Jump To Section:

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

Show more...Show more...Show more...

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-05-17 01:24:21 UTC

Update Date

2022-03-07 03:17:45 UTC

HMDB ID

HMDB0060487

Secondary Accession Numbers

HMDB60487

Metabolite Identification

Common Name

Menaquinol

Description

Menaquinol belongs to the class of organic compounds known as prenylated hydroquinones. These are quinones with a structure characterized by the hydroquinone ring substituted by an prenyl side-chain. Menaquinol is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

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

HMDB0060487
     RDKit          3D
Menaquinol
 49 50  0  0  0  0  0  0  0  0999 V2000
   -5.9010    0.2617    1.1047 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5791    1.1822    0.0009 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4957    2.3018   -0.3100 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4875    1.0211   -0.7091 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5793   -0.1235   -0.3659 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2413    0.4211    0.0142 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2766   -0.6549    0.3729 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6059   -1.5602    1.4757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1727   -0.7818   -0.3042 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9116   -1.7542   -0.1302 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1926   -1.0224    0.0154 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5469   -0.4348    1.2022 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6516   -0.5852    2.3540 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7473    0.2517    1.2237 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1666    0.8658    2.3708 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5596    0.3397    0.0873 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7434    1.0328    0.1542 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5644    1.1392   -0.9460 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1564    0.5284   -2.1076 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9868   -0.1718   -2.2205 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1741   -0.2655   -1.0969 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9939   -0.9478   -1.1423 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5649   -1.5648   -2.2883 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8985    0.4881    1.5677 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9918   -0.8111    0.7751 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1073    0.2402    1.9078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1633    3.2685    0.1515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5464    2.0891   -0.0286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4127    2.5036   -1.4187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2081    1.6798   -1.5371 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9842   -0.7050    0.4626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4946   -0.7870   -1.2750 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8703    1.0640   -0.8014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3900    1.0970    0.8920 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5835   -2.0846    1.2648 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8710   -0.8977    2.3548 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8367   -2.2348    1.8236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0168   -0.0581   -1.1331 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8061   -2.4493    0.7174 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9377   -2.3575   -1.0833 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1208   -0.3510    3.3432 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3457   -1.6708    2.4885 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7283   -0.0080    2.3082 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6273    0.8416    3.2037 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0478    1.5102    1.0856 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4888    1.6941   -0.8533 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8267    0.6259   -2.9737 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7419   -0.6193   -3.1633 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0831   -1.5469   -3.1290 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  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
 14 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 22 11  1  0
 21 16  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  0
  3 28  1  0
  3 29  1  0
  4 30  1  0
  5 31  1  0
  5 32  1  0
  6 33  1  0
  6 34  1  0
  8 35  1  0
  8 36  1  0
  8 37  1  0
  9 38  1  0
 10 39  1  0
 10 40  1  0
 13 41  1  0
 13 42  1  0
 13 43  1  0
 15 44  1  0
 17 45  1  0
 18 46  1  0
 19 47  1  0
 20 48  1  0
 23 49  1  0
M  END

  Mrv0541 05161318242D          

 23 24  0  0  0  0            999 V2000
    6.4302    7.0125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    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
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    4.5375    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
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    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
    5.0013    3.7125    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
    3.5724    2.0625    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
    2.1434    2.0625    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
    2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  2  0  0  0  0
  8  7  1  0  0  0  0
  9  7  1  0  0  0  0
 10  5  1  0  0  0  0
 11  6  1  0  0  0  0
 13 12  1  0  0  0  0
 14  1  1  0  0  0  0
 14  2  1  0  0  0  0
 14  8  2  0  0  0  0
 15  3  1  0  0  0  0
 15  9  1  0  0  0  0
 15 12  2  0  0  0  0
 16  4  1  0  0  0  0
 17 13  1  0  0  0  0
 17 16  1  0  0  0  0
 18 10  2  0  0  0  0
 19 11  2  0  0  0  0
 19 18  1  0  0  0  0
 20 16  2  0  0  0  0
 20 18  1  0  0  0  0
 21 17  2  0  0  0  0
 21 19  1  0  0  0  0
 22 20  1  0  0  0  0
 23 21  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060487

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)=CCC\C(C)=C\CC1=C(O)C2=CC=CC=C2C(O)=C1C

> <INCHI_IDENTIFIER>
InChI=1S/C21H26O2/c1-14(2)8-7-9-15(3)12-13-17-16(4)20(22)18-10-5-6-11-19(18)21(17)23/h5-6,8,10-12,22-23H,7,9,13H2,1-4H3/b15-12+

> <INCHI_KEY>
CZHYZLLLSCZMRL-NTCAYCPXSA-N

> <FORMULA>
C21H26O2

> <MOLECULAR_WEIGHT>
310.4299

> <EXACT_MASS>
310.193280076

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
37.14454286954629

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-3-methylnaphthalene-1,4-diol

> <ALOGPS_LOGP>
6.01

> <JCHEM_LOGP>
6.257294593

> <ALOGPS_LOGS>
-5.16

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.295748335293982

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.384535433726278

> <JCHEM_PKA_STRONGEST_BASIC>
-5.995354564508905

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
99.55659999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.13e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
menaquinol

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0060487
     RDKit          3D
Menaquinol
 49 50  0  0  0  0  0  0  0  0999 V2000
   -5.9010    0.2617    1.1047 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5791    1.1822    0.0009 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4957    2.3018   -0.3100 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4875    1.0211   -0.7091 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5793   -0.1235   -0.3659 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2413    0.4211    0.0142 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2766   -0.6549    0.3729 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6059   -1.5602    1.4757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1727   -0.7818   -0.3042 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9116   -1.7542   -0.1302 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1926   -1.0224    0.0154 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5469   -0.4348    1.2022 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6516   -0.5852    2.3540 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7473    0.2517    1.2237 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1666    0.8658    2.3708 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5596    0.3397    0.0873 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7434    1.0328    0.1542 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5644    1.1392   -0.9460 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1564    0.5284   -2.1076 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9868   -0.1718   -2.2205 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1741   -0.2655   -1.0969 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9939   -0.9478   -1.1423 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5649   -1.5648   -2.2883 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8985    0.4881    1.5677 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9918   -0.8111    0.7751 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1073    0.2402    1.9078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1633    3.2685    0.1515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5464    2.0891   -0.0286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4127    2.5036   -1.4187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2081    1.6798   -1.5371 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9842   -0.7050    0.4626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4946   -0.7870   -1.2750 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8703    1.0640   -0.8014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3900    1.0970    0.8920 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5835   -2.0846    1.2648 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8710   -0.8977    2.3548 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8367   -2.2348    1.8236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0168   -0.0581   -1.1331 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8061   -2.4493    0.7174 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9377   -2.3575   -1.0833 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1208   -0.3510    3.3432 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3457   -1.6708    2.4885 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7283   -0.0080    2.3082 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6273    0.8416    3.2037 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0478    1.5102    1.0856 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4888    1.6941   -0.8533 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8267    0.6259   -2.9737 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7419   -0.6193   -3.1633 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0831   -1.5469   -3.1290 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  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
 14 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 22 11  1  0
 21 16  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  0
  3 28  1  0
  3 29  1  0
  4 30  1  0
  5 31  1  0
  5 32  1  0
  6 33  1  0
  6 34  1  0
  8 35  1  0
  8 36  1  0
  8 37  1  0
  9 38  1  0
 10 39  1  0
 10 40  1  0
 13 41  1  0
 13 42  1  0
 13 43  1  0
 15 44  1  0
 17 45  1  0
 18 46  1  0
 19 47  1  0
 20 48  1  0
 23 49  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      12.003  13.090   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.337  10.780   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.669   6.160   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.669   9.240   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.669  10.780   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.336   8.470   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.002   6.160   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      12.003  11.550   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.336   6.930   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       5.335   6.160   0.000  0.00  0.00           O+0
CONECT    1   14                                                            
CONECT    2   14                                                            
CONECT    3   15                                                            
CONECT    4   16                                                            
CONECT    5    6   10                                                       
CONECT    6    5   11                                                       
CONECT    7    8    9                                                       
CONECT    8    7   14                                                       
CONECT    9    7   15                                                       
CONECT   10    5   18                                                       
CONECT   11    6   19                                                       
CONECT   12   13   15                                                       
CONECT   13   12   17                                                       
CONECT   14    1    2    8                                                  
CONECT   15    3    9   12                                                  
CONECT   16    4   17   20                                                  
CONECT   17   13   16   21                                                  
CONECT   18   10   19   20                                                  
CONECT   19   11   18   21                                                  
CONECT   20   16   18   22                                                  
CONECT   21   17   19   23                                                  
CONECT   22   20                                                            
CONECT   23   21                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

COMPND    HMDB0060487
HETATM    1  C1  UNL     1      -5.901   0.262   1.105  1.00  0.00           C  
HETATM    2  C2  UNL     1      -5.579   1.182   0.001  1.00  0.00           C  
HETATM    3  C3  UNL     1      -6.496   2.302  -0.310  1.00  0.00           C  
HETATM    4  C4  UNL     1      -4.488   1.021  -0.709  1.00  0.00           C  
HETATM    5  C5  UNL     1      -3.579  -0.123  -0.366  1.00  0.00           C  
HETATM    6  C6  UNL     1      -2.241   0.421   0.014  1.00  0.00           C  
HETATM    7  C7  UNL     1      -1.277  -0.655   0.373  1.00  0.00           C  
HETATM    8  C8  UNL     1      -1.606  -1.560   1.476  1.00  0.00           C  
HETATM    9  C9  UNL     1      -0.173  -0.782  -0.304  1.00  0.00           C  
HETATM   10  C10 UNL     1       0.912  -1.754  -0.130  1.00  0.00           C  
HETATM   11  C11 UNL     1       2.193  -1.022   0.015  1.00  0.00           C  
HETATM   12  C12 UNL     1       2.547  -0.435   1.202  1.00  0.00           C  
HETATM   13  C13 UNL     1       1.652  -0.585   2.354  1.00  0.00           C  
HETATM   14  C14 UNL     1       3.747   0.252   1.224  1.00  0.00           C  
HETATM   15  O1  UNL     1       4.167   0.866   2.371  1.00  0.00           O  
HETATM   16  C15 UNL     1       4.560   0.340   0.087  1.00  0.00           C  
HETATM   17  C16 UNL     1       5.743   1.033   0.154  1.00  0.00           C  
HETATM   18  C17 UNL     1       6.564   1.139  -0.946  1.00  0.00           C  
HETATM   19  C18 UNL     1       6.156   0.528  -2.108  1.00  0.00           C  
HETATM   20  C19 UNL     1       4.987  -0.172  -2.221  1.00  0.00           C  
HETATM   21  C20 UNL     1       4.174  -0.266  -1.097  1.00  0.00           C  
HETATM   22  C21 UNL     1       2.994  -0.948  -1.142  1.00  0.00           C  
HETATM   23  O2  UNL     1       2.565  -1.565  -2.288  1.00  0.00           O  
HETATM   24  H1  UNL     1      -6.898   0.488   1.568  1.00  0.00           H  
HETATM   25  H2  UNL     1      -5.992  -0.811   0.775  1.00  0.00           H  
HETATM   26  H3  UNL     1      -5.107   0.240   1.908  1.00  0.00           H  
HETATM   27  H4  UNL     1      -6.163   3.268   0.152  1.00  0.00           H  
HETATM   28  H5  UNL     1      -7.546   2.089  -0.029  1.00  0.00           H  
HETATM   29  H6  UNL     1      -6.413   2.504  -1.419  1.00  0.00           H  
HETATM   30  H7  UNL     1      -4.208   1.680  -1.537  1.00  0.00           H  
HETATM   31  H8  UNL     1      -3.984  -0.705   0.463  1.00  0.00           H  
HETATM   32  H9  UNL     1      -3.495  -0.787  -1.275  1.00  0.00           H  
HETATM   33  H10 UNL     1      -1.870   1.064  -0.801  1.00  0.00           H  
HETATM   34  H11 UNL     1      -2.390   1.097   0.892  1.00  0.00           H  
HETATM   35  H12 UNL     1      -2.583  -2.085   1.265  1.00  0.00           H  
HETATM   36  H13 UNL     1      -1.871  -0.898   2.355  1.00  0.00           H  
HETATM   37  H14 UNL     1      -0.837  -2.235   1.824  1.00  0.00           H  
HETATM   38  H15 UNL     1      -0.017  -0.058  -1.133  1.00  0.00           H  
HETATM   39  H16 UNL     1       0.806  -2.449   0.717  1.00  0.00           H  
HETATM   40  H17 UNL     1       0.938  -2.357  -1.083  1.00  0.00           H  
HETATM   41  H18 UNL     1       2.121  -0.351   3.343  1.00  0.00           H  
HETATM   42  H19 UNL     1       1.346  -1.671   2.488  1.00  0.00           H  
HETATM   43  H20 UNL     1       0.728  -0.008   2.308  1.00  0.00           H  
HETATM   44  H21 UNL     1       3.627   0.842   3.204  1.00  0.00           H  
HETATM   45  H22 UNL     1       6.048   1.510   1.086  1.00  0.00           H  
HETATM   46  H23 UNL     1       7.489   1.694  -0.853  1.00  0.00           H  
HETATM   47  H24 UNL     1       6.827   0.626  -2.974  1.00  0.00           H  
HETATM   48  H25 UNL     1       4.742  -0.619  -3.163  1.00  0.00           H  
HETATM   49  H26 UNL     1       3.083  -1.547  -3.129  1.00  0.00           H  
CONECT    1    2   24   25   26
CONECT    2    3    4    4
CONECT    3   27   28   29
CONECT    4    5   30
CONECT    5    6   31   32
CONECT    6    7   33   34
CONECT    7    8    9    9
CONECT    8   35   36   37
CONECT    9   10   38
CONECT   10   11   39   40
CONECT   11   12   12   22
CONECT   12   13   14
CONECT   13   41   42   43
CONECT   14   15   16   16
CONECT   15   44
CONECT   16   17   21
CONECT   17   18   18   45
CONECT   18   19   46
CONECT   19   20   20   47
CONECT   20   21   48
CONECT   21   22   22
CONECT   22   23
CONECT   23   49
END

