 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2090    0.3475    2.0218 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1439    1.4832    1.0297 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5373    0.4040   -1.0355 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6531   -0.8691   -0.1749 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0890    2.1673   -0.1824 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1934    1.0047    0.8078 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0533    1.7683   -1.2327 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3514    1.1484   -2.2772 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5608   -0.4110   -2.3564 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0101   -1.1369   -1.6406 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0087   -1.8922   -0.4842 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9989   -0.9331    0.6148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4938    0.1327   -0.8048 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5637    0.9938    0.3956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8231   -1.7172    0.9494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8419   -0.7894    2.0754 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6356    1.1106    1.8971 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1519   -0.4952    2.5617 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0342   -1.3681   -0.6718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7189   -0.9277   -2.1549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3233    1.2547   -0.0922 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
 14 15  2  0
 14 16  1  0
 16 17  1  0
 16 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
 13 45  1  0
 17 46  1  0
 19 47  1  0
M  END

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       4.001 -11.550   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335 -12.320   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.668 -11.550   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.002 -12.320   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.336 -11.550   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.669 -12.320   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.003 -11.550   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      13.337 -12.320   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.671 -11.550   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      16.004 -12.320   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      17.338 -11.550   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      20.005 -11.550   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      18.672 -12.320   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      21.339 -12.320   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      18.672 -13.860   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      21.339 -13.860   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      20.005 -14.630   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      22.673 -11.550   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      17.338 -14.630   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      22.673 -14.630   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      20.005 -16.170   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   13   14                                                       
CONECT   13   11   12   15                                                  
CONECT   14   12   16   18                                                  
CONECT   15   13   17   19                                                  
CONECT   16   14   17   20                                                  
CONECT   17   15   16   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    HMDB0040646
HETATM    1  C1  UNL     1       6.766  -0.261  -0.147  1.00  0.00           C  
HETATM    2  C2  UNL     1       5.954  -0.503   1.104  1.00  0.00           C  
HETATM    3  C3  UNL     1       4.768   0.430   1.073  1.00  0.00           C  
HETATM    4  C4  UNL     1       3.896   0.186  -0.141  1.00  0.00           C  
HETATM    5  C5  UNL     1       2.724   1.116  -0.161  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.809   0.940  -1.332  1.00  0.00           C  
HETATM    7  C7  UNL     1       1.204  -0.406  -1.430  1.00  0.00           C  
HETATM    8  C8  UNL     1       0.369  -0.857  -0.298  1.00  0.00           C  
HETATM    9  C9  UNL     1      -0.827  -0.038   0.029  1.00  0.00           C  
HETATM   10  C10 UNL     1      -1.552  -0.646   1.204  1.00  0.00           C  
HETATM   11  C11 UNL     1      -2.790   0.032   1.624  1.00  0.00           C  
HETATM   12  C12 UNL     1      -3.923  -0.041   0.680  1.00  0.00           C  
HETATM   13  C13 UNL     1      -3.900  -0.746  -0.415  1.00  0.00           C  
HETATM   14  C14 UNL     1      -5.071  -0.769  -1.321  1.00  0.00           C  
HETATM   15  O1  UNL     1      -5.005  -1.461  -2.366  1.00  0.00           O  
HETATM   16  C15 UNL     1      -6.256  -0.007  -0.996  1.00  0.00           C  
HETATM   17  O2  UNL     1      -7.364  -0.026  -1.848  1.00  0.00           O  
HETATM   18  C16 UNL     1      -6.289   0.710   0.113  1.00  0.00           C  
HETATM   19  O3  UNL     1      -7.446   1.441   0.409  1.00  0.00           O  
HETATM   20  C17 UNL     1      -5.159   0.731   0.984  1.00  0.00           C  
HETATM   21  O4  UNL     1      -5.187   1.414   2.041  1.00  0.00           O  
HETATM   22  H1  UNL     1       7.721  -0.811  -0.027  1.00  0.00           H  
HETATM   23  H2  UNL     1       6.965   0.800  -0.321  1.00  0.00           H  
HETATM   24  H3  UNL     1       6.262  -0.706  -1.027  1.00  0.00           H  
HETATM   25  H4  UNL     1       5.569  -1.540   1.103  1.00  0.00           H  
HETATM   26  H5  UNL     1       6.539  -0.259   2.002  1.00  0.00           H  
HETATM   27  H6  UNL     1       4.209   0.347   2.022  1.00  0.00           H  
HETATM   28  H7  UNL     1       5.144   1.483   1.030  1.00  0.00           H  
HETATM   29  H8  UNL     1       4.537   0.404  -1.036  1.00  0.00           H  
HETATM   30  H9  UNL     1       3.653  -0.869  -0.175  1.00  0.00           H  
HETATM   31  H10 UNL     1       3.089   2.167  -0.182  1.00  0.00           H  
HETATM   32  H11 UNL     1       2.193   1.005   0.808  1.00  0.00           H  
HETATM   33  H12 UNL     1       1.053   1.768  -1.233  1.00  0.00           H  
HETATM   34  H13 UNL     1       2.351   1.148  -2.277  1.00  0.00           H  
HETATM   35  H14 UNL     1       0.561  -0.411  -2.356  1.00  0.00           H  
HETATM   36  H15 UNL     1       2.010  -1.137  -1.641  1.00  0.00           H  
HETATM   37  H16 UNL     1       0.009  -1.892  -0.484  1.00  0.00           H  
HETATM   38  H17 UNL     1       0.999  -0.933   0.615  1.00  0.00           H  
HETATM   39  H18 UNL     1      -1.494   0.133  -0.805  1.00  0.00           H  
HETATM   40  H19 UNL     1      -0.564   0.994   0.396  1.00  0.00           H  
HETATM   41  H20 UNL     1      -1.823  -1.717   0.949  1.00  0.00           H  
HETATM   42  H21 UNL     1      -0.842  -0.789   2.075  1.00  0.00           H  
HETATM   43  H22 UNL     1      -2.636   1.111   1.897  1.00  0.00           H  
HETATM   44  H23 UNL     1      -3.152  -0.495   2.562  1.00  0.00           H  
HETATM   45  H24 UNL     1      -3.034  -1.368  -0.672  1.00  0.00           H  
HETATM   46  H25 UNL     1      -7.719  -0.928  -2.155  1.00  0.00           H  
HETATM   47  H26 UNL     1      -8.323   1.255  -0.092  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   45
CONECT   14   15   15   16
CONECT   16   17   18   18
CONECT   17   46
CONECT   18   19   20
CONECT   19   47
CONECT   20   21   21
END

