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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (2) Show 2 proteins XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-05-17 00:55:50 UTC

Update Date

2022-03-07 03:17:43 UTC

HMDB ID

HMDB0060353

Secondary Accession Numbers

HMDB60353

Metabolite Identification

Common Name

2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone

Description

2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone belongs to the class of organic compounds known as prenylquinones. These are quinones with a structure characterized by the quinone ring substituted by an prenyl side-chain. 2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

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

HMDB0060353
     RDKit          3D
2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone
 45 45  0  0  0  0  0  0  0  0999 V2000
    6.4540    1.7512    1.9828 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0331    1.8509    1.8561 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4030    1.2439    0.7691 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8518    1.4416   -0.4593 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2269    0.8296   -1.6226 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6487    1.0134   -2.7942 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0450   -0.0526   -1.4725 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4134   -0.6794   -2.6509 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6120   -0.2399   -0.2599 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4235   -1.1127    0.0062 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3587   -0.3831    0.6943 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8638   -0.2930    0.1711 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1492   -0.9335   -1.1114 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9086    0.4810    0.8716 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1149   -0.2682    1.3213 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9132   -0.9251    0.2765 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1670   -0.5224    0.0774 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7535    0.5903    0.9132 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0155   -1.1548   -0.9670 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2436    0.3799    0.9273 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7999    0.1779    2.0881 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9075    2.2140    1.0796 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7105    0.6565    1.9293 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7758    2.2084    2.9200 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7162    2.0866   -0.5714 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5805   -0.0595   -3.0601 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1786   -1.7425   -2.5474 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1922   -0.6308   -3.4751 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1121   -1.7002   -0.8474 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8164   -1.8707    0.7520 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5109    0.1154    1.6563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3639   -2.0191   -1.0480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3608   -0.7600   -1.8796 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0566   -0.4497   -1.5587 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2851    1.2229    0.0944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4747    1.1109    1.6933 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8438   -1.0430    2.1015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7696    0.4711    1.8650 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5769   -1.7308   -0.3457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7990    0.2999    1.9807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7680    0.8331    0.5402 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1444    1.5172    0.7821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8841   -0.4954   -1.2011 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4003   -1.2878   -1.8785 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4008   -2.1416   -0.6283 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  3
 17 18  1  0
 17 19  1  0
  9 20  1  0
 20 21  2  0
 20  3  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  8 26  1  0
  8 27  1  0
  8 28  1  0
 10 29  1  0
 10 30  1  0
 11 31  1  0
 13 32  1  0
 13 33  1  0
 13 34  1  0
 14 35  1  0
 14 36  1  0
 15 37  1  0
 15 38  1  0
 16 39  1  0
 18 40  1  0
 18 41  1  0
 18 42  1  0
 19 43  1  0
 19 44  1  0
 19 45  1  0
M  END


  Mrv0541 05161317552D          

 21 21  0  0  0  0            999 V2000
   -4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  1  0  0  0  0
  8  6  1  0  0  0  0
 10  9  1  0  0  0  0
 12  1  1  0  0  0  0
 12  2  1  0  0  0  0
 12  7  2  0  0  0  0
 13  3  1  0  0  0  0
 13  8  1  0  0  0  0
 13  9  2  0  0  0  0
 14  4  1  0  0  0  0
 15 10  1  0  0  0  0
 15 14  2  0  0  0  0
 16 11  1  0  0  0  0
 16 14  1  0  0  0  0
 17 11  2  0  0  0  0
 18 15  1  0  0  0  0
 18 17  1  0  0  0  0
 19 16  2  0  0  0  0
 20 18  2  0  0  0  0
 21  5  1  0  0  0  0
 21 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060353

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=CC(=O)C(C)=C(C\C=C(/C)CCC=C(C)C)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C18H24O3/c1-12(2)7-6-8-13(3)9-10-15-14(4)16(19)11-17(21-5)18(15)20/h7,9,11H,6,8,10H2,1-5H3/b13-9+

> <INCHI_KEY>
GKCNNWJPOJGTLV-UKTHLTGXSA-N

> <FORMULA>
C18H24O3

> <MOLECULAR_WEIGHT>
288.3814

> <EXACT_MASS>
288.172544634

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
33.32517296525621

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-5-methoxy-2-methylcyclohexa-2,5-diene-1,4-dione

