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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-05-17 00:56:14 UTC

Update Date

2021-09-14 14:57:44 UTC

HMDB ID

HMDB0060359

Secondary Accession Numbers

HMDB60359

Metabolite Identification

Common Name

2,3-Epoxymenaquinone

Description

2,3-Epoxymenaquinone, also known as vitamin K2 2,3-epoxide, belongs to the class of organic compounds known as menaquinones. These are vitamin K2 compounds consisting of a naphtho-1,4-quinone ring system, which is substituted at the 2-position by an isoprenyl side-chain, and usually, at the 3-position by a methyl group. 2,3-Epoxymenaquinone is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

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

HMDB0060359
     RDKit          3D
2,3-Epoxymenaquinone
 48 50  0  0  0  0  0  0  0  0999 V2000
    6.4881   -0.6667    2.3764 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5134   -0.3385    1.3223 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7550    0.7733    0.3754 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4034   -1.0424    1.2134 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4048   -0.7483    0.1763 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0520   -0.3911    0.7616 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1410   -0.1190   -0.3854 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5074    0.9814   -1.3160 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0384   -0.7920   -0.6207 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8920   -0.5469   -1.7545 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2805   -0.1939   -1.2703 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1632    0.0386   -2.4442 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8533    1.0319   -1.4175 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1270    2.2479   -1.9320 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0619    1.3278   -0.6269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6540    2.4474   -0.7613 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6580    0.4086    0.3331 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7610    0.7544    1.1032 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2882   -0.1396    1.9922 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7232   -1.4008    2.1308 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6229   -1.7438    1.3617 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0731   -0.8408    0.4491 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9240   -1.1744   -0.3662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4715   -2.3572   -0.2841 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4860   -1.7258    2.6740 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5102   -0.3462    2.1043 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2125   -0.0505    3.2770 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8220    0.3902   -0.6733 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7230    1.2743    0.5812 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9656    1.5500    0.4178 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2064   -1.8499    1.8852 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7983    0.0478   -0.4805 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2734   -1.6487   -0.4585 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6955   -1.2521    1.3490 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0875    0.4986    1.3964 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4377    1.4648   -1.0248 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6565    1.7170   -1.3246 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5740    0.6134   -2.3744 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2194   -1.5918    0.0633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9574   -1.5227   -2.3194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5015    0.1859   -2.4815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5240    2.6982   -1.1198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4868    1.9650   -2.8014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8129    3.0317   -2.3077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1836    1.7572    0.9702 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1613    0.1203    2.6085 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1641   -2.1049    2.8528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1871   -2.7381    1.4793 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  1  0
 12 13  1  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  2  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 23 24  2  0
 13 11  1  0
 22 17  1  0
 23 11  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  3 28  1  0
  3 29  1  0
  3 30  1  0
  4 31  1  0
  5 32  1  0
  5 33  1  0
  6 34  1  0
  6 35  1  0
  8 36  1  0
  8 37  1  0
  8 38  1  0
  9 39  1  0
 10 40  1  0
 10 41  1  0
 14 42  1  0
 14 43  1  0
 14 44  1  0
 18 45  1  0
 19 46  1  0
 20 47  1  0
 21 48  1  0
M  END


  Mrv0541 05161317562D          

 24 26  0  0  0  0            999 V2000
    3.9039    5.9368    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    4.5079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914    3.7934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164    0.1105    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
    4.2868    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    4.5079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    5.2224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.5079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    0.4125    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
    1.4289    3.0789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4914    5.2224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164    3.7934    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    1.6500    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
    2.1434    2.0625    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    1.6500    0.0000 C   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
    2.1434    2.8875    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
  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 10  2  0  0  0  0
 17 11  2  0  0  0  0
 17 16  1  0  0  0  0
 18 16  1  0  0  0  0
 19 17  1  0  0  0  0
 20  4  1  0  0  0  0
 20 18  1  0  0  0  0
 21 13  1  0  0  0  0
 21 19  1  0  0  0  0
 21 20  1  0  0  0  0
 22 18  2  0  0  0  0
 23 19  2  0  0  0  0
 24 20  1  0  0  0  0
 24 21  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060359

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)=CCC\C(C)=C\CC12OC1(C)C(=O)C1=CC=CC=C1C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C21H24O3/c1-14(2)8-7-9-15(3)12-13-21-19(23)17-11-6-5-10-16(17)18(22)20(21,4)24-21/h5-6,8,10-12H,7,9,13H2,1-4H3/b15-12+

> <INCHI_KEY>
ZEACJJRPAPKYKW-NTCAYCPXSA-N

> <FORMULA>
C21H24O3

> <MOLECULAR_WEIGHT>
324.4135

> <EXACT_MASS>
324.172544634

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
36.597818635326696

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1a-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-7a-methyl-1aH,2H,7H,7aH-naphtho[2,3-b]oxirene-2,7-dione

> <ALOGPS_LOGP>
4.44

> <JCHEM_LOGP>
4.686481352666667

> <ALOGPS_LOGS>
-4.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.368148124799935

> <JCHEM_POLAR_SURFACE_AREA>
46.67

> <JCHEM_REFRACTIVITY>
96.63329999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.65e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1a-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-7a-methylnaphtho[2,3-b]oxirene-2,7-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0060359
     RDKit          3D
2,3-Epoxymenaquinone
 48 50  0  0  0  0  0  0  0  0999 V2000
    6.4881   -0.6667    2.3764 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5134   -0.3385    1.3223 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7550    0.7733    0.3754 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4034   -1.0424    1.2134 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4048   -0.7483    0.1763 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0520   -0.3911    0.7616 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1410   -0.1190   -0.3854 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5074    0.9814   -1.3160 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0384   -0.7920   -0.6207 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8920   -0.5469   -1.7545 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2805   -0.1939   -1.2703 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1632    0.0386   -2.4442 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8533    1.0319   -1.4175 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1270    2.2479   -1.9320 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0619    1.3278   -0.6269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6540    2.4474   -0.7613 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6580    0.4086    0.3331 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7610    0.7544    1.1032 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2882   -0.1396    1.9922 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7232   -1.4008    2.1308 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6229   -1.7438    1.3617 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0731   -0.8408    0.4491 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9240   -1.1744   -0.3662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4715   -2.3572   -0.2841 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4860   -1.7258    2.6740 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5102   -0.3462    2.1043 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2125   -0.0505    3.2770 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8220    0.3902   -0.6733 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7230    1.2743    0.5812 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9656    1.5500    0.4178 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2064   -1.8499    1.8852 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7983    0.0478   -0.4805 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2734   -1.6487   -0.4585 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6955   -1.2521    1.3490 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0875    0.4986    1.3964 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4377    1.4648   -1.0248 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6565    1.7170   -1.3246 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5740    0.6134   -2.3744 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2194   -1.5918    0.0633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9574   -1.5227   -2.3194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5015    0.1859   -2.4815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5240    2.6982   -1.1198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4868    1.9650   -2.8014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8129    3.0317   -2.3077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1836    1.7572    0.9702 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1613    0.1203    2.6085 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1641   -2.1049    2.8528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1871   -2.7381    1.4793 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  1  0
 12 13  1  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  2  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 23 24  2  0
 13 11  1  0
 22 17  1  0
 23 11  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  3 28  1  0
  3 29  1  0
  3 30  1  0
  4 31  1  0
  5 32  1  0
  5 33  1  0
  6 34  1  0
  6 35  1  0
  8 36  1  0
  8 37  1  0
  8 38  1  0
  9 39  1  0
 10 40  1  0
 10 41  1  0
 14 42  1  0
 14 43  1  0
 14 44  1  0
 18 45  1  0
 19 46  1  0
 20 47  1  0
 21 48  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       7.287  11.082   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.287   8.415   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.357   7.081   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.897   0.206   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.002   3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.207   8.415   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.977   9.748   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667   8.415   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.668   0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.667   5.747   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.897   4.414   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.517   9.748   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.897   7.081   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.335   3.080   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.001   0.770   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       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.667   3.080   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       4.001   5.390   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1   14                                                            
CONECT    2   14                                                            
CONECT    3   15                                                            
CONECT    4   20                                                            
CONECT    5    6   10                                                       
CONECT    6    5   11                                                       
CONECT    7    8    9                                                       
CONECT    8    7   14                                                       
CONECT    9    7   15                                                       
CONECT   10    5   16                                                       
CONECT   11    6   17                                                       
CONECT   12   13   15                                                       
CONECT   13   12   21                                                       
CONECT   14    1    2    8                                                  
CONECT   15    3    9   12                                                  
CONECT   16   10   17   18                                                  
CONECT   17   11   16   19                                                  
CONECT   18   16   20   22                                                  
CONECT   19   17   21   23                                                  
CONECT   20    4   18   21   24                                             
CONECT   21   13   19   20   24                                             
CONECT   22   18                                                            
CONECT   23   19                                                            
CONECT   24   20   21                                                       
MASTER        0    0    0    0    0    0    0    0   24    0   52    0
END

COMPND    HMDB0060359
HETATM    1  C1  UNL     1       6.488  -0.667   2.376  1.00  0.00           C  
HETATM    2  C2  UNL     1       5.513  -0.338   1.322  1.00  0.00           C  
HETATM    3  C3  UNL     1       5.755   0.773   0.375  1.00  0.00           C  
HETATM    4  C4  UNL     1       4.403  -1.042   1.213  1.00  0.00           C  
HETATM    5  C5  UNL     1       3.405  -0.748   0.176  1.00  0.00           C  
HETATM    6  C6  UNL     1       2.052  -0.391   0.762  1.00  0.00           C  
HETATM    7  C7  UNL     1       1.141  -0.119  -0.385  1.00  0.00           C  
HETATM    8  C8  UNL     1       1.507   0.981  -1.316  1.00  0.00           C  
HETATM    9  C9  UNL     1       0.038  -0.792  -0.621  1.00  0.00           C  
HETATM   10  C10 UNL     1      -0.892  -0.547  -1.754  1.00  0.00           C  
HETATM   11  C11 UNL     1      -2.281  -0.194  -1.270  1.00  0.00           C  
HETATM   12  O1  UNL     1      -3.163   0.039  -2.444  1.00  0.00           O  
HETATM   13  C12 UNL     1      -2.853   1.032  -1.417  1.00  0.00           C  
HETATM   14  C13 UNL     1      -2.127   2.248  -1.932  1.00  0.00           C  
HETATM   15  C14 UNL     1      -4.062   1.328  -0.627  1.00  0.00           C  
HETATM   16  O2  UNL     1      -4.654   2.447  -0.761  1.00  0.00           O  
HETATM   17  C15 UNL     1      -4.658   0.409   0.333  1.00  0.00           C  
HETATM   18  C16 UNL     1      -5.761   0.754   1.103  1.00  0.00           C  
HETATM   19  C17 UNL     1      -6.288  -0.140   1.992  1.00  0.00           C  
HETATM   20  C18 UNL     1      -5.723  -1.401   2.131  1.00  0.00           C  
HETATM   21  C19 UNL     1      -4.623  -1.744   1.362  1.00  0.00           C  
HETATM   22  C20 UNL     1      -4.073  -0.841   0.449  1.00  0.00           C  
HETATM   23  C21 UNL     1      -2.924  -1.174  -0.366  1.00  0.00           C  
HETATM   24  O3  UNL     1      -2.471  -2.357  -0.284  1.00  0.00           O  
HETATM   25  H1  UNL     1       6.486  -1.726   2.674  1.00  0.00           H  
HETATM   26  H2  UNL     1       7.510  -0.346   2.104  1.00  0.00           H  
HETATM   27  H3  UNL     1       6.212  -0.050   3.277  1.00  0.00           H  
HETATM   28  H4  UNL     1       5.822   0.390  -0.673  1.00  0.00           H  
HETATM   29  H5  UNL     1       6.723   1.274   0.581  1.00  0.00           H  
HETATM   30  H6  UNL     1       4.966   1.550   0.418  1.00  0.00           H  
HETATM   31  H7  UNL     1       4.206  -1.850   1.885  1.00  0.00           H  
HETATM   32  H8  UNL     1       3.798   0.048  -0.480  1.00  0.00           H  
HETATM   33  H9  UNL     1       3.273  -1.649  -0.458  1.00  0.00           H  
HETATM   34  H10 UNL     1       1.695  -1.252   1.349  1.00  0.00           H  
HETATM   35  H11 UNL     1       2.087   0.499   1.396  1.00  0.00           H  
HETATM   36  H12 UNL     1       2.438   1.465  -1.025  1.00  0.00           H  
HETATM   37  H13 UNL     1       0.656   1.717  -1.325  1.00  0.00           H  
HETATM   38  H14 UNL     1       1.574   0.613  -2.374  1.00  0.00           H  
HETATM   39  H15 UNL     1      -0.219  -1.592   0.063  1.00  0.00           H  
HETATM   40  H16 UNL     1      -0.957  -1.523  -2.319  1.00  0.00           H  
HETATM   41  H17 UNL     1      -0.501   0.186  -2.481  1.00  0.00           H  
HETATM   42  H18 UNL     1      -1.524   2.698  -1.120  1.00  0.00           H  
HETATM   43  H19 UNL     1      -1.487   1.965  -2.801  1.00  0.00           H  
HETATM   44  H20 UNL     1      -2.813   3.032  -2.308  1.00  0.00           H  
HETATM   45  H21 UNL     1      -6.184   1.757   0.970  1.00  0.00           H  
HETATM   46  H22 UNL     1      -7.161   0.120   2.609  1.00  0.00           H  
HETATM   47  H23 UNL     1      -6.164  -2.105   2.853  1.00  0.00           H  
HETATM   48  H24 UNL     1      -4.187  -2.738   1.479  1.00  0.00           H  
CONECT    1    2   25   26   27
CONECT    2    3    4    4
CONECT    3   28   29   30
CONECT    4    5   31
CONECT    5    6   32   33
CONECT    6    7   34   35
CONECT    7    8    9    9
CONECT    8   36   37   38
CONECT    9   10   39
CONECT   10   11   40   41
CONECT   11   12   13   23
CONECT   12   13
CONECT   13   14   15
CONECT   14   42   43   44
CONECT   15   16   16   17
CONECT   17   18   18   22
CONECT   18   19   45
CONECT   19   20   20   46
CONECT   20   21   47
CONECT   21   22   22   48
CONECT   22   23
CONECT   23   24   24
END

HMDB0060359
     RDKit          3D
2,3-Epoxymenaquinone
 48 50  0  0  0  0  0  0  0  0999 V2000
    6.4881   -0.6667    2.3764 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5134   -0.3385    1.3223 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7550    0.7733    0.3754 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4034   -1.0424    1.2134 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4048   -0.7483    0.1763 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0520   -0.3911    0.7616 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1410   -0.1190   -0.3854 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5074    0.9814   -1.3160 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0384   -0.7920   -0.6207 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8920   -0.5469   -1.7545 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2805   -0.1939   -1.2703 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1632    0.0386   -2.4442 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8533    1.0319   -1.4175 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1270    2.2479   -1.9320 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0619    1.3278   -0.6269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6540    2.4474   -0.7613 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6580    0.4086    0.3331 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7610    0.7544    1.1032 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2882   -0.1396    1.9922 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7232   -1.4008    2.1308 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6229   -1.7438    1.3617 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0731   -0.8408    0.4491 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9240   -1.1744   -0.3662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4715   -2.3572   -0.2841 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4860   -1.7258    2.6740 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5102   -0.3462    2.1043 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2125   -0.0505    3.2770 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8220    0.3902   -0.6733 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7230    1.2743    0.5812 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9656    1.5500    0.4178 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2064   -1.8499    1.8852 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7983    0.0478   -0.4805 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2734   -1.6487   -0.4585 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6955   -1.2521    1.3490 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0875    0.4986    1.3964 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4377    1.4648   -1.0248 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6565    1.7170   -1.3246 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5740    0.6134   -2.3744 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2194   -1.5918    0.0633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9574   -1.5227   -2.3194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5015    0.1859   -2.4815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5240    2.6982   -1.1198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4868    1.9650   -2.8014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8129    3.0317   -2.3077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1836    1.7572    0.9702 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1613    0.1203    2.6085 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1641   -2.1049    2.8528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1871   -2.7381    1.4793 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  1  0
 12 13  1  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  2  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 23 24  2  0
 13 11  1  0
 22 17  1  0
 23 11  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  3 28  1  0
  3 29  1  0
  3 30  1  0
  4 31  1  0
  5 32  1  0
  5 33  1  0
  6 34  1  0
  6 35  1  0
  8 36  1  0
  8 37  1  0
  8 38  1  0
  9 39  1  0
 10 40  1  0
 10 41  1  0
 14 42  1  0
 14 43  1  0
 14 44  1  0
 18 45  1  0
 19 46  1  0
 20 47  1  0
 21 48  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Vitamin K2 2,3-epoxide	Kegg
Vitamin K2-2,3-epoxide	HMDB

Chemical Formula

C₂₁H₂₄O₃

Average Molecular Weight

324.4135

Monoisotopic Molecular Weight

324.172544634

IUPAC Name

1a-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-7a-methyl-1aH,2H,7H,7aH-naphtho[2,3-b]oxirene-2,7-dione

Traditional Name

1a-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-7a-methylnaphtho[2,3-b]oxirene-2,7-dione

CAS Registry Number

Not Available

SMILES

CC(C)=CCC\C(C)=C\CC12OC1(C)C(=O)C1=CC=CC=C1C2=O

InChI Identifier

InChI=1S/C21H24O3/c1-14(2)8-7-9-15(3)12-13-21-19(23)17-11-6-5-10-16(17)18(22)20(21,4)24-21/h5-6,8,10-12H,7,9,13H2,1-4H3/b15-12+

InChI Key

ZEACJJRPAPKYKW-NTCAYCPXSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as menaquinones. These are vitamin K2 compounds consisting of a naphtho-1,4-quinone ring system, which is substituted at the 2-position by an isoprenyl side-chain, and usually, at the 3-position by a methyl group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Quinone and hydroquinone lipids

Direct Parent

Menaquinones

Alternative Parents

Substituents

Menaquinone
Naphthoquinone
Aromatic monoterpenoid
Monoterpenoid
Naphthalene
Tetralin
Quinone
Aryl alkyl ketone
Aryl ketone
Benzenoid
Ketone
Oxacycle
Ether
Oxirane
Dialkyl ether
Organoheterocyclic compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0060359)

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	0.0056 g/L	ALOGPS
logP	4.44	ALOGPS
logP	4.69	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Basic)	-4.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	46.67 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	96.63 m³·mol⁻¹	ChemAxon
Polarizability	36.6 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	179.625	31661259
DarkChem	[M-H]-	174.85	31661259
DeepCCS	[M-2H]-	208.762	30932474
DeepCCS	[M+Na]+	184.158	30932474
AllCCS	[M+H]+	181.0	32859911
AllCCS	[M+H-H2O]+	177.9	32859911
AllCCS	[M+NH4]+	183.9	32859911
AllCCS	[M+Na]+	184.8	32859911
AllCCS	[M-H]-	186.8	32859911
AllCCS	[M+Na-2H]-	186.9	32859911
AllCCS	[M+HCOO]-	187.1	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2,3-Epoxymenaquinone	CC(C)=CCC\C(C)=C\CC12OC1(C)C(=O)C1=CC=CC=C1C2=O	3374.7	Standard polar	33892256
2,3-Epoxymenaquinone	CC(C)=CCC\C(C)=C\CC12OC1(C)C(=O)C1=CC=CC=C1C2=O	2440.0	Standard non polar	33892256
2,3-Epoxymenaquinone	CC(C)=CCC\C(C)=C\CC12OC1(C)C(=O)C1=CC=CC=C1C2=O	2428.6	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 2,3-Epoxymenaquinone GC-MS (Non-derivatized) - 70eV, Positive	splash10-0lk9-8943000000-09988d4900b0f59534bc	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2,3-Epoxymenaquinone GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2,3-Epoxymenaquinone 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 - 2,3-Epoxymenaquinone 10V, Positive-QTOF	splash10-004i-0129000000-6c020f5170781e25b0ba	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Epoxymenaquinone 20V, Positive-QTOF	splash10-0lmi-8983000000-f9a13cf6b46481ecf36a	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Epoxymenaquinone 40V, Positive-QTOF	splash10-0aor-9310000000-4475f464c265ee73e5cd	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Epoxymenaquinone 10V, Negative-QTOF	splash10-00di-0009000000-ed9620dbea687e569cc0	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Epoxymenaquinone 20V, Negative-QTOF	splash10-00di-0119000000-8c113c8b5fd7944b6be0	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Epoxymenaquinone 40V, Negative-QTOF	splash10-1000-5962000000-8170859910f9c08c34d7	2017-10-06	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

C20265

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

71448979

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. 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

Enzyme Details

2. Vitamin K epoxide reductase complex subunit 1

General function:: Involved in vitamin-K-epoxide reductase (warfarin-sensi
Specific function:: Involved in vitamin K metabolism. Catalytic subunit of the vitamin K epoxide reductase (VKOR) complex which reduces inactive vitamin K 2,3-epoxide to active vitamin K.
Gene Name:: VKORC1
Uniprot ID:: Q9BQB6
Molecular weight:: 18234.3

Reactions

2,3-Epoxymenaquinone + 1,4-Dithiothreitol → Menatetrenone + Oxidized dithiothreitol + Water	details

Showing metabocard for 2,3-Epoxymenaquinone (HMDB0060359)

MOL for HMDB0060359 (2,3-Epoxymenaquinone)

3D MOL for HMDB0060359 (2,3-Epoxymenaquinone)

3D SDF for HMDB0060359 (2,3-Epoxymenaquinone)

3D-SDF for HMDB0060359 (2,3-Epoxymenaquinone)

PDB for HMDB0060359 (2,3-Epoxymenaquinone)

3D PDB for HMDB0060359 (2,3-Epoxymenaquinone)

SMILES for HMDB0060359 (2,3-Epoxymenaquinone)

INCHI for HMDB0060359 (2,3-Epoxymenaquinone)

Structure for HMDB0060359 (2,3-Epoxymenaquinone)

3D Structure for HMDB0060359 (2,3-Epoxymenaquinone)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

Enzymes

Reactions

Reactions