HMDB0040646
     RDKit          3D
Myrsinone
 47 47  0  0  0  0  0  0  0  0999 V2000
    6.7657   -0.2612   -0.1473 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9543   -0.5027    1.1045 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7676    0.4299    1.0726 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8960    0.1856   -0.1414 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7242    1.1157   -0.1611 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8086    0.9405   -1.3318 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2037   -0.4057   -1.4300 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3694   -0.8570   -0.2978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8267   -0.0376    0.0289 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5518   -0.6459    1.2038 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7898    0.0318    1.6242 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9232   -0.0410    0.6797 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8996   -0.7457   -0.4153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0711   -0.7688   -1.3207 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0055   -1.4613   -2.3661 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2564   -0.0069   -0.9960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3636   -0.0261   -1.8476 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2886    0.7104    0.1134 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4456    1.4407    0.4092 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1589    0.7311    0.9835 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1873    1.4141    2.0415 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7208   -0.8108   -0.0270 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9649    0.8004   -0.3206 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2618   -0.7062   -1.0272 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5694   -1.5402    1.1029 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5390   -0.2586    2.0025 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2090    0.3475    2.0218 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1439    1.4832    1.0297 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5373    0.4040   -1.0355 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6531   -0.8691   -0.1749 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0890    2.1673   -0.1824 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1934    1.0047    0.8078 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0533    1.7683   -1.2327 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3514    1.1484   -2.2772 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5608   -0.4110   -2.3564 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0101   -1.1369   -1.6406 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0087   -1.8922   -0.4842 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9989   -0.9331    0.6148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4938    0.1327   -0.8048 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5637    0.9938    0.3956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8231   -1.7172    0.9494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8419   -0.7894    2.0754 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6356    1.1106    1.8971 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1519   -0.4952    2.5617 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0342   -1.3681   -0.6718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7189   -0.9277   -2.1549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3233    1.2547   -0.0922 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
 14 15  2  0
 14 16  1  0
 16 17  1  0
 16 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
 13 45  1  0
 17 46  1  0
 19 47  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
2,3-Dihydroxy-5-undecyl-2,5-cyclohexadiene-1,4-dione, 9ci	HMDB