HMDB0060487
     RDKit          3D
Menaquinol
 49 50  0  0  0  0  0  0  0  0999 V2000
   -5.9010    0.2617    1.1047 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5791    1.1822    0.0009 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4957    2.3018   -0.3100 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4875    1.0211   -0.7091 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5793   -0.1235   -0.3659 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2413    0.4211    0.0142 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2766   -0.6549    0.3729 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6059   -1.5602    1.4757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1727   -0.7818   -0.3042 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9116   -1.7542   -0.1302 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1926   -1.0224    0.0154 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5469   -0.4348    1.2022 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6516   -0.5852    2.3540 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7473    0.2517    1.2237 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1666    0.8658    2.3708 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5596    0.3397    0.0873 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7434    1.0328    0.1542 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5644    1.1392   -0.9460 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1564    0.5284   -2.1076 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9868   -0.1718   -2.2205 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1741   -0.2655   -1.0969 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9939   -0.9478   -1.1423 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5649   -1.5648   -2.2883 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8985    0.4881    1.5677 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9918   -0.8111    0.7751 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1073    0.2402    1.9078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1633    3.2685    0.1515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5464    2.0891   -0.0286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4127    2.5036   -1.4187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2081    1.6798   -1.5371 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9842   -0.7050    0.4626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4946   -0.7870   -1.2750 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8703    1.0640   -0.8014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3900    1.0970    0.8920 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5835   -2.0846    1.2648 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8710   -0.8977    2.3548 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8367   -2.2348    1.8236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0168   -0.0581   -1.1331 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8061   -2.4493    0.7174 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9377   -2.3575   -1.0833 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1208   -0.3510    3.3432 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3457   -1.6708    2.4885 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7283   -0.0080    2.3082 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6273    0.8416    3.2037 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0478    1.5102    1.0856 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4888    1.6941   -0.8533 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8267    0.6259   -2.9737 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7419   -0.6193   -3.1633 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0831   -1.5469   -3.1290 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  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
 14 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 22 11  1  0
 21 16  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  0
  3 28  1  0
  3 29  1  0
  4 30  1  0
  5 31  1  0
  5 32  1  0
  6 33  1  0
  6 34  1  0
  8 35  1  0
  8 36  1  0
  8 37  1  0
  9 38  1  0
 10 39  1  0
 10 40  1  0
 13 41  1  0
 13 42  1  0
 13 43  1  0
 15 44  1  0
 17 45  1  0
 18 46  1  0
 19 47  1  0
 20 48  1  0
 23 49  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Reduced menaquinone	Kegg
Vitamin K2 hydroquinone	Kegg
Reduced vitamin K2	Kegg