> <ALOGPS_LOGP>
4.16

> <JCHEM_LOGP>
4.284244383

> <ALOGPS_LOGS>
-4.38

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.941732563557345

> <JCHEM_POLAR_SURFACE_AREA>
43.370000000000005

> <JCHEM_REFRACTIVITY>
89.46579999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.20e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-5-methoxy-2-methylcyclohexa-2,5-diene-1,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0060353
     RDKit          3D
2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone
 45 45  0  0  0  0  0  0  0  0999 V2000
    6.4540    1.7512    1.9828 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0331    1.8509    1.8561 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4030    1.2439    0.7691 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8518    1.4416   -0.4593 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2269    0.8296   -1.6226 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6487    1.0134   -2.7942 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0450   -0.0526   -1.4725 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4134   -0.6794   -2.6509 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6120   -0.2399   -0.2599 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4235   -1.1127    0.0062 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3587   -0.3831    0.6943 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8638   -0.2930    0.1711 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1492   -0.9335   -1.1114 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9086    0.4810    0.8716 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1149   -0.2682    1.3213 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9132   -0.9251    0.2765 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1670   -0.5224    0.0774 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7535    0.5903    0.9132 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0155   -1.1548   -0.9670 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2436    0.3799    0.9273 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7999    0.1779    2.0881 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9075    2.2140    1.0796 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7105    0.6565    1.9293 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7758    2.2084    2.9200 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7162    2.0866   -0.5714 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5805   -0.0595   -3.0601 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1786   -1.7425   -2.5474 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1922   -0.6308   -3.4751 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1121   -1.7002   -0.8474 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8164   -1.8707    0.7520 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5109    0.1154    1.6563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3639   -2.0191   -1.0480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3608   -0.7600   -1.8796 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0566   -0.4497   -1.5587 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2851    1.2229    0.0944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4747    1.1109    1.6933 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8438   -1.0430    2.1015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7696    0.4711    1.8650 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5769   -1.7308   -0.3457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7990    0.2999    1.9807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7680    0.8331    0.5402 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1444    1.5172    0.7821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8841   -0.4954   -1.2011 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4003   -1.2878   -1.8785 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4008   -2.1416   -0.6283 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  3
 17 18  1  0
 17 19  1  0
  9 20  1  0
 20 21  2  0
 20  3  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  8 26  1  0
  8 27  1  0
  8 28  1  0
 10 29  1  0
 10 30  1  0
 11 31  1  0
 13 32  1  0
 13 33  1  0
 13 34  1  0
 14 35  1  0
 14 36  1  0
 15 37  1  0
 15 38  1  0
 16 39  1  0
 18 40  1  0
 18 41  1  0
 18 42  1  0
 19 43  1  0
 19 44  1  0
 19 45  1  0
M  END

HEADER    PROTEIN                                 16-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-MAY-13         0                                  
HETATM    1  C   UNK     0      -8.002   4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.335   4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -6.668   3.850   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   1.540   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       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
CONECT    1   12                                                            
CONECT    2   12                                                            
CONECT    3   13                                                            
CONECT    4   14                                                            
CONECT    5   21                                                            
CONECT    6    7    8                                                       
CONECT    7    6   12                                                       
CONECT    8    6   13                                                       
CONECT    9   10   13                                                       
CONECT   10    9   15                                                       
CONECT   11   16   17                                                       
CONECT   12    1    2    7                                                  
CONECT   13    3    8    9                                                  
CONECT   14    4   15   16                                                  
CONECT   15   10   14   18                                                  
CONECT   16   11   14   19                                                  
CONECT   17   11   18   21                                                  
CONECT   18   15   17   20                                                  
CONECT   19   16                                                            
CONECT   20   18                                                            
CONECT   21    5   17                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

