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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 02:28:22 UTC

Update Date

2022-03-07 02:56:46 UTC

HMDB ID

HMDB0040867

Secondary Accession Numbers

HMDB40867

Metabolite Identification

Common Name

5-O-Methylembelin

Description

5-O-Methylembelin 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. 5-O-Methylembelin 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 5-O-Methylembelin.

Structure

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

HMDB0040867
     RDKit          3D
5-O-Methylembelin
 50 50  0  0  0  0  0  0  0  0999 V2000
    7.2189    0.0248    0.3177 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2836   -0.0884    1.4908 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0553   -0.9170    1.1820 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3152   -0.2683    0.0494 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0642   -1.0794   -0.2922 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3084   -0.4389   -1.4322 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8531    0.9627   -1.1239 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9416    1.0401    0.0554 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3261    0.2218   -0.1392 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1746    0.3672    1.1023 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4508   -0.3291    1.0925 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5228   -0.0076    0.1974 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6860    1.0334   -0.5787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7184    2.0034   -0.5780 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8567    1.2058   -1.4459 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9326    2.2377   -2.1602 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8937    0.1917   -1.4617 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7736   -0.8783   -0.6943 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7956   -1.8263   -0.7430 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9892   -1.5134   -0.0472 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6129   -1.0202    0.1465 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5648   -2.0708    0.8549 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9662    0.9441   -0.2421 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2971    0.0575    0.6292 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0853   -0.8451   -0.3660 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9821    0.9336    1.7866 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8620   -0.5331    2.3265 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2854   -1.9579    0.9590 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4113   -0.8744    2.0850 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0527    0.7758    0.3445 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9584   -0.3008   -0.8532 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4363   -2.0582   -0.6579 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4367   -1.2458    0.5900 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9508   -0.4662   -2.3326 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4377   -1.0806   -1.6504 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7185    1.6245   -0.9389 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3548    1.3472   -2.0349 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4431    0.7063    0.9706 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6116    2.0937    0.1610 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0706   -0.8571   -0.1552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8053    0.3288   -1.0929 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5522   -0.1387    1.9108 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2002    1.4226    1.4639 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8724   -0.3089    2.1462 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2161   -1.4355    0.9662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8858    2.9040   -0.1098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7640    0.2986   -2.0928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3792   -0.5731   -0.5027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7228   -2.3412   -0.0964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7050   -1.2656    0.9940 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
 19 20  1  0
 18 21  1  0
 21 22  2  0
 21 12  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  2 26  1  0
  2 27  1  0
  3 28  1  0
  3 29  1  0
  4 30  1  0
  4 31  1  0
  5 32  1  0
  5 33  1  0
  6 34  1  0
  6 35  1  0
  7 36  1  0
  7 37  1  0
  8 38  1  0
  8 39  1  0
  9 40  1  0
  9 41  1  0
 10 42  1  0
 10 43  1  0
 11 44  1  0
 11 45  1  0
 14 46  1  0
 17 47  1  0
 20 48  1  0
 20 49  1  0
 20 50  1  0
M  END


  Mrv0541 05061312122D          

 22 22  0  0  0  0            999 V2000
    6.4302    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1473    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8605    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5749    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7184    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2894    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0039    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7184    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2894    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0039    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0039    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5749    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0039    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4328    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  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
 12 11  1  0  0  0  0
 14 12  1  0  0  0  0
 15 13  1  0  0  0  0
 16 13  2  0  0  0  0
 17 14  2  0  0  0  0
 17 15  1  0  0  0  0
 18 14  1  0  0  0  0
 18 16  1  0  0  0  0
 19 15  2  0  0  0  0
 20 17  1  0  0  0  0
 21 18  2  0  0  0  0
 22  2  1  0  0  0  0
 22 16  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0040867

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C18H28O4/c1-3-4-5-6-7-8-9-10-11-12-14-17(20)15(19)13-16(22-2)18(14)21/h13,20H,3-12H2,1-2H3

> <INCHI_KEY>
KHBJLRRAMCJZLZ-UHFFFAOYSA-N

> <FORMULA>
C18H28O4

> <MOLECULAR_WEIGHT>
308.4125

> <EXACT_MASS>
308.198759384

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
36.545068315513454

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
4.47

> <JCHEM_LOGP>
4.940862977333335

> <ALOGPS_LOGS>
-5.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.190878539724274

> <JCHEM_PKA_STRONGEST_BASIC>
-4.145569726815219

> <JCHEM_POLAR_SURFACE_AREA>
63.599999999999994

> <JCHEM_REFRACTIVITY>
90.08189999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.91e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-O-methylembelin

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0040867
     RDKit          3D
5-O-Methylembelin
 50 50  0  0  0  0  0  0  0  0999 V2000
    7.2189    0.0248    0.3177 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2836   -0.0884    1.4908 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0553   -0.9170    1.1820 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3152   -0.2683    0.0494 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0642   -1.0794   -0.2922 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3084   -0.4389   -1.4322 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8531    0.9627   -1.1239 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9416    1.0401    0.0554 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3261    0.2218   -0.1392 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1746    0.3672    1.1023 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4508   -0.3291    1.0925 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5228   -0.0076    0.1974 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6860    1.0334   -0.5787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7184    2.0034   -0.5780 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8567    1.2058   -1.4459 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9326    2.2377   -2.1602 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8937    0.1917   -1.4617 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7736   -0.8783   -0.6943 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7956   -1.8263   -0.7430 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9892   -1.5134   -0.0472 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6129   -1.0202    0.1465 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5648   -2.0708    0.8549 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9662    0.9441   -0.2421 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2971    0.0575    0.6292 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0853   -0.8451   -0.3660 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9821    0.9336    1.7866 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8620   -0.5331    2.3265 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2854   -1.9579    0.9590 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4113   -0.8744    2.0850 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0527    0.7758    0.3445 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9584   -0.3008   -0.8532 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4363   -2.0582   -0.6579 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4367   -1.2458    0.5900 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9508   -0.4662   -2.3326 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4377   -1.0806   -1.6504 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7185    1.6245   -0.9389 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3548    1.3472   -2.0349 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4431    0.7063    0.9706 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6116    2.0937    0.1610 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0706   -0.8571   -0.1552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8053    0.3288   -1.0929 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5522   -0.1387    1.9108 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2002    1.4226    1.4639 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8724   -0.3089    2.1462 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2161   -1.4355    0.9662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8858    2.9040   -0.1098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7640    0.2986   -2.0928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3792   -0.5731   -0.5027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7228   -2.3412   -0.0964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7050   -1.2656    0.9940 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
 19 20  1  0
 18 21  1  0
 21 22  2  0
 21 12  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  2 26  1  0
  2 27  1  0
  3 28  1  0
  3 29  1  0
  4 30  1  0
  4 31  1  0
  5 32  1  0
  5 33  1  0
  6 34  1  0
  6 35  1  0
  7 36  1  0
  7 37  1  0
  8 38  1  0
  8 39  1  0
  9 40  1  0
  9 41  1  0
 10 42  1  0
 10 43  1  0
 11 44  1  0
 11 45  1  0
 14 46  1  0
 17 47  1  0
 20 48  1  0
 20 49  1  0
 20 50  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      12.003   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      32.008   3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      13.337   3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      14.671   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      16.004   3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      17.338   2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      18.672   3.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      20.005   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      21.339   3.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      22.673   2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      24.006   3.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      25.340   2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      29.341   4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      26.674   3.080   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      28.007   5.390   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      29.341   3.080   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      26.674   4.620   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      28.007   2.310   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      28.007   6.930   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      25.340   5.390   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      28.007   0.770   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      30.675   2.310   0.000  0.00  0.00           O+0
CONECT    1    3                                                            
CONECT    2   22                                                            
CONECT    3    1    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   12                                                       
CONECT   12   11   14                                                       
CONECT   13   15   16                                                       
CONECT   14   12   17   18                                                  
CONECT   15   13   17   19                                                  
CONECT   16   13   18   22                                                  
CONECT   17   14   15   20                                                  
CONECT   18   14   16   21                                                  
CONECT   19   15                                                            
CONECT   20   17                                                            
CONECT   21   18                                                            
CONECT   22    2   16                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

COMPND    HMDB0040867
HETATM    1  C1  UNL     1       7.219   0.025   0.318  1.00  0.00           C  
HETATM    2  C2  UNL     1       6.284  -0.088   1.491  1.00  0.00           C  
HETATM    3  C3  UNL     1       5.055  -0.917   1.182  1.00  0.00           C  
HETATM    4  C4  UNL     1       4.315  -0.268   0.049  1.00  0.00           C  
HETATM    5  C5  UNL     1       3.064  -1.079  -0.292  1.00  0.00           C  
HETATM    6  C6  UNL     1       2.308  -0.439  -1.432  1.00  0.00           C  
HETATM    7  C7  UNL     1       1.853   0.963  -1.124  1.00  0.00           C  
HETATM    8  C8  UNL     1       0.942   1.040   0.055  1.00  0.00           C  
HETATM    9  C9  UNL     1      -0.326   0.222  -0.139  1.00  0.00           C  
HETATM   10  C10 UNL     1      -1.175   0.367   1.102  1.00  0.00           C  
HETATM   11  C11 UNL     1      -2.451  -0.329   1.093  1.00  0.00           C  
HETATM   12  C12 UNL     1      -3.523  -0.008   0.197  1.00  0.00           C  
HETATM   13  C13 UNL     1      -3.686   1.033  -0.579  1.00  0.00           C  
HETATM   14  O1  UNL     1      -2.718   2.003  -0.578  1.00  0.00           O  
HETATM   15  C14 UNL     1      -4.857   1.206  -1.446  1.00  0.00           C  
HETATM   16  O2  UNL     1      -4.933   2.238  -2.160  1.00  0.00           O  
HETATM   17  C15 UNL     1      -5.894   0.192  -1.462  1.00  0.00           C  
HETATM   18  C16 UNL     1      -5.774  -0.878  -0.694  1.00  0.00           C  
HETATM   19  O3  UNL     1      -6.796  -1.826  -0.743  1.00  0.00           O  
HETATM   20  C17 UNL     1      -7.989  -1.513  -0.047  1.00  0.00           C  
HETATM   21  C18 UNL     1      -4.613  -1.020   0.147  1.00  0.00           C  
HETATM   22  O4  UNL     1      -4.565  -2.071   0.855  1.00  0.00           O  
HETATM   23  H1  UNL     1       6.966   0.944  -0.242  1.00  0.00           H  
HETATM   24  H2  UNL     1       8.297   0.058   0.629  1.00  0.00           H  
HETATM   25  H3  UNL     1       7.085  -0.845  -0.366  1.00  0.00           H  
HETATM   26  H4  UNL     1       5.982   0.934   1.787  1.00  0.00           H  
HETATM   27  H5  UNL     1       6.862  -0.533   2.326  1.00  0.00           H  
HETATM   28  H6  UNL     1       5.285  -1.958   0.959  1.00  0.00           H  
HETATM   29  H7  UNL     1       4.411  -0.874   2.085  1.00  0.00           H  
HETATM   30  H8  UNL     1       4.053   0.776   0.344  1.00  0.00           H  
HETATM   31  H9  UNL     1       4.958  -0.301  -0.853  1.00  0.00           H  
HETATM   32  H10 UNL     1       3.436  -2.058  -0.658  1.00  0.00           H  
HETATM   33  H11 UNL     1       2.437  -1.246   0.590  1.00  0.00           H  
HETATM   34  H12 UNL     1       2.951  -0.466  -2.333  1.00  0.00           H  
HETATM   35  H13 UNL     1       1.438  -1.081  -1.650  1.00  0.00           H  
HETATM   36  H14 UNL     1       2.718   1.625  -0.939  1.00  0.00           H  
HETATM   37  H15 UNL     1       1.355   1.347  -2.035  1.00  0.00           H  
HETATM   38  H16 UNL     1       1.443   0.706   0.971  1.00  0.00           H  
HETATM   39  H17 UNL     1       0.612   2.094   0.161  1.00  0.00           H  
HETATM   40  H18 UNL     1       0.071  -0.857  -0.155  1.00  0.00           H  
HETATM   41  H19 UNL     1      -0.805   0.329  -1.093  1.00  0.00           H  
HETATM   42  H20 UNL     1      -0.552  -0.139   1.911  1.00  0.00           H  
HETATM   43  H21 UNL     1      -1.200   1.423   1.464  1.00  0.00           H  
HETATM   44  H22 UNL     1      -2.872  -0.309   2.146  1.00  0.00           H  
HETATM   45  H23 UNL     1      -2.216  -1.435   0.966  1.00  0.00           H  
HETATM   46  H24 UNL     1      -2.886   2.904  -0.110  1.00  0.00           H  
HETATM   47  H25 UNL     1      -6.764   0.299  -2.093  1.00  0.00           H  
HETATM   48  H26 UNL     1      -8.379  -0.573  -0.503  1.00  0.00           H  
HETATM   49  H27 UNL     1      -8.723  -2.341  -0.096  1.00  0.00           H  
HETATM   50  H28 UNL     1      -7.705  -1.266   0.994  1.00  0.00           H  
CONECT    1    2   23   24   25
CONECT    2    3   26   27
CONECT    3    4   28   29
CONECT    4    5   30   31
CONECT    5    6   32   33
CONECT    6    7   34   35
CONECT    7    8   36   37
CONECT    8    9   38   39
CONECT    9   10   40   41
CONECT   10   11   42   43
CONECT   11   12   44   45
CONECT   12   13   13   21
CONECT   13   14   15
CONECT   14   46
CONECT   15   16   16   17
CONECT   17   18   18   47
CONECT   18   19   21
CONECT   19   20
CONECT   20   48   49   50
CONECT   21   22   22
END