Chemical Formula

C₂₁H₂₆O₂

Average Molecular Weight

310.4299

Monoisotopic Molecular Weight

310.193280076

IUPAC Name

2-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-3-methylnaphthalene-1,4-diol

Traditional Name

menaquinol

CAS Registry Number

Not Available

SMILES

CC(C)=CCC\C(C)=C\CC1=C(O)C2=CC=CC=C2C(O)=C1C

InChI Identifier

InChI=1S/C21H26O2/c1-14(2)8-7-9-15(3)12-13-17-16(4)20(22)18-10-5-6-11-19(18)21(17)23/h5-6,8,10-12,22-23H,7,9,13H2,1-4H3/b15-12+

InChI Key

CZHYZLLLSCZMRL-NTCAYCPXSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as prenylated hydroquinones. These are quinones with a structure characterized by the hydroquinone 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

Prenylated hydroquinones

Alternative Parents

Substituents

Prenylbenzoquinol
1-naphthol
Naphthalene
Monoterpenoid
Bicyclic monoterpenoid
Aromatic monoterpenoid
Hydroquinone
Benzenoid
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0060487)

Source

Exogenous

Exogenous (HMDB: HMDB0060487)

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	0.0021 g/L	ALOGPS
logP	6.01	ALOGPS
logP	6.26	ChemAxon
logS	-5.2	ALOGPS
pKa (Strongest Acidic)	9.38	ChemAxon
pKa (Strongest Basic)	-6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	40.46 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	99.56 m³·mol⁻¹	ChemAxon
Polarizability	37.14 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	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]+	174.989	30932474
DeepCCS	[M-H]-	172.631	30932474
DeepCCS	[M-2H]-	206.222	30932474
DeepCCS	[M+Na]+	181.764	30932474
AllCCS	[M+H]+	178.4	32859911
AllCCS	[M+H-H2O]+	175.1	32859911
AllCCS	[M+NH4]+	181.5	32859911
AllCCS	[M+Na]+	182.4	32859911
AllCCS	[M-H]-	178.9	32859911
AllCCS	[M+Na-2H]-	178.6	32859911
AllCCS	[M+HCOO]-	178.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Menaquinol	CC(C)=CCC\C(C)=C\CC1=C(O)C2=CC=CC=C2C(O)=C1C	3822.3	Standard polar	33892256
Menaquinol	CC(C)=CCC\C(C)=C\CC1=C(O)C2=CC=CC=C2C(O)=C1C	2561.8	Standard non polar	33892256
Menaquinol	CC(C)=CCC\C(C)=C\CC1=C(O)C2=CC=CC=C2C(O)=C1C	2701.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Menaquinol,1TMS,isomer #1	CC(C)=CCC/C(C)=C/CC1=C(C)C(O)=C2C=CC=CC2=C1O[Si](C)(C)C	2688.1	Semi standard non polar	33892256
Menaquinol,1TMS,isomer #2	CC(C)=CCC/C(C)=C/CC1=C(C)C(O[Si](C)(C)C)=C2C=CC=CC2=C1O	2686.6	Semi standard non polar	33892256
Menaquinol,2TMS,isomer #1	CC(C)=CCC/C(C)=C/CC1=C(C)C(O[Si](C)(C)C)=C2C=CC=CC2=C1O[Si](C)(C)C	2729.1	Semi standard non polar	33892256
Menaquinol,1TBDMS,isomer #1	CC(C)=CCC/C(C)=C/CC1=C(C)C(O)=C2C=CC=CC2=C1O[Si](C)(C)C(C)(C)C	2921.5	Semi standard non polar	33892256
Menaquinol,1TBDMS,isomer #2	CC(C)=CCC/C(C)=C/CC1=C(C)C(O[Si](C)(C)C(C)(C)C)=C2C=CC=CC2=C1O	2910.3	Semi standard non polar	33892256
Menaquinol,2TBDMS,isomer #1	CC(C)=CCC/C(C)=C/CC1=C(C)C(O[Si](C)(C)C(C)(C)C)=C2C=CC=CC2=C1O[Si](C)(C)C(C)(C)C	3138.3	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 - Menaquinol GC-MS (Non-derivatized) - 70eV, Positive	splash10-05mn-5390000000-22415fc15498d35c6c7c	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Menaquinol GC-MS (2 TMS) - 70eV, Positive	splash10-000i-5108900000-dced8995d9d9618fe806	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Menaquinol 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 - Menaquinol 10V, Positive-QTOF	splash10-03di-0339000000-71c7e0bf895c9ad9f6a5	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Menaquinol 20V, Positive-QTOF	splash10-0839-5931000000-9f1a8b7a710ef2117682	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Menaquinol 40V, Positive-QTOF	splash10-066r-9310000000-8404d53fc4ce1372e4b3	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Menaquinol 10V, Negative-QTOF	splash10-0a4i-0009000000-10ec0ed6440aee398c46	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Menaquinol 20V, Negative-QTOF	splash10-0a4i-0119000000-edd4499fcb81e4de4361	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Menaquinol 40V, Negative-QTOF	splash10-00dl-1940000000-b1cf94b6e2c3590e495f	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Menaquinol 10V, Positive-QTOF	splash10-03di-0119000000-a21e0c561587cd772b99	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Menaquinol 20V, Positive-QTOF	splash10-053i-6941000000-d555b2680363c1ebfd97	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Menaquinol 40V, Positive-QTOF	splash10-0573-9700000000-d08c44d8aeb1eea92ff8	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Menaquinol 10V, Negative-QTOF	splash10-0a4i-0009000000-d834b990dbff0e00d266	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Menaquinol 20V, Negative-QTOF	splash10-0a4i-0129000000-83184eaaa68be604d1d8	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Menaquinol 40V, Negative-QTOF	splash10-0002-0920000000-208dfa69e4df42af067a	2021-10-12	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