Chemical Formula

C₁₇H₂₆O₄

Average Molecular Weight

294.3859

Monoisotopic Molecular Weight

294.18310932

IUPAC Name

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

Traditional Name

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

CAS Registry Number

145040-57-9

SMILES

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

InChI Identifier

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

InChI Key

JPFXYNDBKFIYLX-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as ubiquinones. These are coenzyme Q derivatives containing a 5, 6-dimethoxy-3-methyl(1,4-benzoquinone) moiety to which an isoprenyl group is attached at ring position 2(or 6).

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Quinone and hydroquinone lipids

Direct Parent

Ubiquinones

Alternative Parents

Substituents

Ubiquinone skeleton
Quinone
P-benzoquinone
Vinylogous acid
Cyclic ketone
Ketone
Enediol
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
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: HMDB0040646)

Source

Endogenous

Endogenous (HMDB: HMDB0040646)

Animal

Animal (HMDB: HMDB0040646)

Exogenous

Food

Food (HMDB: HMDB0040646)

Exogenous (HMDB: HMDB0040646)

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid Peroxidation (HMDB: HMDB0040646)

Biochemical pathway

Metabolic pathway

Fatty Acid Metabolism (HMDB: HMDB0040646)

Lipid metabolism pathway (HMDB: HMDB0040646)

Cellular process

Cell signaling (HMDB: HMDB0040646)

Biochemical process

Lipid transport (HMDB: HMDB0040646)

