Showing NP-Card for Phylloquinone (NP0334583)

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Record Information
Version2.0
Created at2024-09-10 19:00:51 UTC
Updated at2024-09-10 19:00:51 UTC
NP-MRD IDNP0334583
Secondary Accession NumbersNone
Natural Product Identification
Common NamePhylloquinone
DescriptionPhylloquinone 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
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0334583 (Phylloquinone)

  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
Download

3D MOL for NP0334583 (Phylloquinone)

Download
3D SDF for NP0334583 (Phylloquinone)
  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

$$$$

Download
3D-SDF for NP0334583 (Phylloquinone)
Download
PDB for NP0334583 (Phylloquinone)
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

Download
3D PDB for NP0334583 (Phylloquinone)
Download
SMILES for NP0334583 (Phylloquinone)
CC(C)CCC[C@@H](C)CCC[C@@H](C)CCC\C(C)=C\CC1=C(C)C(=O)C2=CC=CC=C2C1=O
Download
INCHI for NP0334583 (Phylloquinone)
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
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View in JSmol
SynonymsNot Available
Chemical FormulaC31H46O2
Average Mass450.7070 Da
Monoisotopic Mass450.34978 Da
IUPAC Name2-methyl-3-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]-1,4-dihydronaphthalene-1,4-dione
Traditional Namephytonadione
CAS Registry NumberNot 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 KeyMBWXNTAXLNYFJB-CCNXOCMANA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
DescriptionThis 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.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassPrenol lipids  
Sub ClassQuinone and hydroquinone lipids  
Direct ParentVitamin 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 FrameworkAromatic homopolycyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP9.7ChemAxon
pKa (Strongest Basic)-7.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area34.14 ŲChemAxon
Rotatable Bond Count14ChemAxon
Refractivity142.96 m³·mol⁻¹ChemAxon
Polarizability56.95 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00002868  
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPhytomenadione  
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. 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  ] 
  2. 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  ] 
  3. Aaseth JO, Finnes TE, Askim M, Alexander J: The Importance of Vitamin K and the Combination of Vitamins K and D for Calcium Metabolism and Bone Health: A Review. Nutrients. 2024 Jul 25;16(15):2420. doi: 10.3390/nu16152420. [PubMed:39125301  ]