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Showing metabocard for Vitamin K2 (HMDB0259856)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (4) Show 4 proteinsXML
enzymes (4) Show 4 proteins
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 22:48:01 UTC
Update Date2022-11-23 22:29:21 UTC
HMDB IDHMDB0259856
Secondary Accession NumbersNone
Metabolite Identification
Common NameVitamin K2
Description2-methyl-3-(3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl)-1,4-dihydronaphthalene-1,4-dione belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. Based on a literature review very few articles have been published on 2-methyl-3-(3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl)-1,4-dihydronaphthalene-1,4-dione. This compound has been identified in human blood as reported by (PMID: 31557052 ). Vitamin k2 is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Vitamin K2 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0259856 (Vitamin K2)


  Mrv1652309122100482D          

 33 34  0  0  0  0            999 V2000
    0.0000   -1.6500    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   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   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
    2.8579    0.0000    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
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    2.8579   -1.6500    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
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 31 33  1  0  0  0  0
M  END
Download

3D MOL for HMDB0259856 (Vitamin K2)

HMDB0259856
     RDKit          3D
vitamin K2
 73 74  0  0  0  0  0  0  0  0999 V2000
   -9.8326   -0.9527   -0.0597 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.7631    1.0625   -0.9981 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6392    0.4776   -1.7731 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.4150    0.8314    1.2902 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2752    1.9109    0.7018 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2604    1.2544   -0.1934 C   0  0  0  0  0  0  0  0  0  0  0  0
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    6.1932    1.0008   -2.3983 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0259856 (Vitamin K2)


  Mrv1652309122100482D          

 33 34  0  0  0  0            999 V2000
    0.0000   -1.6500    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   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   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
    2.8579    0.0000    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   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.1434   -1.2375    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
    1.4289   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  -10.0026   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7171   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0026    0.8250    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  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
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  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  6 11  1  0  0  0  0
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  2 12  1  0  0  0  0
 12 13  2  0  0  0  0
  3 14  1  0  0  0  0
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 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
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 20 19  1  4  0  0  0
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 25 26  2  0  0  0  0
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 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 31 33  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0259856

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C31H40O2/c1-22(2)12-9-13-23(3)14-10-15-24(4)16-11-17-25(5)20-21-27-26(6)30(32)28-18-7-8-19-29(28)31(27)33/h7-8,12,14,16,18-20H,9-11,13,15,17,21H2,1-6H3

> <INCHI_KEY>
DKHGMERMDICWDU-UHFFFAOYSA-N

> <FORMULA>
C31H40O2

> <MOLECULAR_WEIGHT>
444.659

> <EXACT_MASS>
444.302830528

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
55.25237139800855

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-methyl-3-(3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl)-1,4-dihydronaphthalene-1,4-dione

> <ALOGPS_LOGP>
7.24

> <JCHEM_LOGP>
8.479707364333333

> <ALOGPS_LOGS>
-5.96

> <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>
145.50680000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.89e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-methyl-3-(3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl)naphthalene-1,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0259856 (Vitamin K2)

HMDB0259856
     RDKit          3D
vitamin K2
 73 74  0  0  0  0  0  0  0  0999 V2000
   -9.8326   -0.9527   -0.0597 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9570    0.0305   -0.7254 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4918    0.9341   -1.7846 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6671    0.0929   -0.3552 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7631    1.0625   -0.9981 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6392    0.4776   -1.7731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6867   -0.3695   -1.0426 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1255   -1.6397   -0.4248 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4190   -0.0096   -0.9685 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3472   -0.7603   -0.2681 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7067    0.0721    0.8249 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6464   -0.7575    1.4696 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9878   -2.0313    2.1219 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6270   -0.2981    1.4320 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6545   -1.1239    2.0688 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4602   -0.4418    3.1260 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3147    0.6192    2.5718 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0833    1.4728    3.5606 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4150    0.8314    1.2902 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2752    1.9109    0.7018 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2604    1.2544   -0.1934 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2466    1.6174   -1.4833 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3036    2.6153   -1.9874 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1932    1.0008   -2.3983 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1998    1.3301   -3.6329 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1533    0.0061   -1.9667 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0405   -0.5585   -2.8724 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9277   -1.4960   -2.4051 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9851   -1.9066   -1.0868 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0834   -1.3162   -0.2274 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1748   -0.3726   -0.6452 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2120    0.2649    0.2478 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2377   -0.0861    1.4524 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4183   -0.4040    0.7137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2632   -1.7974    0.3833 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5717   -1.3920   -0.7689 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5551    0.6885   -1.9333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9600    0.8337   -2.7324 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3658    1.9902   -1.4058 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3354   -0.5618    0.4185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3792    1.6657   -1.7346 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3651    1.7901   -0.2223 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1222   -0.2131   -2.5405 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1210    1.2353   -2.4147 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0829   -2.0311   -0.8804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2399   -1.5984    0.6689 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3956   -2.4680   -0.6257 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1183    0.9169   -1.4595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6838   -1.7290    0.1236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5522   -0.9709   -1.0200 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5037    0.3500    1.5386 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2674    0.9545    0.3604 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4069   -2.8434    1.6410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0814   -2.2105    2.0105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7197   -2.0055    3.2001 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8364    0.6414    0.9647 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3758   -1.5689    1.3454 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2077   -2.0372    2.5723 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1603   -1.2018    3.5880 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8232   -0.0720    3.9707 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1136    1.6618    3.2386 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1215    0.9559    4.5181 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4753    2.4060    3.6622 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9140    0.2123    0.5713 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5742    2.5455    0.1220 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7530    2.5464    1.4479 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2439    2.3062   -1.9160 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5106    2.8084   -3.0553 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3759    3.5961   -1.4745 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0094   -0.2450   -3.9215 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6289   -1.9503   -3.0913 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6934   -2.6513   -0.7277 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1135   -1.6258    0.8101 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
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  2  3
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 17 19  2  3
 19 20  1  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 22 24  1  0
 24 25  2  0
 24 26  1  0
 26 27  2  0
 27 28  1  0
 28 29  2  0
 29 30  1  0
 30 31  2  0
 31 32  1  0
 32 33  2  0
 32 21  1  0
 31 26  1  0
  1 34  1  0
  1 35  1  0
  1 36  1  0
  3 37  1  0
  3 38  1  0
  3 39  1  0
  4 40  1  0
  5 41  1  0
  5 42  1  0
  6 43  1  0
  6 44  1  0
  8 45  1  0
  8 46  1  0
  8 47  1  0
  9 48  1  0
 10 49  1  0
 10 50  1  0
 11 51  1  0
 11 52  1  0
 13 53  1  0
 13 54  1  0
 13 55  1  0
 14 56  1  0
 15 57  1  0
 15 58  1  0
 16 59  1  0
 16 60  1  0
 18 61  1  0
 18 62  1  0
 18 63  1  0
 19 64  1  0
 20 65  1  0
 20 66  1  0
 23 67  1  0
 23 68  1  0
 23 69  1  0
 27 70  1  0
 28 71  1  0
 29 72  1  0
 30 73  1  0
M  END
Download

PDB for HMDB0259856 (Vitamin K2)

HEADER    PROTEIN                                 12-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-21         0                                  
HETATM    1  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.667   1.540   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      -5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -8.002   1.540   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0     -10.669  -0.000   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0     -12.003  -0.770   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0     -13.337  -0.000   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0     -13.337   1.540   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0     -14.670  -0.770   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0     -16.004  -0.000   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0     -17.338  -0.770   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0     -18.672  -0.000   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0     -20.005  -0.770   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0     -18.672   1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4   14                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    6   12                                                  
CONECT   12   11    2   13                                                  
CONECT   13   12                                                            
CONECT   14    3   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   68    0
END
Download

3D PDB for HMDB0259856 (Vitamin K2)

COMPND    HMDB0259856
HETATM    1  C1  UNL     1      -9.833  -0.953  -0.060  1.00  0.00           C  
HETATM    2  C2  UNL     1      -8.957   0.031  -0.725  1.00  0.00           C  
HETATM    3  C3  UNL     1      -9.492   0.934  -1.785  1.00  0.00           C  
HETATM    4  C4  UNL     1      -7.667   0.093  -0.355  1.00  0.00           C  
HETATM    5  C5  UNL     1      -6.763   1.062  -0.998  1.00  0.00           C  
HETATM    6  C6  UNL     1      -5.639   0.478  -1.773  1.00  0.00           C  
HETATM    7  C7  UNL     1      -4.687  -0.370  -1.043  1.00  0.00           C  
HETATM    8  C8  UNL     1      -5.126  -1.640  -0.425  1.00  0.00           C  
HETATM    9  C9  UNL     1      -3.419  -0.010  -0.969  1.00  0.00           C  
HETATM   10  C10 UNL     1      -2.347  -0.760  -0.268  1.00  0.00           C  
HETATM   11  C11 UNL     1      -1.707   0.072   0.825  1.00  0.00           C  
HETATM   12  C12 UNL     1      -0.646  -0.758   1.470  1.00  0.00           C  
HETATM   13  C13 UNL     1      -0.988  -2.031   2.122  1.00  0.00           C  
HETATM   14  C14 UNL     1       0.627  -0.298   1.432  1.00  0.00           C  
HETATM   15  C15 UNL     1       1.655  -1.124   2.069  1.00  0.00           C  
HETATM   16  C16 UNL     1       2.460  -0.442   3.126  1.00  0.00           C  
HETATM   17  C17 UNL     1       3.315   0.619   2.572  1.00  0.00           C  
HETATM   18  C18 UNL     1       4.083   1.473   3.561  1.00  0.00           C  
HETATM   19  C19 UNL     1       3.415   0.831   1.290  1.00  0.00           C  
HETATM   20  C20 UNL     1       4.275   1.911   0.702  1.00  0.00           C  
HETATM   21  C21 UNL     1       5.260   1.254  -0.193  1.00  0.00           C  
HETATM   22  C22 UNL     1       5.247   1.617  -1.483  1.00  0.00           C  
HETATM   23  C23 UNL     1       4.304   2.615  -1.987  1.00  0.00           C  
HETATM   24  C24 UNL     1       6.193   1.001  -2.398  1.00  0.00           C  
HETATM   25  O1  UNL     1       6.200   1.330  -3.633  1.00  0.00           O  
HETATM   26  C25 UNL     1       7.153   0.006  -1.967  1.00  0.00           C  
HETATM   27  C26 UNL     1       8.040  -0.558  -2.872  1.00  0.00           C  
HETATM   28  C27 UNL     1       8.928  -1.496  -2.405  1.00  0.00           C  
HETATM   29  C28 UNL     1       8.985  -1.907  -1.087  1.00  0.00           C  
HETATM   30  C29 UNL     1       8.083  -1.316  -0.227  1.00  0.00           C  
HETATM   31  C30 UNL     1       7.175  -0.373  -0.645  1.00  0.00           C  
HETATM   32  C31 UNL     1       6.212   0.265   0.248  1.00  0.00           C  
HETATM   33  O2  UNL     1       6.238  -0.086   1.452  1.00  0.00           O  
HETATM   34  H1  UNL     1     -10.418  -0.404   0.714  1.00  0.00           H  
HETATM   35  H2  UNL     1      -9.263  -1.797   0.383  1.00  0.00           H  
HETATM   36  H3  UNL     1     -10.572  -1.392  -0.769  1.00  0.00           H  
HETATM   37  H4  UNL     1     -10.555   0.689  -1.933  1.00  0.00           H  
HETATM   38  H5  UNL     1      -8.960   0.834  -2.732  1.00  0.00           H  
HETATM   39  H6  UNL     1      -9.366   1.990  -1.406  1.00  0.00           H  
HETATM   40  H7  UNL     1      -7.335  -0.562   0.418  1.00  0.00           H  
HETATM   41  H8  UNL     1      -7.379   1.666  -1.735  1.00  0.00           H  
HETATM   42  H9  UNL     1      -6.365   1.790  -0.222  1.00  0.00           H  
