NP-MRD: Showing NP-Card for vitamin k (NP0147102)

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Record Information

Version

2.0

Created at

2022-09-02 02:38:13 UTC

Updated at

2022-09-02 02:38:14 UTC

NP-MRD ID

NP0147102

Secondary Accession Numbers

None

Natural Product Identification

Common Name

vitamin k

Description

Vitamin K1, also known as phytonadione or mephyton, belongs to the class of organic compounds known as vitamin k compounds. These are quinone lipids containing a methylated naphthoquinone ring structure, and vary in the aliphatic side chain attached at the 3-position. It is also required for the formation of anticoagulant factors protein C and S. It is commonly used to treat warfarin toxicity, and as an antidote for coumatetralyl. Vitamin K1 is an extremely weak basic (essentially neutral) compound (based on its pKa). In humans, vitamin K1 is involved in warfarin action pathway. Outside of the human body, Vitamin K1 is found, on average, in the highest concentration within a few different foods, such as highbush blueberries, common thymes, and common sages and in a lower concentration in hot chocolates, narrowleaf cattails, and napa cabbages. Vitamin K1 has also been detected, but not quantified in, several different foods, such as bamboo shoots, vanilla, green vegetables, american lobsters, and butter substitutes. This could make vitamin K1 a potential biomarker for the consumption of these foods. It is on the World Health Organization's List of Essential Medicines, the most effective and safe medicines needed in a health system. Use is typically recommended by mouth or injection under the skin. vitamin k is found in Homo sapiens, Prunus domestica and Secale cereale. vitamin k was first documented in 1982 (PMID: 7086539). Vitamin K is required for bone protein formation.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305271900322D          

 33 34  0  0  0  0            999 V2000
   26.4422  -11.6182    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.4422   -8.3182    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.8686  -10.7932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5831  -10.3807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.7265  -10.7932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.2976  -10.7932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.0120  -10.3807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1541  -10.3807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.4410  -10.3807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4397  -10.7932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7252  -10.3807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8686  -11.6182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.1555  -10.7932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.7265  -11.6182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0107  -10.7932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.8699  -10.3807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0107  -11.6182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2963  -10.3807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.5844  -10.7932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.2989  -10.3807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.5844  -11.6182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.0133  -10.7932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.7278  -10.3807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.7278   -9.5557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.4422  -10.7932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.1568  -10.3807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.1568   -9.5557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.4422   -9.1432    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.0133   -9.1432    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.8942  -10.8219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.8942   -9.1146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.6418  -10.3979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.6418   -9.5386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 25  2  0  0  0  0
  2 28  2  0  0  0  0
  3  4  1  0  0  0  0
  3  8  1  0  0  0  0
  3 12  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  0  0  0  0
  5  9  1  0  0  0  0
  5 14  1  0  0  0  0
  6  7  1  0  0  0  0
  8 10  1  0  0  0  0
  9 13  1  0  0  0  0
 10 11  1  0  0  0  0
 11 15  1  0  0  0  0
 13 16  1  0  0  0  0
 15 17  1  0  0  0  0
 15 18  1  0  0  0  0
 16 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 24 28  1  0  0  0  0
 24 29  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 30  2  0  0  0  0
 27 28  1  0  0  0  0
 27 31  2  0  0  0  0
 30 32  1  0  0  0  0
 31 33  1  0  0  0  0
 32 33  2  0  0  0  0
M  END


  Mrv1652305271900322D          

 33 34  0  0  0  0            999 V2000
   26.4422  -11.6182    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.4422   -8.3182    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.8686  -10.7932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5831  -10.3807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.7265  -10.7932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.2976  -10.7932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.0120  -10.3807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1541  -10.3807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.4410  -10.3807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4397  -10.7932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7252  -10.3807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8686  -11.6182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.1555  -10.7932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.7265  -11.6182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0107  -10.7932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.8699  -10.3807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0107  -11.6182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2963  -10.3807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.5844  -10.7932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.2989  -10.3807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.5844  -11.6182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.0133  -10.7932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.7278  -10.3807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.7278   -9.5557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.4422  -10.7932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.1568  -10.3807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.1568   -9.5557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.4422   -9.1432    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.0133   -9.1432    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.8942  -10.8219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.8942   -9.1146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.6418  -10.3979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.6418   -9.5386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 25  2  0  0  0  0
  2 28  2  0  0  0  0
  3  4  1  0  0  0  0
  3  8  1  0  0  0  0
  3 12  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  0  0  0  0
  5  9  1  0  0  0  0
  5 14  1  0  0  0  0
  6  7  1  0  0  0  0
  8 10  1  0  0  0  0
  9 13  1  0  0  0  0
 10 11  1  0  0  0  0
 11 15  1  0  0  0  0
 13 16  1  0  0  0  0
 15 17  1  0  0  0  0
 15 18  1  0  0  0  0
 16 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 24 28  1  0  0  0  0
 24 29  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 30  2  0  0  0  0
 27 28  1  0  0  0  0
 27 31  2  0  0  0  0
 30 32  1  0  0  0  0
 31 33  1  0  0  0  0
 32 33  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0147102

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)CCCC(C)CCCC(C)CCC\C(C)=C\CC1=C(C)C(=O)C2=CC=CC=C2C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C31H46O2/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/h7-8,18-20,22-24H,9-17,21H2,1-6H3/b25-20+

> <INCHI_KEY>
MBWXNTAXLNYFJB-LKUDQCMESA-N

> <FORMULA>
C31H46O2

> <MOLECULAR_WEIGHT>
450.6957

> <EXACT_MASS>
450.349780716

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
79

> <JCHEM_AVERAGE_POLARIZABILITY>
56.796606195944925

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-methyl-3-[(2E)-3,7,11,15-tetramethylhexadec-2-en-1-yl]-1,4-dihydronaphthalene-1,4-dione

> <ALOGPS_LOGP>
8.48

> <JCHEM_LOGP>
9.696445808333333

> <ALOGPS_LOGS>
-6.88

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-7.224343412034619

> <JCHEM_POLAR_SURFACE_AREA>
34.14

> <JCHEM_REFRACTIVITY>
142.95679999999993

> <JCHEM_ROTATABLE_BOND_COUNT>
14

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.92e-05 g/l

> <JCHEM_TRADITIONAL_IUPAC>
vitamin k1

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  O   UNK     0      49.359 -21.687   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      49.359 -15.527   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      33.355 -20.147   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      34.688 -19.377   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      38.689 -20.147   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      36.022 -20.147   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      37.356 -19.377   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      32.021 -19.377   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      40.023 -19.377   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      30.687 -20.147   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      29.354 -19.377   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      33.355 -21.687   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      41.357 -20.147   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      38.689 -21.687   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      28.020 -20.147   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      42.690 -19.377   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      28.020 -21.687   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      26.686 -19.377   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      44.024 -20.147   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      45.358 -19.377   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      44.024 -21.687   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      46.691 -20.147   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      48.025 -19.377   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      48.025 -17.837   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      49.359 -20.147   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      50.693 -19.377   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      50.693 -17.837   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      49.359 -17.067   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      46.691 -17.067   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      52.069 -20.201   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      52.069 -17.014   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      53.465 -19.409   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      53.465 -17.805   0.000  0.00  0.00           C+0
CONECT    1   25                                                            
CONECT    2   28                                                            
CONECT    3    4    8   12                                                  
CONECT    4    3    6                                                       
CONECT    5    7    9   14                                                  
CONECT    6    4    7                                                       
CONECT    7    5    6                                                       
CONECT    8    3   10                                                       
CONECT    9    5   13                                                       
CONECT   10    8   11                                                       
CONECT   11   10   15                                                       
CONECT   12    3                                                            
CONECT   13    9   16                                                       
CONECT   14    5                                                            
CONECT   15   11   17   18                                                  
CONECT   16   13   19                                                       
CONECT   17   15                                                            
CONECT   18   15                                                            
CONECT   19   16   20   21                                                  
CONECT   20   19   22                                                       
CONECT   21   19                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23   28   29                                                  
CONECT   25    1   23   26                                                  
CONECT   26   25   27   30                                                  
CONECT   27   26   28   31                                                  
CONECT   28    2   24   27                                                  
CONECT   29   24                                                            
CONECT   30   26   32                                                       
CONECT   31   27   33                                                       
CONECT   32   30   33                                                       
CONECT   33   31   32                                                       
MASTER        0    0    0    0    0    0    0    0   33    0   68    0
END

View in JSmol

Synonyms

Value	Source
Phytonadione	Kegg
2-Methyl-3-phytyl-1,4-naphthoquinone	Kegg
Phytomenadione	Kegg
Mephyton	Kegg
2',3'-trans-Vitamin K1	HMDB
2-Methyl-3-phythyl-1,4-naphthochinon	HMDB
2-Methyl-3-phytyl-1,4-naphthochinon	HMDB
2-Methyl-3-phytyl-1,4-napthoquinone	HMDB
2-Methyl-3-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]naphthalene-1,4-dione	HMDB
3-Phytylmenadione	HMDB
a-Phylloquinone	HMDB
alpha-Phylloquinone	HMDB
Antihemorrhagic vitamin	HMDB
Aqua mephyton	HMDB
Aqua-mephytin	HMDB
Aquamephyton	HMDB, MeSH
Combinal K1	HMDB
Fitomenadiona	HMDB
Fitomenadione	HMDB
K-Ject	HMDB
Kativ N	HMDB
Kephton	HMDB
Kinadion	HMDB
Konakion	HMDB, MeSH
mono-Kay	HMDB
Monodion	HMDB
Phyllochinon	HMDB
Phyllochinonum	HMDB
Phylloquinone	HMDB
Phythyl-menadion	HMDB
Phytomenadionum	HMDB
Phytonadionum	HMDB
Phytylmenadione	HMDB
Synthex P	HMDB
trans-Phylloquinone	HMDB
Vitamin K 1	MeSH, HMDB
Phyllohydroquinone	MeSH, HMDB
Vitamin K1	KEGG
Vitamin K	MeSH, HMDB

Chemical Formula

C₃₁H₄₆O₂

Average Mass

450.6957 Da

Monoisotopic Mass

450.34978 Da

IUPAC Name

2-methyl-3-[(2E)-3,7,11,15-tetramethylhexadec-2-en-1-yl]-1,4-dihydronaphthalene-1,4-dione

Traditional Name

vitamin k1

CAS Registry Number

Not Available

SMILES

CC(C)CCCC(C)CCCC(C)CCC\C(C)=C\CC1=C(C)C(=O)C2=CC=CC=C2C1=O

InChI Identifier

InChI=1S/C31H46O2/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/h7-8,18-20,22-24H,9-17,21H2,1-6H3/b25-20+

InChI Key

MBWXNTAXLNYFJB-LKUDQCMESA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 90 MHz, CDCl₃, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Homo sapiens	LOTUS Database	35616633
Prunus domestica	LOTUS Database	35616633
Secale cereale	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as vitamin k compounds. These are quinone lipids containing a methylated naphthoquinone ring structure, and vary in the aliphatic side chain attached at the 3-position.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Quinone and hydroquinone lipids

Direct Parent

Vitamin K compounds

Alternative Parents

Substituents

Diterpenoid
Naphthoquinone
Naphthalene
Aryl ketone
Quinone
Benzenoid
Ketone
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic compounds

External Descriptors

vitamin K (C02059 )
Fat-soluble vitamins (C02059 )

Physical Properties

State

Not Available

Experimental 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

Predicted Properties

Property	Value	Source
logP	8.48	ALOGPS
logP	9.7	ChemAxon
logS	-6.9	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	14	ChemAxon
Refractivity	142.96 m³·mol⁻¹	ChemAxon
Polarizability	56.8 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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB012357

KNApSAcK ID

C00002868

Chemspider ID

Not Available

KEGG Compound ID

C02059

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Phytomenadione

METLIN ID

Not Available

PubChem Compound

5280483

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Haroon Y, Shearer MJ, Rahim S, Gunn WG, McEnery G, Barkhan P: The content of phylloquinone (vitamin K1) in human milk, cows' milk and infant formula foods determined by high-performance liquid chromatography. J Nutr. 1982 Jun;112(6):1105-17. doi: 10.1093/jn/112.6.1105. [PubMed:7086539 ]
LOTUS database [Link]

Showing NP-Card for vitamin k (NP0147102)

MOL for NP0147102 (vitamin k)

3D MOL for NP0147102 (vitamin k)

3D SDF for NP0147102 (vitamin k)

3D-SDF for NP0147102 (vitamin k)

PDB for NP0147102 (vitamin k)

3D PDB for NP0147102 (vitamin k)

SMILES for NP0147102 (vitamin k)

INCHI for NP0147102 (vitamin k)

Structure for NP0147102 (vitamin k)

3D Structure for NP0147102 (vitamin k)