COMPND    HMDB0060353
HETATM    1  C1  UNL     1       6.454   1.751   1.983  1.00  0.00           C  
HETATM    2  O1  UNL     1       5.033   1.851   1.856  1.00  0.00           O  
HETATM    3  C2  UNL     1       4.403   1.244   0.769  1.00  0.00           C  
HETATM    4  C3  UNL     1       4.852   1.442  -0.459  1.00  0.00           C  
HETATM    5  C4  UNL     1       4.227   0.830  -1.623  1.00  0.00           C  
HETATM    6  O2  UNL     1       4.649   1.013  -2.794  1.00  0.00           O  
HETATM    7  C5  UNL     1       3.045  -0.053  -1.473  1.00  0.00           C  
HETATM    8  C6  UNL     1       2.413  -0.679  -2.651  1.00  0.00           C  
HETATM    9  C7  UNL     1       2.612  -0.240  -0.260  1.00  0.00           C  
HETATM   10  C8  UNL     1       1.423  -1.113   0.006  1.00  0.00           C  
HETATM   11  C9  UNL     1       0.359  -0.383   0.694  1.00  0.00           C  
HETATM   12  C10 UNL     1      -0.864  -0.293   0.171  1.00  0.00           C  
HETATM   13  C11 UNL     1      -1.149  -0.933  -1.111  1.00  0.00           C  
HETATM   14  C12 UNL     1      -1.909   0.481   0.872  1.00  0.00           C  
HETATM   15  C13 UNL     1      -3.115  -0.268   1.321  1.00  0.00           C  
HETATM   16  C14 UNL     1      -3.913  -0.925   0.277  1.00  0.00           C  
HETATM   17  C15 UNL     1      -5.167  -0.522   0.077  1.00  0.00           C  
HETATM   18  C16 UNL     1      -5.754   0.590   0.913  1.00  0.00           C  
HETATM   19  C17 UNL     1      -6.015  -1.155  -0.967  1.00  0.00           C  
HETATM   20  C18 UNL     1       3.244   0.380   0.927  1.00  0.00           C  
HETATM   21  O3  UNL     1       2.800   0.178   2.088  1.00  0.00           O  
HETATM   22  H1  UNL     1       6.908   2.214   1.080  1.00  0.00           H  
HETATM   23  H2  UNL     1       6.711   0.656   1.929  1.00  0.00           H  
HETATM   24  H3  UNL     1       6.776   2.208   2.920  1.00  0.00           H  
HETATM   25  H4  UNL     1       5.716   2.087  -0.571  1.00  0.00           H  
HETATM   26  H5  UNL     1       1.580  -0.060  -3.060  1.00  0.00           H  
HETATM   27  H6  UNL     1       2.179  -1.743  -2.547  1.00  0.00           H  
HETATM   28  H7  UNL     1       3.192  -0.631  -3.475  1.00  0.00           H  
HETATM   29  H8  UNL     1       1.112  -1.700  -0.847  1.00  0.00           H  
HETATM   30  H9  UNL     1       1.816  -1.871   0.752  1.00  0.00           H  
HETATM   31  H10 UNL     1       0.511   0.115   1.656  1.00  0.00           H  
HETATM   32  H11 UNL     1      -1.364  -2.019  -1.048  1.00  0.00           H  
HETATM   33  H12 UNL     1      -0.361  -0.760  -1.880  1.00  0.00           H  
HETATM   34  H13 UNL     1      -2.057  -0.450  -1.559  1.00  0.00           H  
HETATM   35  H14 UNL     1      -2.285   1.223   0.094  1.00  0.00           H  
HETATM   36  H15 UNL     1      -1.475   1.111   1.693  1.00  0.00           H  
HETATM   37  H16 UNL     1      -2.844  -1.043   2.102  1.00  0.00           H  
HETATM   38  H17 UNL     1      -3.770   0.471   1.865  1.00  0.00           H  
HETATM   39  H18 UNL     1      -3.577  -1.731  -0.346  1.00  0.00           H  
HETATM   40  H19 UNL     1      -5.799   0.300   1.981  1.00  0.00           H  
HETATM   41  H20 UNL     1      -6.768   0.833   0.540  1.00  0.00           H  
HETATM   42  H21 UNL     1      -5.144   1.517   0.782  1.00  0.00           H  
HETATM   43  H22 UNL     1      -6.884  -0.495  -1.201  1.00  0.00           H  
HETATM   44  H23 UNL     1      -5.400  -1.288  -1.878  1.00  0.00           H  
HETATM   45  H24 UNL     1      -6.401  -2.142  -0.628  1.00  0.00           H  
CONECT    1    2   22   23   24
CONECT    2    3
CONECT    3    4    4   20
CONECT    4    5   25
CONECT    5    6    6    7
CONECT    7    8    9    9
CONECT    8   26   27   28
CONECT    9   10   20
CONECT   10   11   29   30
CONECT   11   12   12   31
CONECT   12   13   14
CONECT   13   32   33   34
CONECT   14   15   35   36
CONECT   15   16   37   38
CONECT   16   17   17   39
CONECT   17   18   19
CONECT   18   40   41   42
CONECT   19   43   44   45
CONECT   20   21   21
END

HMDB0060353
     RDKit          3D
2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone
 45 45  0  0  0  0  0  0  0  0999 V2000
    6.4540    1.7512    1.9828 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0331    1.8509    1.8561 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4030    1.2439    0.7691 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8518    1.4416   -0.4593 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2269    0.8296   -1.6226 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6487    1.0134   -2.7942 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0450   -0.0526   -1.4725 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4134   -0.6794   -2.6509 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6120   -0.2399   -0.2599 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4235   -1.1127    0.0062 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3587   -0.3831    0.6943 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8638   -0.2930    0.1711 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1492   -0.9335   -1.1114 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9086    0.4810    0.8716 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1149   -0.2682    1.3213 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9132   -0.9251    0.2765 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1670   -0.5224    0.0774 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7535    0.5903    0.9132 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0155   -1.1548   -0.9670 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2436    0.3799    0.9273 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7999    0.1779    2.0881 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9075    2.2140    1.0796 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7105    0.6565    1.9293 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7758    2.2084    2.9200 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7162    2.0866   -0.5714 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5805   -0.0595   -3.0601 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1786   -1.7425   -2.5474 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1922   -0.6308   -3.4751 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1121   -1.7002   -0.8474 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8164   -1.8707    0.7520 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5109    0.1154    1.6563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3639   -2.0191   -1.0480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3608   -0.7600   -1.8796 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0566   -0.4497   -1.5587 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2851    1.2229    0.0944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4747    1.1109    1.6933 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8438   -1.0430    2.1015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7696    0.4711    1.8650 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5769   -1.7308   -0.3457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7990    0.2999    1.9807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7680    0.8331    0.5402 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1444    1.5172    0.7821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8841   -0.4954   -1.2011 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4003   -1.2878   -1.8785 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4008   -2.1416   -0.6283 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  3
 17 18  1  0
 17 19  1  0
  9 20  1  0
 20 21  2  0
 20  3  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  8 26  1  0
  8 27  1  0
  8 28  1  0
 10 29  1  0
 10 30  1  0
 11 31  1  0
 13 32  1  0
 13 33  1  0
 13 34  1  0
 14 35  1  0
 14 36  1  0
 15 37  1  0
 15 38  1  0
 16 39  1  0
 18 40  1  0
 18 41  1  0
 18 42  1  0
 19 43  1  0
 19 44  1  0
 19 45  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Alkanesulfonic acid	Generator
Alkanesulphonate	Generator
Alkanesulphonic acid	Generator

Chemical Formula

C₁₈H₂₄O₃

Average Molecular Weight

288.3814

Monoisotopic Molecular Weight

288.172544634

IUPAC Name

3-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-5-methoxy-2-methylcyclohexa-2,5-diene-1,4-dione

Traditional Name

3-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-5-methoxy-2-methylcyclohexa-2,5-diene-1,4-dione

CAS Registry Number

Not Available

SMILES

COC1=CC(=O)C(C)=C(C\C=C(/C)CCC=C(C)C)C1=O

InChI Identifier

InChI=1S/C18H24O3/c1-12(2)7-6-8-13(3)9-10-15-14(4)16(19)11-17(21-5)18(15)20/h7,9,11H,6,8,10H2,1-5H3/b13-9+

InChI Key

GKCNNWJPOJGTLV-UKTHLTGXSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as prenylquinones. These are quinones with a structure characterized by the quinone ring substituted by an prenyl side-chain.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Quinone and hydroquinone lipids

Direct Parent

Prenylquinones

Alternative Parents

Substituents

Prenylbenzoquinone
Monoterpenoid
Monocyclic monoterpenoid
Quinone
P-benzoquinone
Vinylogous ester
Cyclic ketone
Ketone
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

Membrane (HMDB: HMDB0060353)

Source

Exogenous

Exogenous (HMDB: HMDB0060353)

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
Water Solubility	0.012 g/L	ALOGPS
logP	4.16	ALOGPS
logP	4.28	ChemAxon
logS	-4.4	ALOGPS
pKa (Strongest Basic)	-4.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	43.37 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	89.47 m³·mol⁻¹	ChemAxon
Polarizability	33.33 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]+	177.787	30932474
DeepCCS	[M-H]-	175.429	30932474
DeepCCS	[M-2H]-	208.316	30932474
DeepCCS	[M+Na]+	183.881	30932474
AllCCS	[M+H]+	171.7	32859911
AllCCS	[M+H-H2O]+	168.4	32859911
AllCCS	[M+NH4]+	174.8	32859911
AllCCS	[M+Na]+	175.7	32859911
AllCCS	[M-H]-	175.9	32859911
AllCCS	[M+Na-2H]-	176.4	32859911
AllCCS	[M+HCOO]-	177.1	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 √ó 2.1 mm; 1.7 Œºmparticle diameter). Predicted by Afia on May 17, 2022.	9.18 minutes	32390414
Predicted by Siyang on May 30, 2022	18.0282 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	0.57 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2955.4 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	495.6 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	219.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	260.9 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	80.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	645.8 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	802.9 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	68.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1540.2 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	618.3 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	1395.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	431.3 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	418.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	275.3 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	468.9 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	8.0 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone	COC1=CC(=O)C(C)=C(C\C=C(/C)CCC=C(C)C)C1=O	2873.1	Standard polar	33892256
2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone	COC1=CC(=O)C(C)=C(C\C=C(/C)CCC=C(C)C)C1=O	2116.0	Standard non polar	33892256
2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone	COC1=CC(=O)C(C)=C(C\C=C(/C)CCC=C(C)C)C1=O	2231.7	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 - 2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone GC-MS (Non-derivatized) - 70eV, Positive	splash10-00y0-6690000000-7a5287477e7efa6ad42d	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone 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 - 2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone 10V, Positive-QTOF	splash10-000i-0390000000-13adeaaa7fe56e8df717	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone 20V, Positive-QTOF	splash10-01b9-3970000000-7b43a420c387498f12a3	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone 40V, Positive-QTOF	splash10-014i-9300000000-aacb5ea6317d88b890f9	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone 10V, Negative-QTOF	splash10-000i-0190000000-5cdd985c9ca7f6895528	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone 20V, Negative-QTOF	splash10-000i-1190000000-bca4f086f15a17ab5f0d	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone 40V, Negative-QTOF	splash10-0aor-9560000000-3809915958556191d17a	2015-09-15	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane (predicted from logP)

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C17561

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10902296

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]
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 ]
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Enzymes

Enzyme Details

1. Ubiquinone biosynthesis protein COQ7 homolog

General function:: Involved in oxidoreductase activity
Specific function:: Involved in lifespan determination in ubiquinone-independent manner. Involved in ubiquinone biosynthesis. Potential central metabolic regulator (By similarity).
Gene Name:: COQ7
Uniprot ID:: Q99807
Molecular weight:: Not Available

Reactions

2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone + Oxygen + NADPH + Hydrogen Ion → 2-Polyprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone + NADP + Water	details

Enzyme Details

2. 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial

General function:: Involved in methyltransferase activity
Specific function:: Methyltransferase required for the conversion of 2-polyprenyl-6-methoxy-1,4-benzoquinol (DDMQH2) to 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinol (DMQH2) (By similarity).
Gene Name:: COQ5
Uniprot ID:: Q5HYK3
Molecular weight:: 37140.17

Reactions

2-Polyprenyl-6-methoxy-1,4-benzoquinone + S-Adenosylmethionine → 2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone + S-Adenosylhomocysteine	details

Showing metabocard for 2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone (HMDB0060353)

MOL for HMDB0060353 (2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone)

3D MOL for HMDB0060353 (2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone)

3D SDF for HMDB0060353 (2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone)

3D-SDF for HMDB0060353 (2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone)

PDB for HMDB0060353 (2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone)

3D PDB for HMDB0060353 (2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone)

SMILES for HMDB0060353 (2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone)

INCHI for HMDB0060353 (2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone)

Structure for HMDB0060353 (2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone)

3D Structure for HMDB0060353 (2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

Enzymes

Reactions

Reactions