HMDB0040867
     RDKit          3D
5-O-Methylembelin
 50 50  0  0  0  0  0  0  0  0999 V2000
    7.2189    0.0248    0.3177 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2836   -0.0884    1.4908 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0553   -0.9170    1.1820 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3152   -0.2683    0.0494 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0642   -1.0794   -0.2922 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3084   -0.4389   -1.4322 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8531    0.9627   -1.1239 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9416    1.0401    0.0554 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3261    0.2218   -0.1392 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1746    0.3672    1.1023 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4508   -0.3291    1.0925 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5228   -0.0076    0.1974 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6860    1.0334   -0.5787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7184    2.0034   -0.5780 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8567    1.2058   -1.4459 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9326    2.2377   -2.1602 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8937    0.1917   -1.4617 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7736   -0.8783   -0.6943 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7956   -1.8263   -0.7430 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9892   -1.5134   -0.0472 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6129   -1.0202    0.1465 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5648   -2.0708    0.8549 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9662    0.9441   -0.2421 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2971    0.0575    0.6292 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0853   -0.8451   -0.3660 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9821    0.9336    1.7866 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8620   -0.5331    2.3265 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2854   -1.9579    0.9590 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4113   -0.8744    2.0850 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0527    0.7758    0.3445 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9584   -0.3008   -0.8532 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4363   -2.0582   -0.6579 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4367   -1.2458    0.5900 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9508   -0.4662   -2.3326 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4377   -1.0806   -1.6504 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7185    1.6245   -0.9389 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3548    1.3472   -2.0349 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4431    0.7063    0.9706 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6116    2.0937    0.1610 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0706   -0.8571   -0.1552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8053    0.3288   -1.0929 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5522   -0.1387    1.9108 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2002    1.4226    1.4639 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8724   -0.3089    2.1462 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2161   -1.4355    0.9662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8858    2.9040   -0.1098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7640    0.2986   -2.0928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3792   -0.5731   -0.5027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7228   -2.3412   -0.0964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7050   -1.2656    0.9940 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
 19 20  1  0
 18 21  1  0
 21 22  2  0
 21 12  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  2 26  1  0
  2 27  1  0
  3 28  1  0
  3 29  1  0
  4 30  1  0
  4 31  1  0
  5 32  1  0
  5 33  1  0
  6 34  1  0
  6 35  1  0
  7 36  1  0
  7 37  1  0
  8 38  1  0
  8 39  1  0
  9 40  1  0
  9 41  1  0
 10 42  1  0
 10 43  1  0
 11 44  1  0
 11 45  1  0
 14 46  1  0
 17 47  1  0
 20 48  1  0
 20 49  1  0
 20 50  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
2-Hydroxy-5-methoxy-3-undecyl-1,4-benzoquinone	ChEBI
5-O-Methylembelin	MeSH

Chemical Formula

C₁₈H₂₈O₄

Average Molecular Weight

308.4125

Monoisotopic Molecular Weight

308.198759384

IUPAC Name

2-hydroxy-5-methoxy-3-undecylcyclohexa-2,5-diene-1,4-dione

Traditional Name

5-O-methylembelin

CAS Registry Number

56005-10-8

SMILES

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

InChI Identifier

InChI=1S/C18H28O4/c1-3-4-5-6-7-8-9-10-11-12-14-17(20)15(19)13-16(22-2)18(14)21/h13,20H,3-12H2,1-2H3

InChI Key

KHBJLRRAMCJZLZ-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 ester
Vinylogous acid
Enol
Organic oxide
Hydrocarbon derivative
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

hydroxybenzoquinone (CHEBI:65842 )
enol ether (CHEBI:65842 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0040867)
Cell membrane (HMDB: HMDB0040867)

Source

Exogenous

Exogenous (HMDB: HMDB0040867)