HETATM   43  H10 UNL     1      -6.122  -0.213  -2.541  1.00  0.00           H  
HETATM   44  H11 UNL     1      -5.121   1.235  -2.415  1.00  0.00           H  
HETATM   45  H12 UNL     1      -6.083  -2.031  -0.880  1.00  0.00           H  
HETATM   46  H13 UNL     1      -5.240  -1.598   0.669  1.00  0.00           H  
HETATM   47  H14 UNL     1      -4.396  -2.468  -0.626  1.00  0.00           H  
HETATM   48  H15 UNL     1      -3.118   0.917  -1.460  1.00  0.00           H  
HETATM   49  H16 UNL     1      -2.684  -1.729   0.124  1.00  0.00           H  
HETATM   50  H17 UNL     1      -1.552  -0.971  -1.020  1.00  0.00           H  
HETATM   51  H18 UNL     1      -2.504   0.350   1.539  1.00  0.00           H  
HETATM   52  H19 UNL     1      -1.267   0.954   0.360  1.00  0.00           H  
HETATM   53  H20 UNL     1      -0.407  -2.843   1.641  1.00  0.00           H  
HETATM   54  H21 UNL     1      -2.081  -2.210   2.010  1.00  0.00           H  
HETATM   55  H22 UNL     1      -0.720  -2.005   3.200  1.00  0.00           H  
HETATM   56  H23 UNL     1       0.836   0.641   0.965  1.00  0.00           H  
HETATM   57  H24 UNL     1       2.376  -1.569   1.345  1.00  0.00           H  
HETATM   58  H25 UNL     1       1.208  -2.037   2.572  1.00  0.00           H  
HETATM   59  H26 UNL     1       3.160  -1.202   3.588  1.00  0.00           H  
HETATM   60  H27 UNL     1       1.823  -0.072   3.971  1.00  0.00           H  
HETATM   61  H28 UNL     1       5.114   1.662   3.239  1.00  0.00           H  
HETATM   62  H29 UNL     1       4.121   0.956   4.518  1.00  0.00           H  
HETATM   63  H30 UNL     1       3.475   2.406   3.662  1.00  0.00           H  
HETATM   64  H31 UNL     1       2.914   0.212   0.571  1.00  0.00           H  
HETATM   65  H32 UNL     1       3.574   2.545   0.122  1.00  0.00           H  
HETATM   66  H33 UNL     1       4.753   2.546   1.448  1.00  0.00           H  
HETATM   67  H34 UNL     1       3.244   2.306  -1.916  1.00  0.00           H  
HETATM   68  H35 UNL     1       4.511   2.808  -3.055  1.00  0.00           H  
HETATM   69  H36 UNL     1       4.376   3.596  -1.474  1.00  0.00           H  
HETATM   70  H37 UNL     1       8.009  -0.245  -3.922  1.00  0.00           H  
HETATM   71  H38 UNL     1       9.629  -1.950  -3.091  1.00  0.00           H  
HETATM   72  H39 UNL     1       9.693  -2.651  -0.728  1.00  0.00           H  
HETATM   73  H40 UNL     1       8.114  -1.626   0.810  1.00  0.00           H  
CONECT    1    2   34   35   36
CONECT    2    3    4    4
CONECT    3   37   38   39
CONECT    4    5   40
CONECT    5    6   41   42
CONECT    6    7   43   44
CONECT    7    8    9    9
CONECT    8   45   46   47
CONECT    9   10   48
CONECT   10   11   49   50
CONECT   11   12   51   52
CONECT   12   13   14   14
CONECT   13   53   54   55
CONECT   14   15   56
CONECT   15   16   57   58
CONECT   16   17   59   60
CONECT   17   18   19   19
CONECT   18   61   62   63
CONECT   19   20   64
CONECT   20   21   65   66
CONECT   21   22   22   32
CONECT   22   23   24
CONECT   23   67   68   69
CONECT   24   25   25   26
CONECT   26   27   27   31
CONECT   27   28   70
CONECT   28   29   29   71
CONECT   29   30   72
CONECT   30   31   31   73
CONECT   31   32
CONECT   32   33   33
END
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SMILES for HMDB0259856 (Vitamin K2)

CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCC1=C(C)C(=O)C2=CC=CC=C2C1=O
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INCHI for HMDB0259856 (Vitamin K2)

InChI=1S/C31H40O2/c1-22(2)12-9-13-23(3)14-10-15-24(4)16-11-17-25(5)20-21-27-26(6)30(32)28-18-7-8-19-29(28)31(27)33/h7-8,12,14,16,18-20H,9-11,13,15,17,21H2,1-6H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
MenaquinoneMeSH
MenaquinonesMeSH
Vitamin K 2MeSH
Vitamin K quinoneMeSH
Chemical FormulaC31H40O2
Average Molecular Weight444.659
Monoisotopic Molecular Weight444.302830528
IUPAC Name2-methyl-3-(3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl)-1,4-dihydronaphthalene-1,4-dione
Traditional Name2-methyl-3-(3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl)naphthalene-1,4-dione
CAS Registry NumberNot Available
SMILES
CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCC1=C(C)C(=O)C2=CC=CC=C2C1=O
InChI Identifier
InChI=1S/C31H40O2/c1-22(2)12-9-13-23(3)14-10-15-24(4)16-11-17-25(5)20-21-27-26(6)30(32)28-18-7-8-19-29(28)31(27)33/h7-8,12,14,16,18-20H,9-11,13,15,17,21H2,1-6H3
InChI KeyDKHGMERMDICWDU-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassDiterpenoids
Direct ParentDiterpenoids
Alternative Parents
Substituents
  • Diterpenoid
  • Naphthalene
  • Benzenoid
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aromatic homopolycyclic compound
Molecular FrameworkAromatic homopolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP7.24ALOGPS
logP8.48ChemAxon
logS-6ALOGPS
pKa (Strongest Basic)-7.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area34.14 ŲChemAxon
Rotatable Bond Count11ChemAxon
Refractivity145.51 m³·mol⁻¹ChemAxon
Polarizability55.25 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+220.80932859911
AllCCS[M+H-H2O]+218.61532859911
AllCCS[M+Na]+223.41332859911
AllCCS[M+NH4]+222.83332859911
AllCCS[M-H]-203.78832859911
AllCCS[M+Na-2H]-205.23632859911
AllCCS[M+HCOO]-207.00532859911
DeepCCS[M+H]+206.24430932474
DeepCCS[M-H]-203.88630932474
DeepCCS[M-2H]-238.04530932474
DeepCCS[M+Na]+214.130932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
vitamin K2CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCC1=C(C)C(=O)C2=CC=CC=C2C1=O4335.1Standard polar33892256
vitamin K2CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCC1=C(C)C(=O)C2=CC=CC=C2C1=O3405.7Standard non polar33892256
vitamin K2CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCC1=C(C)C(=O)C2=CC=CC=C2C1=O3458.4Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Vitamin K2 GC-MS (Non-derivatized) - 70eV, Positivesplash10-056r-3495400000-652d9c83366bc511f5252021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Vitamin K2 GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID3916
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound4056
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]

Enzymes

Enzyme Details
1. Leukotriene-B(4) omega-hydroxylase 1
General function:
Involved in monooxygenase activity
Specific function:
Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.
Gene Name:
CYP4F2
Uniprot ID:
P78329
Molecular weight:
59852.825
Enzyme Details
2. Cytochrome P450 4F11
General function:
Secondary metabolites biosynthesis, transport and catabolism
Specific function:
Not Available
Gene Name:
CYP4F11
Uniprot ID:
Q9HBI6
Molecular weight:
60145.165
Enzyme Details
3. UbiA prenyltransferase domain-containing protein 1
General function:
Not Available
Specific function:
Prenyltransferase that mediates the formation of menaquinone-4 (MK-4) and coenzyme Q10. MK-4 is a vitamin K2 isoform present at high concentrations in the brain, kidney and pancreas, and is required for endothelial cell development. Mediates the conversion of phylloquinone (PK) into MK-4, probably by cleaving the side chain of phylloquinone (PK) to release 2-methyl-1,4-naphthoquinone (menadione; K3) and then prenylating it with geranylgeranyl pyrophosphate (GGPP) to form MK-4. Also plays a role in cardiovascular development independently of MK-4 biosynthesis, by acting as a coenzyme Q10 biosynthetic enzyme: coenzyme Q10, also named ubiquinone, plays an important antioxidant role in the cardiovascular system. Mediates biosynthesis of coenzyme Q10 in the Golgi membrane, leading to protect cardiovascular tissues from NOS3/eNOS-dependent oxidative stress.
Gene Name:
UBIAD1
Uniprot ID:
Q9Y5Z9
Molecular weight:
36830.745
Enzyme Details
4. UbiA prenyltransferase domain-containing protein 1
General function:
Not Available
Specific function:
Prenyltransferase that mediates the formation of menaquinone-4 (MK-4) and coenzyme Q10. MK-4 is a vitamin K2 isoform required for endothelial cell development. Mediates the conversion of phylloquinone (PK) into MK-4, probably by cleaving the side chain of phylloquinone (PK) to release 2-methyl-1,4-naphthoquinone (menadione; K3) and then prenylating it with geranylgeranyl pyrophosphate (GGPP) to form MK-4. Also plays a role in cardiovascular development independently of MK-4 biosynthesis, by acting as a coenzyme Q10 biosynthetic enzyme: coenzyme Q10, also named ubiquinone, plays an important antioxidant role in the cardiovascular system. Mediates biosynthesis of coenzyme Q10 in the Golgi membrane, leading to protect cardiovascular tissues from nos3/eNOS-dependent oxidative stress.
Gene Name:
UBIAD1
Uniprot ID:
E7FB98
Molecular weight:
36213.585