C05819

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5280839

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. NAD(P)H dehydrogenase [quinone] 1

General function:: Involved in electron carrier activity
Specific function:: The enzyme apparently serves as a quinone reductase in connection with conjugation reactions of hydroquinons involved in detoxification pathways as well as in biosynthetic processes such as the vitamin K-dependent gamma-carboxylation of glutamate residues in prothrombin synthesis.
Gene Name:: NQO1
Uniprot ID:: P15559
Molecular weight:: 30867.405

Reactions

Menatetrenone + Hydrogen Ion + NADH → Menaquinol + NAD	details

Enzyme Details

2. Vitamin K-dependent gamma-carboxylase

General function:: Involved in gamma-glutamyl carboxylase activity
Specific function:: Mediates the vitamin K-dependent carboxylation of glutamate residues to calcium-binding gamma-carboxyglutamate (Gla) residues with the concomitant conversion of the reduced hydroquinone form of vitamin K to vitamin K epoxide.
Gene Name:: GGCX
Uniprot ID:: P38435
Molecular weight:: 87560.065

Reactions

2,3-Epoxymenaquinone + Gla protein + Water → Menaquinol + Gla protein precursor + Carbon dioxide + Oxygen	details

Showing metabocard for Menaquinol (HMDB0060487)

MOL for HMDB0060487 (Menaquinol)

3D MOL for HMDB0060487 (Menaquinol)

3D SDF for HMDB0060487 (Menaquinol)

3D-SDF for HMDB0060487 (Menaquinol)

PDB for HMDB0060487 (Menaquinol)

3D PDB for HMDB0060487 (Menaquinol)

SMILES for HMDB0060487 (Menaquinol)

INCHI for HMDB0060487 (Menaquinol)

Structure for HMDB0060487 (Menaquinol)

3D Structure for HMDB0060487 (Menaquinol)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

Enzymes

Reactions

Reactions