Food

Food (HMDB: HMDB0040867)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0040867)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	95 - 96 °C	Not Available
Boiling Point	439.50 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	1.27 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	5.940 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.0029 g/L	ALOGPS
logP	4.47	ALOGPS
logP	4.94	ChemAxon
logS	-5	ALOGPS
pKa (Strongest Acidic)	8.19	ChemAxon
pKa (Strongest Basic)	-4.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	63.6 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	90.08 m³·mol⁻¹	ChemAxon
Polarizability	36.55 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]+	182.792	30932474
DeepCCS	[M-H]-	180.434	30932474
DeepCCS	[M-2H]-	213.408	30932474
DeepCCS	[M+Na]+	189.095	30932474
AllCCS	[M+H]+	180.3	32859911
AllCCS	[M+H-H2O]+	177.2	32859911
AllCCS	[M+NH4]+	183.1	32859911
AllCCS	[M+Na]+	184.0	32859911
AllCCS	[M-H]-	181.1	32859911
AllCCS	[M+Na-2H]-	181.9	32859911
AllCCS	[M+HCOO]-	182.8	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.	10.57 minutes	32390414
Predicted by Siyang on May 30, 2022	20.3093 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	0.84 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	3061.1 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	545.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	225.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	282.2 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	479.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	945.6 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	949.4 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	119.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1863.8 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	600.6 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	1866.3 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	561.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	512.7 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	543.4 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	473.4 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	8.7 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-O-Methylembelin	CCCCCCCCCCCC1=C(O)C(=O)C=C(OC)C1=O	3480.1	Standard polar	33892256
5-O-Methylembelin	CCCCCCCCCCCC1=C(O)C(=O)C=C(OC)C1=O	2251.5	Standard non polar	33892256
5-O-Methylembelin	CCCCCCCCCCCC1=C(O)C(=O)C=C(OC)C1=O	2278.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5-O-Methylembelin,1TMS,isomer #1	CCCCCCCCCCCC1=C(O[Si](C)(C)C)C(=O)C=C(OC)C1=O	2516.8	Semi standard non polar	33892256
5-O-Methylembelin,1TBDMS,isomer #1	CCCCCCCCCCCC1=C(O[Si](C)(C)C(C)(C)C)C(=O)C=C(OC)C1=O	2752.2	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 - 5-O-Methylembelin GC-MS (Non-derivatized) - 70eV, Positive	splash10-0abm-9460000000-3b5f25533d774c6cb813	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-O-Methylembelin GC-MS (1 TMS) - 70eV, Positive	splash10-006t-9433000000-19e59d48d20a7d4bcefc	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-O-Methylembelin 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 - 5-O-Methylembelin 10V, Positive-QTOF	splash10-0a4i-1339000000-6b2ebcc08f23b314a5ad	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-O-Methylembelin 20V, Positive-QTOF	splash10-0a4l-5982000000-b3e408c35e8a67ee1267	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-O-Methylembelin 40V, Positive-QTOF	splash10-052f-9500000000-68961cb83c647a7e6681	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-O-Methylembelin 10V, Negative-QTOF	splash10-0a4i-0009000000-003d1a9976505c6c1ef4	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-O-Methylembelin 20V, Negative-QTOF	splash10-0a4i-2397000000-e4711e3fd67cdbb9ea8d	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-O-Methylembelin 40V, Negative-QTOF	splash10-059x-9360000000-dd6ae394c363820addc8	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-O-Methylembelin 10V, Negative-QTOF	splash10-0a4i-0009000000-f75c458667804d661acb	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-O-Methylembelin 20V, Negative-QTOF	splash10-0a4i-0309000000-2b3dfc7139f8e7b708b7	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-O-Methylembelin 40V, Negative-QTOF	splash10-006t-5970000000-88edb6c8086ecdb44f2f	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-O-Methylembelin 10V, Positive-QTOF	splash10-0a4i-0109000000-4455e61e094f5558496d	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-O-Methylembelin 20V, Positive-QTOF	splash10-0aor-6914000000-ffb489284db7568c06fb	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-O-Methylembelin 40V, Positive-QTOF	splash10-067i-9500000000-bc181806b1221e1faaad	2021-09-22	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

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

171489

PDB ID

Not Available

ChEBI ID

65842

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1440601

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for 5-O-Methylembelin (HMDB0040867)

MOL for HMDB0040867 (5-O-Methylembelin)

3D MOL for HMDB0040867 (5-O-Methylembelin)

3D SDF for HMDB0040867 (5-O-Methylembelin)

3D-SDF for HMDB0040867 (5-O-Methylembelin)

PDB for HMDB0040867 (5-O-Methylembelin)

3D PDB for HMDB0040867 (5-O-Methylembelin)

SMILES for HMDB0040867 (5-O-Methylembelin)

INCHI for HMDB0040867 (5-O-Methylembelin)

Structure for HMDB0040867 (5-O-Methylembelin)

3D Structure for HMDB0040867 (5-O-Methylembelin)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra