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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 13:44:43 UTC

Update Date

2021-09-26 23:08:25 UTC

HMDB ID

HMDB0254434

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Menaquinone 6

Description

2-(3,7,11,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaen-1-yl)-3-methyl-1,4-dihydronaphthalene-1,4-dione belongs to the class of organic compounds known as sesterterpenoids. These are terpenes composed of five consecutive isoprene units. 2-(3,7,11,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaen-1-yl)-3-methyl-1,4-dihydronaphthalene-1,4-dione is an extremely weak basic (essentially neutral) compound (based on its pKa). This compound has been identified in human blood as reported by (PMID: 31557052 ). Menaquinone 6 is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Menaquinone 6 is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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


  Mrv1533004161505202D          

 43 44  0  0  0  0            999 V2000
   -7.8592  -16.0875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8592  -15.2625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447  -14.8500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447  -14.0250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302  -13.6125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302  -12.7875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158  -12.3750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158  -11.5500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013  -11.1375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013  -10.3125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -9.9000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -9.0750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -7.8375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.1447  -12.3750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5737  -14.8500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  4  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
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 12 13  1  0  0  0  0
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 25 36  1  0  0  0  0
 36 37  2  0  0  0  0
 22 38  1  0  0  0  0
 18 39  1  0  0  0  0
 14 40  1  0  0  0  0
 10 41  1  0  0  0  0
  6 42  1  0  0  0  0
  2 43  1  0  0  0  0
M  END

HMDB0254434
     RDKit          3D
Menaquinone 6
 99100  0  0  0  0  0  0  0  0999 V2000
    9.9465    1.0835   -3.5321 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6071   -0.0605   -2.8455 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7793   -0.7103   -3.5407 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1987   -0.5101   -1.6746 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0423    0.0848   -0.9424 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0097   -0.9339   -0.5857 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8947   -0.2779    0.1637 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7256   -1.1105    0.6386 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9122    1.0197    0.4130 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8630    1.7667    1.1466 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1776    2.8294    0.3537 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2008    3.5384    1.1921 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7218    4.2395    2.4207 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0
  2  3  1  0
  2  4  2  3
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M  END


  Mrv1533004161505202D          

 43 44  0  0  0  0            999 V2000
   -7.8592  -16.0875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
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  3  4  1  0  0  0  0
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M  END
> <DATABASE_ID>
HMDB0254434

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCC1=C(C)C(=O)C2=CC=CC=C2C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C41H56O2/c1-30(2)16-11-17-31(3)18-12-19-32(4)20-13-21-33(5)22-14-23-34(6)24-15-25-35(7)28-29-37-36(8)40(42)38-26-9-10-27-39(38)41(37)43/h9-10,16,18,20,22,24,26-28H,11-15,17,19,21,23,25,29H2,1-8H3

> <INCHI_KEY>
PFRQBZFETXBLTP-UHFFFAOYSA-N

> <FORMULA>
C41H56O2

> <MOLECULAR_WEIGHT>
580.897

> <EXACT_MASS>
580.428031043

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
99

> <JCHEM_AVERAGE_POLARIZABILITY>
73.3002687518553

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(3,7,11,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaen-1-yl)-3-methyl-1,4-dihydronaphthalene-1,4-dione

> <ALOGPS_LOGP>
9.01

> <JCHEM_LOGP>
11.79913591433333

> <ALOGPS_LOGS>
-6.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-7.224343414413889

> <JCHEM_POLAR_SURFACE_AREA>
34.14

> <JCHEM_REFRACTIVITY>
193.11200000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
17

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.66e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(3,7,11,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaen-1-yl)-3-methylnaphthalene-1,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0254434
     RDKit          3D
Menaquinone 6
 99100  0  0  0  0  0  0  0  0999 V2000
    9.9465    1.0835   -3.5321 C   0  0  0  0  0  0  0  0  0  0  0  0
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  8 55  1  0
  8 56  1  0
  8 57  1  0
  9 58  1  0
 10 59  1  0
 10 60  1  0
 11 61  1  0
 11 62  1  0
 13 63  1  0
 13 64  1  0
 13 65  1  0
 14 66  1  0
 15 67  1  0
 15 68  1  0
 16 69  1  0
 16 70  1  0
 18 71  1  0
 18 72  1  0
 18 73  1  0
 19 74  1  0
 20 75  1  0
 20 76  1  0
 21 77  1  0
 21 78  1  0
 23 79  1  0
 23 80  1  0
 23 81  1  0
 24 82  1  0
 25 83  1  0
 25 84  1  0
 26 85  1  0
 26 86  1  0
 28 87  1  0
 28 88  1  0
 28 89  1  0
 29 90  1  0
 30 91  1  0
 30 92  1  0
 33 93  1  0
 33 94  1  0
 33 95  1  0
 37 96  1  0
 38 97  1  0
 39 98  1  0
 40 99  1  0
M  END

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  C   UNK     0     -14.670 -30.030   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0     -14.670 -28.490   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0     -13.337 -27.720   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -13.337 -26.180   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0     -12.003 -25.410   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0     -12.003 -23.870   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0     -10.669 -23.100   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0     -10.669 -21.560   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -9.336 -20.790   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -9.336 -19.250   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -8.002 -18.480   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -8.002 -16.940   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -6.668 -16.170   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -6.668 -14.630   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -5.335 -13.860   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -5.335 -12.320   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -8.002 -13.860   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0     -10.669 -18.480   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0     -13.337 -23.100   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0     -16.004 -27.720   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   43                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   42                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   41                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   40                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   39                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   38                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   36                                                  
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31   35                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   30   36                                                  
CONECT   36   35   25   37                                                  
CONECT   37   36                                                            
CONECT   38   22                                                            
CONECT   39   18                                                            
CONECT   40   14                                                            
CONECT   41   10                                                            
CONECT   42    6                                                            
CONECT   43    2                                                            
MASTER        0    0    0    0    0    0    0    0   43    0   88    0
END

COMPND    HMDB0254434
HETATM    1  C1  UNL     1       9.947   1.083  -3.532  1.00  0.00           C  
HETATM    2  C2  UNL     1      10.607  -0.060  -2.845  1.00  0.00           C  
HETATM    3  C3  UNL     1      11.779  -0.710  -3.541  1.00  0.00           C  
HETATM    4  C4  UNL     1      10.199  -0.510  -1.675  1.00  0.00           C  
HETATM    5  C5  UNL     1       9.042   0.085  -0.942  1.00  0.00           C  
HETATM    6  C6  UNL     1       8.010  -0.934  -0.586  1.00  0.00           C  
HETATM    7  C7  UNL     1       6.895  -0.278   0.164  1.00  0.00           C  
HETATM    8  C8  UNL     1       5.726  -1.110   0.639  1.00  0.00           C  
HETATM    9  C9  UNL     1       6.912   1.020   0.413  1.00  0.00           C  
HETATM   10  C10 UNL     1       5.863   1.767   1.147  1.00  0.00           C  
HETATM   11  C11 UNL     1       5.178   2.829   0.354  1.00  0.00           C  
HETATM   12  C12 UNL     1       4.201   3.538   1.192  1.00  0.00           C  
HETATM   13  C13 UNL     1       4.722   4.240   2.421  1.00  0.00           C  
HETATM   14  C14 UNL     1       2.899   3.603   0.969  1.00  0.00           C  
HETATM   15  C15 UNL     1       2.155   2.995  -0.131  1.00  0.00           C  
HETATM   16  C16 UNL     1       1.009   2.139   0.372  1.00  0.00           C  
HETATM   17  C17 UNL     1       1.463   1.076   1.254  1.00  0.00           C  
HETATM   18  C18 UNL     1       2.041   1.417   2.628  1.00  0.00           C  
HETATM   19  C19 UNL     1       1.339  -0.205   0.984  1.00  0.00           C  
HETATM   20  C20 UNL     1       0.733  -0.783  -0.222  1.00  0.00           C  
HETATM   21  C21 UNL     1      -0.433  -1.678   0.199  1.00  0.00           C  
HETATM   22  C22 UNL     1      -1.519  -0.990   0.889  1.00  0.00           C  
HETATM   23  C23 UNL     1      -1.249  -0.259   2.186  1.00  0.00           C  
HETATM   24  C24 UNL     1      -2.770  -0.952   0.476  1.00  0.00           C  
HETATM   25  C25 UNL     1      -3.229  -1.608  -0.749  1.00  0.00           C  
HETATM   26  C26 UNL     1      -4.036  -2.831  -0.502  1.00  0.00           C  
HETATM   27  C27 UNL     1      -5.262  -2.666   0.305  1.00  0.00           C  
HETATM   28  C28 UNL     1      -5.146  -2.247   1.734  1.00  0.00           C  
HETATM   29  C29 UNL     1      -6.471  -2.930  -0.181  1.00  0.00           C  
HETATM   30  C30 UNL     1      -7.660  -2.758   0.634  1.00  0.00           C  
HETATM   31  C31 UNL     1      -8.709  -1.879   0.054  1.00  0.00           C  
HETATM   32  C32 UNL     1      -9.929  -2.308  -0.211  1.00  0.00           C  
HETATM   33  C33 UNL     1     -10.316  -3.723   0.065  1.00  0.00           C  
HETATM   34  C34 UNL     1     -10.896  -1.362  -0.788  1.00  0.00           C  
HETATM   35  O1  UNL     1     -12.061  -1.767  -1.041  1.00  0.00           O  
HETATM   36  C35 UNL     1     -10.582   0.015  -1.082  1.00  0.00           C  
HETATM   37  C36 UNL     1     -11.494   0.903  -1.631  1.00  0.00           C  
HETATM   38  C37 UNL     1     -11.178   2.215  -1.913  1.00  0.00           C  
HETATM   39  C38 UNL     1      -9.902   2.649  -1.633  1.00  0.00           C  
HETATM   40  C39 UNL     1      -8.979   1.780  -1.085  1.00  0.00           C  
HETATM   41  C40 UNL     1      -9.294   0.467  -0.802  1.00  0.00           C  
HETATM   42  C41 UNL     1      -8.360  -0.493  -0.231  1.00  0.00           C  
HETATM   43  O2  UNL     1      -7.186  -0.107   0.031  1.00  0.00           O  
HETATM   44  H1  UNL     1       9.734   1.865  -2.767  1.00  0.00           H  
HETATM   45  H2  UNL     1       9.028   0.707  -4.012  1.00  0.00           H  
HETATM   46  H3  UNL     1      10.614   1.488  -4.330  1.00  0.00           H  
HETATM   47  H4  UNL     1      11.437  -1.512  -4.217  1.00  0.00           H  
HETATM   48  H5  UNL     1      12.297   0.055  -4.156  1.00  0.00           H  
HETATM   49  H6  UNL     1      12.495  -1.062  -2.780  1.00  0.00           H  
HETATM   50  H7  UNL     1      10.738  -1.357  -1.228  1.00  0.00           H  
HETATM   51  H8  UNL     1       8.526   0.841  -1.582  1.00  0.00           H  
HETATM   52  H9  UNL     1       9.460   0.512  -0.013  1.00  0.00           H  
HETATM   53  H10 UNL     1       8.445  -1.715   0.108  1.00  0.00           H  
HETATM   54  H11 UNL     1       7.589  -1.492  -1.445  1.00  0.00           H  
HETATM   55  H12 UNL     1       6.038  -2.182   0.603  1.00  0.00           H  
HETATM   56  H13 UNL     1       4.883  -1.034  -0.077  1.00  0.00           H  
HETATM   57  H14 UNL     1       5.425  -0.885   1.666  1.00  0.00           H  
HETATM   58  H15 UNL     1       7.773   1.609   0.057  1.00  0.00           H  
HETATM   59  H16 UNL     1       6.347   2.280   2.022  1.00  0.00           H  
HETATM   60  H17 UNL     1       5.101   1.068   1.529  1.00  0.00           H  
HETATM   61  H18 UNL     1       5.987   3.540   0.023  1.00  0.00           H  
HETATM   62  H19 UNL     1       4.665   2.400  -0.528  1.00  0.00           H  
HETATM   63  H20 UNL     1       5.815   4.386   2.352  1.00  0.00           H  
HETATM   64  H21 UNL     1       4.255   5.221   2.554  1.00  0.00           H  
HETATM   65  H22 UNL     1       4.510   3.640   3.326  1.00  0.00           H  
HETATM   66  H23 UNL     1       2.289   4.197   1.678  1.00  0.00           H  
HETATM   67  H24 UNL     1       2.731   2.367  -0.821  1.00  0.00           H  
HETATM   68  H25 UNL     1       1.713   3.816  -0.793  1.00  0.00           H  
HETATM   69  H26 UNL     1       0.505   1.748  -0.528  1.00  0.00           H  
HETATM   70  H27 UNL     1       0.243   2.808   0.878  1.00  0.00           H  
HETATM   71  H28 UNL     1       1.635   2.385   2.953  1.00  0.00           H  
HETATM   72  H29 UNL     1       1.660   0.641   3.348  1.00  0.00           H  
HETATM   73  H30 UNL     1       3.116   1.323   2.609  1.00  0.00           H  
HETATM   74  H31 UNL     1       1.747  -0.929   1.737  1.00  0.00           H  
HETATM   75  H32 UNL     1       0.439  -0.102  -1.006  1.00  0.00           H  
HETATM   76  H33 UNL     1       1.523  -1.453  -0.700  1.00  0.00           H  
HETATM   77  H34 UNL     1      -0.037  -2.489   0.881  1.00  0.00           H  
HETATM   78  H35 UNL     1      -0.752  -2.217  -0.705  1.00  0.00           H  
HETATM   79  H36 UNL     1      -1.284   0.823   1.988  1.00  0.00           H  
HETATM   80  H37 UNL     1      -0.368  -0.640   2.694  1.00  0.00           H  
HETATM   81  H38 UNL     1      -2.124  -0.524   2.850  1.00  0.00           H  
HETATM   82  H39 UNL     1      -3.501  -0.378   1.060  1.00  0.00           H  
HETATM   83  H40 UNL     1      -3.875  -0.821  -1.275  1.00  0.00           H  
HETATM   84  H41 UNL     1      -2.455  -1.846  -1.497  1.00  0.00           H  
HETATM   85  H42 UNL     1      -3.355  -3.546   0.057  1.00  0.00           H  
HETATM   86  H43 UNL     1      -4.237  -3.363  -1.463  1.00  0.00           H  
HETATM   87  H44 UNL     1      -4.096  -2.331   2.089  1.00  0.00           H  
HETATM   88  H45 UNL     1      -5.726  -2.995   2.367  1.00  0.00           H  
HETATM   89  H46 UNL     1      -5.511  -1.244   1.948  1.00  0.00           H  
HETATM   90  H47 UNL     1      -6.530  -3.279  -1.204  1.00  0.00           H  
HETATM   91  H48 UNL     1      -8.164  -3.733   0.882  1.00  0.00           H  
HETATM   92  H49 UNL     1      -7.388  -2.262   1.607  1.00  0.00           H  
HETATM   93  H50 UNL     1     -10.152  -4.026   1.117  1.00  0.00           H  
HETATM   94  H51 UNL     1     -11.432  -3.829  -0.076  1.00  0.00           H  
HETATM   95  H52 UNL     1      -9.862  -4.414  -0.681  1.00  0.00           H  
HETATM   96  H53 UNL     1     -12.490   0.544  -1.843  1.00  0.00           H  
HETATM   97  H54 UNL     1     -11.874   2.921  -2.341  1.00  0.00           H  
HETATM   98  H55 UNL     1      -9.638   3.698  -1.859  1.00  0.00           H  
HETATM   99  H56 UNL     1      -7.975   2.108  -0.862  1.00  0.00           H  
CONECT    1    2   44   45   46
CONECT    2    3    4    4
CONECT    3   47   48   49
CONECT    4    5   50
CONECT    5    6   51   52
CONECT    6    7   53   54
CONECT    7    8    9    9
CONECT    8   55   56   57
CONECT    9   10   58
CONECT   10   11   59   60
CONECT   11   12   61   62
CONECT   12   13   14   14
CONECT   13   63   64   65
CONECT   14   15   66
CONECT   15   16   67   68
CONECT   16   17   69   70
CONECT   17   18   19   19
CONECT   18   71   72   73
CONECT   19   20   74
CONECT   20   21   75   76
CONECT   21   22   77   78
CONECT   22   23   24   24
CONECT   23   79   80   81
CONECT   24   25   82
CONECT   25   26   83   84
CONECT   26   27   85   86
CONECT   27   28   29   29
CONECT   28   87   88   89
CONECT   29   30   90
CONECT   30   31   91   92
CONECT   31   32   32   42
CONECT   32   33   34
CONECT   33   93   94   95
CONECT   34   35   35   36
CONECT   36   37   37   41
CONECT   37   38   96
CONECT   38   39   39   97
CONECT   39   40   98
CONECT   40   41   41   99
CONECT   41   42
CONECT   42   43   43
END

HMDB0254434
     RDKit          3D
Menaquinone 6
 99100  0  0  0  0  0  0  0  0999 V2000
    9.9465    1.0835   -3.5321 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6071   -0.0605   -2.8455 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7793   -0.7103   -3.5407 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1987   -0.5101   -1.6746 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0423    0.0848   -0.9424 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0097   -0.9339   -0.5857 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8947   -0.2779    0.1637 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7256   -1.1105    0.6386 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9122    1.0197    0.4130 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8630    1.7667    1.1466 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1776    2.8294    0.3537 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2008    3.5384    1.1921 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7218    4.2395    2.4207 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8986    3.6030    0.9692 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1554    2.9946   -0.1310 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0089    2.1393    0.3721 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4628    1.0756    1.2540 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0413    1.4169    2.6281 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3392   -0.2047    0.9841 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7335   -0.7830   -0.2224 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4328   -1.6778    0.1987 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5192   -0.9899    0.8885 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2489   -0.2595    2.1864 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7698   -0.9518    0.4761 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2292   -1.6081   -0.7490 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0362   -2.8306   -0.5022 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2617   -2.6655    0.3047 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1461   -2.2474    1.7337 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4707   -2.9303   -0.1815 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6600   -2.7582    0.6342 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7088   -1.8791    0.0537 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9290   -2.3085   -0.2113 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3159   -3.7234    0.0650 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.8960   -1.3619   -0.7881 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0607   -1.7672   -1.0410 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5822    0.0153   -1.0823 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.4941    0.9031   -1.6308 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1780    2.2150   -1.9128 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9017    2.6491   -1.6334 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9792    1.7803   -1.0851 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2942    0.4668   -0.8024 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3600   -0.4930   -0.2313 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1860   -0.1065    0.0308 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7338    1.8655   -2.7672 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0282    0.7068   -4.0115 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.6138    1.4877   -4.3303 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.4371   -1.5117   -4.2166 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.2974    0.0551   -4.1564 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.4954   -1.0616   -2.7799 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.7382   -1.3570   -1.2282 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5256    0.8407   -1.5820 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.4605    0.5120   -0.0126 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4447   -1.7147    0.1083 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5892   -1.4918   -1.4448 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0382   -2.1822    0.6033 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8827   -1.0342   -0.0769 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4247   -0.8847    1.6655 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7734    1.6088    0.0571 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3474    2.2805    2.0221 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1015    1.0678    1.5288 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9870    3.5398    0.0228 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6645    2.4001   -0.5280 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8151    4.3864    2.3522 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2549    5.2209    2.5538 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5103    3.6401    3.3263 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2892    4.1974    1.6776 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7308    2.3668   -0.8213 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7131    3.8158   -0.7929 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5048    1.7478   -0.5280 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2428    2.8075    0.8778 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6349    2.3848    2.9532 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6599    0.6413    3.3477 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1158    1.3229    2.6092 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7470   -0.9295    1.7371 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4393   -0.1017   -1.0057 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5234   -1.4529   -0.6996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0366   -2.4895    0.8807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7523   -2.2173   -0.7055 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2835    0.8226    1.9882 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3675   -0.6401    2.6938 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1243   -0.5238    2.8504 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5006   -0.3777    1.0603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8749   -0.8211   -1.2751 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4553   -1.8463   -1.4968 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3553   -3.5464    0.0574 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2369   -3.3630   -1.4631 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0958   -2.3307    2.0889 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7261   -2.9953    2.3669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5107   -1.2443    1.9477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5301   -3.2789   -1.2043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1638   -3.7332    0.8823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3877   -2.2625    1.6072 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1523   -4.0261    1.1169 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.4318   -3.8289   -0.0757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8616   -4.4142   -0.6808 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.4898    0.5437   -1.8426 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.8736    2.9212   -2.3414 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6381    3.6983   -1.8592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9751    2.1078   -0.8622 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  3
  9 10  1  0
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 40 99  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₄₁H₅₆O₂

Average Molecular Weight

580.897

Monoisotopic Molecular Weight

580.428031043

IUPAC Name

2-(3,7,11,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaen-1-yl)-3-methyl-1,4-dihydronaphthalene-1,4-dione

Traditional Name

2-(3,7,11,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaen-1-yl)-3-methylnaphthalene-1,4-dione

CAS Registry Number

Not Available

SMILES

CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCC1=C(C)C(=O)C2=CC=CC=C2C1=O

InChI Identifier

InChI=1S/C41H56O2/c1-30(2)16-11-17-31(3)18-12-19-32(4)20-13-21-33(5)22-14-23-34(6)24-15-25-35(7)28-29-37-36(8)40(42)38-26-9-10-27-39(38)41(37)43/h9-10,16,18,20,22,24,26-28H,11-15,17,19,21,23,25,29H2,1-8H3

InChI Key

PFRQBZFETXBLTP-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sesterterpenoids. These are terpenes composed of five consecutive isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesterterpenoids

Direct Parent

Sesterterpenoids

Alternative Parents

Substituents

Sesterterpenoid
Naphthalene
Benzenoid
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic compounds

External Descriptors

a menaquinone (CPD-9724 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (HMDB: HMDB0254434)

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
logP	9.01	ALOGPS
logP	11.8	ChemAxon
logS	-6.3	ALOGPS
pKa (Strongest Basic)	-7.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	34.14 Å²	ChemAxon
Rotatable Bond Count	17	ChemAxon
Refractivity	193.11 m³·mol⁻¹	ChemAxon
Polarizability	73.3 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	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]+	229.884	30932474
DeepCCS	[M-H]-	227.489	30932474
DeepCCS	[M-2H]-	260.372	30932474
DeepCCS	[M+Na]+	235.797	30932474
AllCCS	[M+H]+	252.1	32859911
AllCCS	[M+H-H2O]+	250.7	32859911
AllCCS	[M+NH4]+	253.3	32859911
AllCCS	[M+Na]+	253.7	32859911
AllCCS	[M-H]-	226.0	32859911
AllCCS	[M+Na-2H]-	228.8	32859911
AllCCS	[M+HCOO]-	232.1	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	38.0605 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	0.68 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	4867.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	1079.8 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	450.5 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	533.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	326.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	1496.0 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	1389.8 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	115.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	3347.9 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	1243.2 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	2235.5 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	1271.7 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	756.5 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	313.4 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	1047.7 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	10.2 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Menaquinone 6	CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCC1=C(C)C(=O)C2=CC=CC=C2C1=O	5149.2	Standard polar	33892256
Menaquinone 6	CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCC1=C(C)C(=O)C2=CC=CC=C2C1=O	4272.2	Standard non polar	33892256
Menaquinone 6	CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCC1=C(C)C(=O)C2=CC=CC=C2C1=O	4348.8	Semi standard non polar	33892256

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Menaquinone 6 10V, Positive-QTOF	splash10-001i-1102490000-2e736246395907869caf	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Menaquinone 6 20V, Positive-QTOF	splash10-0019-1309710000-c0ffe460a791df64629f	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Menaquinone 6 40V, Positive-QTOF	splash10-052s-2915400000-10ada8609fdbe4921e46	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Menaquinone 6 10V, Negative-QTOF	splash10-004i-0000090000-e02f4c9509bc27ca251e	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Menaquinone 6 20V, Negative-QTOF	splash10-004r-0911370000-7fa01552af19c0511e2a	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Menaquinone 6 40V, Negative-QTOF	splash10-0f9g-2901640000-593c20c59ef09807f54f	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

92731

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

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for Menaquinone 6 (HMDB0254434)

MOL for HMDB0254434 (Menaquinone 6)

3D MOL for HMDB0254434 (Menaquinone 6)

3D SDF for HMDB0254434 (Menaquinone 6)

3D-SDF for HMDB0254434 (Menaquinone 6)

PDB for HMDB0254434 (Menaquinone 6)

3D PDB for HMDB0254434 (Menaquinone 6)

SMILES for HMDB0254434 (Menaquinone 6)

INCHI for HMDB0254434 (Menaquinone 6)

Structure for HMDB0254434 (Menaquinone 6)

3D Structure for HMDB0254434 (Menaquinone 6)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

MS/MS Spectra