NP-MRD: Showing NP-Card for Phylloquinone (NP0334583)

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Record Information

Version

2.0

Created at

2024-09-10 19:00:51 UTC

Updated at

2024-09-10 19:00:51 UTC

NP-MRD ID

NP0334583

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Phylloquinone

Description

Phylloquinone 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. Phylloquinone was first documented in 2024 (PMID: 39299070). Based on a literature review a small amount of articles have been published on Phylloquinone (PMID: 39271942) (PMID: 39125301).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 05252321333D          

 33 34  0  0  0  0            999 V2000
   10.4273   -0.3037   -2.3278 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9001   -0.7819   -0.0100 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7970    1.6347    1.5994 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7827    1.5306    2.0491 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6954   -0.8752    1.5128 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9399   -0.7458   -2.3458 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.9864   -0.3129   -0.6491 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.8039    0.3466    0.5451 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0043    0.2528   -0.6682 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2354    0.0962    1.6723 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8679    0.0488    0.0494 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0714   -0.1294   -1.5922 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9391   -0.3732    0.6653 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4371   -0.3068    0.8147 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9515   -0.3706    1.0211 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5172   -0.5125    1.3756 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1229   -0.4810   -0.5601 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.9084   -0.6545   -1.4409 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5250    0.6564    0.9299 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3615    0.4677   -0.3454 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6277    0.6973    0.2792 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4814    0.1147   -1.1716 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.7194    0.1391    1.4298 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8100    0.0453    1.8937 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3714   -0.2861    0.1962 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0572   -0.3479   -1.4419 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8856    0.2771   -0.3103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6156   -0.3509   -1.0697 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4350    0.3072    0.1223 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4421   -0.6777   -1.8481 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0820    0.6221    0.5054 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6188   -1.2861   -2.9489 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9507    1.2355    1.6218 O   0  0  0  0  0  0  0  0  0  0  0  0
  1 22  1  0  0  0  0
  2 22  1  0  0  0  0
 23  3  1  6  0  0  0
 24  4  1  6  0  0  0
  5 25  1  0  0  0  0
  6 26  1  0  0  0  0
  7  8  2  0  0  0  0
  7 18  1  0  0  0  0
  8 19  1  0  0  0  0
  9 12  1  0  0  0  0
  9 13  1  0  0  0  0
 10 14  1  0  0  0  0
 10 15  1  0  0  0  0
 11 16  1  0  0  0  0
 11 17  1  0  0  0  0
 12 22  1  0  0  0  0
 13 23  1  0  0  0  0
 14 23  1  0  0  0  0
 15 24  1  0  0  0  0
 16 24  1  0  0  0  0
 17 25  1  0  0  0  0
 18 28  2  0  0  0  0
 19 29  2  0  0  0  0
 20 21  1  0  0  0  0
 20 25  2  0  0  0  0
 21 27  1  0  0  0  0
 26 27  2  0  0  0  0
 26 30  1  0  0  0  0
 27 31  1  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
 29 31  1  0  0  0  0
 30 32  2  0  0  0  0
 31 33  2  0  0  0  0
M  END


  Mrv2104 05252321333D          

 33 34  0  0  0  0            999 V2000
   10.4273   -0.3037   -2.3278 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9001   -0.7819   -0.0100 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7970    1.6347    1.5994 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7827    1.5306    2.0491 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6954   -0.8752    1.5128 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9399   -0.7458   -2.3458 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.9864   -0.3129   -0.6491 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.8039    0.3466    0.5451 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0043    0.2528   -0.6682 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2354    0.0962    1.6723 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8679    0.0488    0.0494 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0714   -0.1294   -1.5922 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9391   -0.3732    0.6653 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4371   -0.3068    0.8147 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9515   -0.3706    1.0211 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5172   -0.5125    1.3756 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1229   -0.4810   -0.5601 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.9084   -0.6545   -1.4409 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5250    0.6564    0.9299 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3615    0.4677   -0.3454 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6277    0.6973    0.2792 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4814    0.1147   -1.1716 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.7194    0.1391    1.4298 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8100    0.0453    1.8937 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3714   -0.2861    0.1962 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0572   -0.3479   -1.4419 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8856    0.2771   -0.3103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6156   -0.3509   -1.0697 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4350    0.3072    0.1223 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4421   -0.6777   -1.8481 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0820    0.6221    0.5054 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6188   -1.2861   -2.9489 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9507    1.2355    1.6218 O   0  0  0  0  0  0  0  0  0  0  0  0
  1 22  1  0  0  0  0
  2 22  1  0  0  0  0
 23  3  1  6  0  0  0
 24  4  1  6  0  0  0
  5 25  1  0  0  0  0
  6 26  1  0  0  0  0
  7  8  2  0  0  0  0
  7 18  1  0  0  0  0
  8 19  1  0  0  0  0
  9 12  1  0  0  0  0
  9 13  1  0  0  0  0
 10 14  1  0  0  0  0
 10 15  1  0  0  0  0
 11 16  1  0  0  0  0
 11 17  1  0  0  0  0
 12 22  1  0  0  0  0
 13 23  1  0  0  0  0
 14 23  1  0  0  0  0
 15 24  1  0  0  0  0
 16 24  1  0  0  0  0
 17 25  1  0  0  0  0
 18 28  2  0  0  0  0
 19 29  2  0  0  0  0
 20 21  1  0  0  0  0
 20 25  2  0  0  0  0
 21 27  1  0  0  0  0
 26 27  2  0  0  0  0
 26 30  1  0  0  0  0
 27 31  1  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
 29 31  1  0  0  0  0
 30 32  2  0  0  0  0
 31 33  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0334583

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)CCC[C@@H](C)CCC[C@@H](C)CCC\C(C)=C\CC1=C(C)C(=O)C2=CC=CC=C2C1=O

> <INCHI_IDENTIFIER>
InChI=1/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+/t23-,24-/s2

> <INCHI_KEY>
MBWXNTAXLNYFJB-CCNXOCMANA-N

> <FORMULA>
C31H46O2

> <MOLECULAR_WEIGHT>
450.707

> <EXACT_MASS>
450.349780721

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
79

> <JCHEM_AVERAGE_POLARIZABILITY>
56.95077558064732

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
9.696445808333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-7.22434341203462

> <JCHEM_POLAR_SURFACE_AREA>
34.14

> <JCHEM_REFRACTIVITY>
142.9568

> <JCHEM_ROTATABLE_BOND_COUNT>
14

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
phytonadione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-MAY-23         0                                  
HETATM    1  C   UNK     0      10.427  -0.304  -2.328  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.900  -0.782  -0.010  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.797   1.635   1.599  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.783   1.531   2.049  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.695  -0.875   1.513  0.00  0.00           C+0
HETATM    6  C   UNK     0      -5.940  -0.746  -2.346  0.00  0.00           C+0
HETATM    7  C   UNK     0     -11.986  -0.313  -0.649  0.00  0.00           C+0
HETATM    8  C   UNK     0     -11.804   0.347   0.545  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.004   0.253  -0.668  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.235   0.096   1.672  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.868   0.049   0.049  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.071  -0.129  -1.592  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.939  -0.373   0.665  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.437  -0.307   0.815  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.952  -0.371   1.021  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.517  -0.513   1.376  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.123  -0.481  -0.560  0.00  0.00           C+0
HETATM   18  C   UNK     0     -10.908  -0.655  -1.441  0.00  0.00           C+0
HETATM   19  C   UNK     0     -10.525   0.656   0.930  0.00  0.00           C+0
HETATM   20  C   UNK     0      -4.362   0.468  -0.345  0.00  0.00           C+0
HETATM   21  C   UNK     0      -5.628   0.697   0.279  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.481   0.115  -1.172  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.719   0.139   1.430  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.810   0.045   1.894  0.00  0.00           C+0
HETATM   25  C   UNK     0      -3.371  -0.286   0.196  0.00  0.00           C+0
HETATM   26  C   UNK     0      -7.057  -0.348  -1.442  0.00  0.00           C+0
HETATM   27  C   UNK     0      -6.886   0.277  -0.310  0.00  0.00           C+0
HETATM   28  C   UNK     0      -9.616  -0.351  -1.070  0.00  0.00           C+0
HETATM   29  C   UNK     0      -9.435   0.307   0.122  0.00  0.00           C+0
HETATM   30  C   UNK     0      -8.442  -0.678  -1.848  0.00  0.00           C+0
HETATM   31  C   UNK     0      -8.082   0.622   0.505  0.00  0.00           C+0
HETATM   32  O   UNK     0      -8.619  -1.286  -2.949  0.00  0.00           O+0
HETATM   33  O   UNK     0      -7.951   1.236   1.622  0.00  0.00           O+0
CONECT    1   22                                                            
CONECT    2   22                                                            
CONECT    3   23                                                            
CONECT    4   24                                                            
CONECT    5   25                                                            
CONECT    6   26                                                            
CONECT    7    8   18                                                       
CONECT    8    7   19                                                       
CONECT    9   12   13                                                       
CONECT   10   14   15                                                       
CONECT   11   16   17                                                       
CONECT   12    9   22                                                       
CONECT   13    9   23                                                       
CONECT   14   10   23                                                       
CONECT   15   10   24                                                       
CONECT   16   11   24                                                       
CONECT   17   11   25                                                       
CONECT   18    7   28                                                       
CONECT   19    8   29                                                       
CONECT   20   21   25                                                       
CONECT   21   20   27                                                       
CONECT   22    1    2   12                                                  
CONECT   23    3   13   14                                                  
CONECT   24    4   15   16                                                  
CONECT   25    5   17   20                                                  
CONECT   26    6   27   30                                                  
CONECT   27   21   26   31                                                  
CONECT   28   18   29   30                                                  
CONECT   29   19   28   31                                                  
CONECT   30   26   28   32                                                  
CONECT   31   27   29   33                                                  
CONECT   32   30                                                            
CONECT   33   31                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   68    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₁H₄₆O₂

Average Mass

450.7070 Da

Monoisotopic Mass

450.34978 Da

IUPAC Name

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

Traditional Name

phytonadione

CAS Registry Number

Not Available

SMILES

CC(C)CCC[C@@H](C)CCC[C@@H](C)CCC\C(C)=C\CC1=C(C)C(=O)C2=CC=CC=C2C1=O

InChI Identifier

InChI=1/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+/t23-,24-/s2

InChI Key

MBWXNTAXLNYFJB-CCNXOCMANA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

This compound 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

phylloquinones (CHEBI:18067 )
Vitamin K (LMPR02030028 )

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	9.7	ChemAxon
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	56.95 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

Not Available

KNApSAcK ID

C00002868

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Phytomenadione

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Akman F: A detailed TD-DFT and intermolecular interaction study of vitamin K in soluble, poorly soluble and insoluble solvents, as well as an ADME and molecular docking study. Spectrochim Acta A Mol Biomol Spectrosc. 2024 Sep 18;325:125130. doi: 10.1016/j.saa.2024.125130. [PubMed:39299070 ]
Tiwari A, Mamedov F, Fitzpatrick D, Gunell S, Tikkanen M, Aro EM: Differential FeS cluster photodamage plays a critical role in regulating excess electron flow through photosystem I. Nat Plants. 2024 Sep 13. doi: 10.1038/s41477-024-01780-2. [PubMed:39271942 ]
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Showing NP-Card for Phylloquinone (NP0334583)

MOL for NP0334583 (Phylloquinone)

3D MOL for NP0334583 (Phylloquinone)

3D SDF for NP0334583 (Phylloquinone)

3D-SDF for NP0334583 (Phylloquinone)

PDB for NP0334583 (Phylloquinone)

3D PDB for NP0334583 (Phylloquinone)

SMILES for NP0334583 (Phylloquinone)

INCHI for NP0334583 (Phylloquinone)

Structure for NP0334583 (Phylloquinone)

3D Structure for NP0334583 (Phylloquinone)