Role

Biological role

Energy source (HMDB: HMDB0040646)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	120 - 122 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	1.15 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	0.0038 g/L	ALOGPS
logP	4.28	ALOGPS
logP	4.83	ChemAxon
logS	-4.9	ALOGPS
pKa (Strongest Acidic)	8.01	ChemAxon
pKa (Strongest Basic)	-4.1	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	34.58 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
DarkChem	[M+H]+	174.219	31661259
DarkChem	[M-H]-	172.785	31661259
DeepCCS	[M+H]+	178.379	30932474
DeepCCS	[M-H]-	175.829	30932474
DeepCCS	[M-2H]-	209.436	30932474
DeepCCS	[M+Na]+	186.061	30932474
AllCCS	[M+H]+	175.7	32859911
AllCCS	[M+H-H2O]+	172.5	32859911
AllCCS	[M+NH4]+	178.7	32859911
AllCCS	[M+Na]+	179.5	32859911
AllCCS	[M-H]-	176.6	32859911
AllCCS	[M+Na-2H]-	177.1	32859911
AllCCS	[M+HCOO]-	177.9	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	10.39 minutes	32390414
Predicted by Siyang on May 30, 2022	20.7763 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	0.92 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	3191.9 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	578.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	228.9 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	316.9 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	540.5 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	1082.7 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	928.4 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	107.0 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1863.3 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	567.2 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1961.4 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	680.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	598.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	685.8 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	578.0 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	16.3 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Myrsinone	CCCCCCCCCCCC1=CC(=O)C(O)=C(O)C1=O	3516.1	Standard polar	33892256
Myrsinone	CCCCCCCCCCCC1=CC(=O)C(O)=C(O)C1=O	2095.8	Standard non polar	33892256
Myrsinone	CCCCCCCCCCCC1=CC(=O)C(O)=C(O)C1=O	2123.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Myrsinone,1TMS,isomer #1	CCCCCCCCCCCC1=CC(=O)C(O[Si](C)(C)C)=C(O)C1=O	2476.8	Semi standard non polar	33892256
Myrsinone,1TMS,isomer #2	CCCCCCCCCCCC1=CC(=O)C(O)=C(O[Si](C)(C)C)C1=O	2488.5	Semi standard non polar	33892256
Myrsinone,2TMS,isomer #1	CCCCCCCCCCCC1=CC(=O)C(O[Si](C)(C)C)=C(O[Si](C)(C)C)C1=O	2536.8	Semi standard non polar	33892256
Myrsinone,1TBDMS,isomer #1	CCCCCCCCCCCC1=CC(=O)C(O[Si](C)(C)C(C)(C)C)=C(O)C1=O	2760.9	Semi standard non polar	33892256
Myrsinone,1TBDMS,isomer #2	CCCCCCCCCCCC1=CC(=O)C(O)=C(O[Si](C)(C)C(C)(C)C)C1=O	2765.6	Semi standard non polar	33892256
Myrsinone,2TBDMS,isomer #1	CCCCCCCCCCCC1=CC(=O)C(O[Si](C)(C)C(C)(C)C)=C(O[Si](C)(C)C(C)(C)C)C1=O	3038.6	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 - Myrsinone GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a6r-9680000000-54fd3d2f599abb3cef56	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Myrsinone GC-MS (2 TMS) - 70eV, Positive	splash10-00dj-9604400000-6043594d0948b4167288	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Myrsinone 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 - Myrsinone 10V, Positive-QTOF	splash10-0002-0190000000-2532f91006677750200d	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Myrsinone 20V, Positive-QTOF	splash10-00mn-3960000000-b34136d8a7f011379595	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Myrsinone 40V, Positive-QTOF	splash10-054o-9620000000-34cd3714203286cc40db	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Myrsinone 10V, Negative-QTOF	splash10-0006-0090000000-75feb871888a755ab8d1	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Myrsinone 20V, Negative-QTOF	splash10-052o-0090000000-efd73fe35fab2777ad83	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Myrsinone 40V, Negative-QTOF	splash10-0a4i-6980000000-89e1d2710f8ea0eabd08	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Myrsinone 10V, Positive-QTOF	splash10-0002-0190000000-1c4491975c34be6e5735	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Myrsinone 20V, Positive-QTOF	splash10-0ka5-8920000000-45b6ee73dc5355b49da2	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Myrsinone 40V, Positive-QTOF	splash10-0pba-9400000000-e5b7b7f1625148a18079	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Myrsinone 10V, Negative-QTOF	splash10-0006-1090000000-c9d4e7fb5074354944ae	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Myrsinone 20V, Negative-QTOF	splash10-0006-0190000000-bc9915369b6d469d46ad	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Myrsinone 40V, Negative-QTOF	splash10-0a4i-3940000000-e17f02c89ede3d1bba99	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

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

FDB020439

KNApSAcK ID

C00057067

Chemspider ID

30777500

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

137177207

PDB ID

Not Available

ChEBI ID

174796

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1885041

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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

Showing metabocard for Myrsinone (HMDB0040646)

MOL for HMDB0040646 (Myrsinone)

3D MOL for HMDB0040646 (Myrsinone)

3D SDF for HMDB0040646 (Myrsinone)

3D-SDF for HMDB0040646 (Myrsinone)

PDB for HMDB0040646 (Myrsinone)

3D PDB for HMDB0040646 (Myrsinone)

SMILES for HMDB0040646 (Myrsinone)

INCHI for HMDB0040646 (Myrsinone)

Structure for HMDB0040646 (Myrsinone)

3D Structure for HMDB0040646 (Myrsinone)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra