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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2006-08-24 09:02:29 UTC

Update Date

2021-09-14 15:20:04 UTC

HMDB ID

HMDB0004810

Secondary Accession Numbers

HMDB04810

Metabolite Identification

Common Name

5C-aglycone

Description

5C-aglycone is one of the two major aglycone urinary water-soluble metabolites of Phylloquinone (Vitamin K1) and menaquinones (vitamin K2), usually excreted as glucuronide conjugates; their structure suggests that they are formed by an oxidative degradation of the phytyl side chain involving enzymes of omega- and beta-oxidation. Newborn infants as a group, are known to have precariously low vitamin K stores and are routinely given vitamin K prophylaxis at birth. (PMIDs 7306367, 4833371, 15722567).

Structure

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

HMDB0004810
     RDKit          3D
5C-aglycone
 36 37  0  0  0  0  0  0  0  0999 V2000
    0.3537   -2.8040    0.9322 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0129   -1.4821    0.6467 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3068   -0.3860    0.4417 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1593   -0.4758    0.4972 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8628   -0.0949   -0.7409 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3524   -0.2386   -0.5297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0085    0.1463   -1.8647 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8209    0.8007    0.4544 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0670    1.6996    0.8852 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1311    0.7796    0.9105 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9653    0.8971    0.1642 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2086    1.8840   -0.0173 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4162    0.9787    0.1109 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0279    2.1877   -0.1504 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4015    2.2803   -0.2039 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1246    1.1136    0.0150 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5295   -0.1008    0.2769 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1537   -0.1675    0.3253 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4727   -1.4469    0.6026 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1477   -2.5032    0.8003 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1106   -3.6125    0.9382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2979   -3.0265    0.0466 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2658   -2.7745    1.8339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4541   -1.5111    0.7633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4821    0.1522    1.3450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5777   -0.8275   -1.5452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6916    0.9503   -1.0733 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6308   -1.2636   -0.2208 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6585   -0.5167   -2.6596 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1032    0.0643   -1.7897 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7170    1.1957   -2.0410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6575    1.5860    1.1606 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4414    3.0906   -0.3191 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9170    3.2109   -0.4062 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2083    1.2028   -0.0306 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1397   -0.9884    0.4419 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
  3 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 19  2  1  0
 18 13  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  4 24  1  0
  4 25  1  0
  5 26  1  0
  5 27  1  0
  6 28  1  0
  7 29  1  0
  7 30  1  0
  7 31  1  0
 10 32  1  0
 14 33  1  0
 15 34  1  0
 16 35  1  0
 17 36  1  0
M  END

7C-aglycone.mol
  Mrv0541 02231219592D          

 20 21  0  0  0  0            999 V2000
   -1.0717    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5006   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2151   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2151    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5006    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5006   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5006    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2151   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572    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  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  1 10  1  0  0  0  0
  5 10  2  0  0  0  0
  4 11  2  0  0  0  0
  1 12  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 15 17  1  0  0  0  0
  3 13  1  0  0  0  0
  2 20  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0004810

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(CCC1=C(C)C(=O)C2=C(C=CC=C2)C1=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C16H16O4/c1-9(16(19)20)7-8-11-10(2)14(17)12-5-3-4-6-13(12)15(11)18/h3-6,9H,7-8H2,1-2H3,(H,19,20)

> <INCHI_KEY>
ALLYVKRLOHDVKI-UHFFFAOYSA-N

> <FORMULA>
C16H16O4

> <MOLECULAR_WEIGHT>
272.2958

> <EXACT_MASS>
272.104859

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
28.592988100054306

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-methyl-4-(3-methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl)butanoic acid

> <ALOGPS_LOGP>
2.38

> <JCHEM_LOGP>
2.8418694376666664

> <ALOGPS_LOGS>
-3.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.9053555081283307

> <JCHEM_PKA_STRONGEST_BASIC>
-7.215270896918987

> <JCHEM_POLAR_SURFACE_AREA>
71.44

> <JCHEM_REFRACTIVITY>
74.9403

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.76e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5c-aglycone

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0004810
     RDKit          3D
5C-aglycone
 36 37  0  0  0  0  0  0  0  0999 V2000
    0.3537   -2.8040    0.9322 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0129   -1.4821    0.6467 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3068   -0.3860    0.4417 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1593   -0.4758    0.4972 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8628   -0.0949   -0.7409 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3524   -0.2386   -0.5297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0085    0.1463   -1.8647 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8209    0.8007    0.4544 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0670    1.6996    0.8852 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1311    0.7796    0.9105 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9653    0.8971    0.1642 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2086    1.8840   -0.0173 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4162    0.9787    0.1109 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0279    2.1877   -0.1504 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4015    2.2803   -0.2039 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1246    1.1136    0.0150 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5295   -0.1008    0.2769 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1537   -0.1675    0.3253 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4727   -1.4469    0.6026 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1477   -2.5032    0.8003 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1106   -3.6125    0.9382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2979   -3.0265    0.0466 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2658   -2.7745    1.8339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4541   -1.5111    0.7633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4821    0.1522    1.3450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5777   -0.8275   -1.5452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6916    0.9503   -1.0733 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6308   -1.2636   -0.2208 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6585   -0.5167   -2.6596 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1032    0.0643   -1.7897 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7170    1.1957   -2.0410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6575    1.5860    1.1606 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4414    3.0906   -0.3191 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9170    3.2109   -0.4062 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2083    1.2028   -0.0306 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1397   -0.9884    0.4419 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
  3 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 19  2  1  0
 18 13  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  4 24  1  0
  4 25  1  0
  5 26  1  0
  5 27  1  0
  6 28  1  0
  7 29  1  0
  7 30  1  0
  7 31  1  0
 10 32  1  0
 14 33  1  0
 15 34  1  0
 16 35  1  0
 17 36  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 7C-aglycone.mol                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      -2.001   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.667   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.667  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.001  -1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.668  -1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -6.002  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -6.002   0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.668   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.334   0.770   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -2.001  -3.080   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -2.001   3.080   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.667  -1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.001  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.334  -1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.334  -3.080   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.668  -0.770   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.668   0.770   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       6.002  -1.540   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       0.667   1.540   0.000  0.00  0.00           C+0
CONECT    1    2   10   12                                                  
CONECT    2    1    3   20                                                  
CONECT    3    2    4   13                                                  
CONECT    4    3    5   11                                                  
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    1    5                                                  
CONECT   11    4                                                            
CONECT   12    1                                                            
CONECT   13   14    3                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   18   19   15                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20    2                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

COMPND    HMDB0004810
HETATM    1  C1  UNL     1       0.354  -2.804   0.932  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.013  -1.482   0.647  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.307  -0.386   0.442  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.159  -0.476   0.497  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.863  -0.095  -0.741  1.00  0.00           C  
HETATM    6  C6  UNL     1      -3.352  -0.239  -0.530  1.00  0.00           C  
HETATM    7  C7  UNL     1      -4.008   0.146  -1.865  1.00  0.00           C  
HETATM    8  C8  UNL     1      -3.821   0.801   0.454  1.00  0.00           C  
HETATM    9  O1  UNL     1      -3.067   1.700   0.885  1.00  0.00           O  
HETATM   10  O2  UNL     1      -5.131   0.780   0.911  1.00  0.00           O  
HETATM   11  C9  UNL     1       0.965   0.897   0.164  1.00  0.00           C  
HETATM   12  O3  UNL     1       0.209   1.884  -0.017  1.00  0.00           O  
HETATM   13  C10 UNL     1       2.416   0.979   0.111  1.00  0.00           C  
HETATM   14  C11 UNL     1       3.028   2.188  -0.150  1.00  0.00           C  
HETATM   15  C12 UNL     1       4.401   2.280  -0.204  1.00  0.00           C  
HETATM   16  C13 UNL     1       5.125   1.114   0.015  1.00  0.00           C  
HETATM   17  C14 UNL     1       4.529  -0.101   0.277  1.00  0.00           C  
HETATM   18  C15 UNL     1       3.154  -0.167   0.325  1.00  0.00           C  
HETATM   19  C16 UNL     1       2.473  -1.447   0.603  1.00  0.00           C  
HETATM   20  O4  UNL     1       3.148  -2.503   0.800  1.00  0.00           O  
HETATM   21  H1  UNL     1       1.111  -3.612   0.938  1.00  0.00           H  
HETATM   22  H2  UNL     1      -0.298  -3.027   0.047  1.00  0.00           H  
HETATM   23  H3  UNL     1      -0.266  -2.774   1.834  1.00  0.00           H  
HETATM   24  H4  UNL     1      -1.454  -1.511   0.763  1.00  0.00           H  
HETATM   25  H5  UNL     1      -1.482   0.152   1.345  1.00  0.00           H  
HETATM   26  H6  UNL     1      -1.578  -0.827  -1.545  1.00  0.00           H  
HETATM   27  H7  UNL     1      -1.692   0.950  -1.073  1.00  0.00           H  
HETATM   28  H8  UNL     1      -3.631  -1.264  -0.221  1.00  0.00           H  
HETATM   29  H9  UNL     1      -3.658  -0.517  -2.660  1.00  0.00           H  
HETATM   30  H10 UNL     1      -5.103   0.064  -1.790  1.00  0.00           H  
HETATM   31  H11 UNL     1      -3.717   1.196  -2.041  1.00  0.00           H  
HETATM   32  H12 UNL     1      -5.658   1.586   1.161  1.00  0.00           H  
HETATM   33  H13 UNL     1       2.441   3.091  -0.319  1.00  0.00           H  
HETATM   34  H14 UNL     1       4.917   3.211  -0.406  1.00  0.00           H  
HETATM   35  H15 UNL     1       6.208   1.203  -0.031  1.00  0.00           H  
HETATM   36  H16 UNL     1       5.140  -0.988   0.442  1.00  0.00           H  
CONECT    1    2   21   22   23
CONECT    2    3    3   19
CONECT    3    4   11
CONECT    4    5   24   25
CONECT    5    6   26   27
CONECT    6    7    8   28
CONECT    7   29   30   31
CONECT    8    9    9   10
CONECT   10   32
CONECT   11   12   12   13
CONECT   13   14   14   18
CONECT   14   15   33
CONECT   15   16   16   34
CONECT   16   17   35
CONECT   17   18   18   36
CONECT   18   19
CONECT   19   20   20
END

HMDB0004810
     RDKit          3D
5C-aglycone
 36 37  0  0  0  0  0  0  0  0999 V2000
    0.3537   -2.8040    0.9322 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0129   -1.4821    0.6467 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3068   -0.3860    0.4417 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1593   -0.4758    0.4972 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8628   -0.0949   -0.7409 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3524   -0.2386   -0.5297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0085    0.1463   -1.8647 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8209    0.8007    0.4544 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0670    1.6996    0.8852 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1311    0.7796    0.9105 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9653    0.8971    0.1642 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2086    1.8840   -0.0173 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4162    0.9787    0.1109 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0279    2.1877   -0.1504 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4015    2.2803   -0.2039 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1246    1.1136    0.0150 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5295   -0.1008    0.2769 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1537   -0.1675    0.3253 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4727   -1.4469    0.6026 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1477   -2.5032    0.8003 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1106   -3.6125    0.9382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2979   -3.0265    0.0466 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2658   -2.7745    1.8339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4541   -1.5111    0.7633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4821    0.1522    1.3450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5777   -0.8275   -1.5452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6916    0.9503   -1.0733 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6308   -1.2636   -0.2208 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6585   -0.5167   -2.6596 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1032    0.0643   -1.7897 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7170    1.1957   -2.0410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6575    1.5860    1.1606 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4414    3.0906   -0.3191 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9170    3.2109   -0.4062 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2083    1.2028   -0.0306 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1397   -0.9884    0.4419 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
  3 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 19  2  1  0
 18 13  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  4 24  1  0
  4 25  1  0
  5 26  1  0
  5 27  1  0
  6 28  1  0
  7 29  1  0
  7 30  1  0
  7 31  1  0
 10 32  1  0
 14 33  1  0
 15 34  1  0
 16 35  1  0
 17 36  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
2-Methyl-3-(3'-carboxy-3'-methylpropyl)-1,4-naphthoquinone	MeSH
Vitamin K1 aglycone II	MeSH
Phylloquinone aglycone II	MeSH
1,4-dihydro-a,3-Dimethyl-1,4-dioxo-2-naphthalenebutanoate	HMDB
1,4-dihydro-a,3-Dimethyl-1,4-dioxo-2-naphthalenebutanoic acid	HMDB
2-Methyl-3-(3'-3'-carboxymethylpropyl)-1,4-naphthoquinone	HMDB
2-Methyl-3-(3'-carboxybutyl)-1,4-naphthoquinone	HMDB
2-Methyl-3-(3-carboxybutyl)-1,4-naphthoquinone	HMDB
2-Methyl-4-(3-methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl)butanoate	Generator, HMDB

Chemical Formula

C₁₆H₁₆O₄

Average Molecular Weight

272.2958

Monoisotopic Molecular Weight

272.104859

IUPAC Name

2-methyl-4-(3-methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl)butanoic acid

Traditional Name

5c-aglycone

CAS Registry Number

34927-45-2

SMILES

CC(CCC1=C(C)C(=O)C2=C(C=CC=C2)C1=O)C(O)=O

InChI Identifier

InChI=1S/C16H16O4/c1-9(16(19)20)7-8-11-10(2)14(17)12-5-3-4-6-13(12)15(11)18/h3-6,9H,7-8H2,1-2H3,(H,19,20)

InChI Key

ALLYVKRLOHDVKI-UHFFFAOYSA-N

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

Naphthoquinone
Naphthalene
Aryl ketone
Quinone
Benzenoid
Ketone
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (HMDB: HMDB0004810)

Cellular substructure

Excreta

Biofluid or Excreta

Urine (PMID: 17585028)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0004810)

Source

Endogenous

Endogenous (HMDB: HMDB0004810)

Animal

Animal (HMDB: HMDB0004810)

Exogenous

Food

Food (HMDB: HMDB0004810)

Animal origin

Poultry

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid Peroxidation (HMDB: HMDB0004810)

Biochemical pathway

Metabolic pathway

Fatty Acid Metabolism (HMDB: HMDB0004810)

Lipid metabolism pathway (HMDB: HMDB0004810)

Cellular process

Cell signaling (HMDB: HMDB0004810)

Biochemical process

Lipid transport (HMDB: HMDB0004810)

Role

Biological role

Energy source (HMDB: HMDB0004810)

Physical Properties

State

Solid

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
Water Solubility	0.068 g/L	ALOGPS
logP	2.38	ALOGPS
logP	2.84	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	3.91	ChemAxon
pKa (Strongest Basic)	-7.2	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	71.44 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	74.94 m³·mol⁻¹	ChemAxon
Polarizability	28.59 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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
DarkChem	[M+H]+	163.413	31661259
DarkChem	[M-H]-	158.843	31661259
DeepCCS	[M+H]+	169.415	30932474
DeepCCS	[M-H]-	167.057	30932474
DeepCCS	[M-2H]-	199.943	30932474
DeepCCS	[M+Na]+	175.508	30932474
AllCCS	[M+H]+	162.9	32859911
AllCCS	[M+H-H2O]+	159.3	32859911
AllCCS	[M+NH4]+	166.2	32859911
AllCCS	[M+Na]+	167.2	32859911
AllCCS	[M-H]-	167.1	32859911
AllCCS	[M+Na-2H]-	167.0	32859911
AllCCS	[M+HCOO]-	166.9	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5C-aglycone	CC(CCC1=C(C)C(=O)C2=C(C=CC=C2)C1=O)C(O)=O	3774.1	Standard polar	33892256
5C-aglycone	CC(CCC1=C(C)C(=O)C2=C(C=CC=C2)C1=O)C(O)=O	2002.7	Standard non polar	33892256
5C-aglycone	CC(CCC1=C(C)C(=O)C2=C(C=CC=C2)C1=O)C(O)=O	2305.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5C-aglycone,1TMS,isomer #1	CC1=C(CCC(C)C(=O)O[Si](C)(C)C)C(=O)C2=CC=CC=C2C1=O	2381.0	Semi standard non polar	33892256
5C-aglycone,1TBDMS,isomer #1	CC1=C(CCC(C)C(=O)O[Si](C)(C)C(C)(C)C)C(=O)C2=CC=CC=C2C1=O	2652.5	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 5C-aglycone GC-MS (Non-derivatized) - 70eV, Positive	splash10-054o-4490000000-73cacce0d4ef97b05e92	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5C-aglycone GC-MS (1 TMS) - 70eV, Positive	splash10-00bi-9544000000-3602db57cbb78741da08	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5C-aglycone GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5C-aglycone 10V, Positive-QTOF	splash10-05fr-0190000000-463324fdd2c715fd816e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5C-aglycone 20V, Positive-QTOF	splash10-0a4r-3960000000-21c1791e79025a6764a8	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5C-aglycone 40V, Positive-QTOF	splash10-014i-9200000000-e94f15ae4f0fb45668d5	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5C-aglycone 10V, Negative-QTOF	splash10-00di-0090000000-902e52700c099a8e7343	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5C-aglycone 20V, Negative-QTOF	splash10-00fr-0190000000-a0b5e022e540719a24de	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5C-aglycone 40V, Negative-QTOF	splash10-00di-9830000000-da8088aae199017aac7f	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5C-aglycone 10V, Positive-QTOF	splash10-00dr-0390000000-36945061956f0529d3ab	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5C-aglycone 20V, Positive-QTOF	splash10-000i-0910000000-e5944af6e9276ef24a04	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5C-aglycone 40V, Positive-QTOF	splash10-0a4i-3900000000-28c91d12c029a31ae909	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5C-aglycone 10V, Negative-QTOF	splash10-00b9-0090000000-774fb9d9aaa581701042	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5C-aglycone 20V, Negative-QTOF	splash10-00a9-0980000000-8fb2cf64ffa57ba6471a	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5C-aglycone 40V, Negative-QTOF	splash10-000t-0900000000-27fa3802fe36aee8df09	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane (predicted from logP)

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details
Urine	Detected and Quantified	0.001 +/- 0.00012 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	17585028	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Urine	Detected and Quantified	0.00069 +/- 0.00026 umol/mmol creatinine	Adult (>18 years old)	Both	After 15 day of phylloquinone restriction	17585028	details

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

FDB023421

KNApSAcK ID

Not Available

Chemspider ID

2339843

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

7074

PubChem Compound

3082405

PDB ID

Not Available

ChEBI ID

89486

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

Harrington DJ, Soper R, Edwards C, Savidge GF, Hodges SJ, Shearer MJ: Determination of the urinary aglycone metabolites of vitamin K by HPLC with redox-mode electrochemical detection. J Lipid Res. 2005 May;46(5):1053-60. Epub 2005 Feb 1. [PubMed:15722567 ]
Watanabe M, Toyoda M, Imada I, Morimoto H: Ubiquinone and related compounds. XXVI. The urinary metabolites of phylloquinone and alpha-tocopherol. Chem Pharm Bull (Tokyo). 1974 Jan;22(1):176-82. [PubMed:4833371 ]
McBurney A, Shearer MJ, Barkhan P: Preparative isolation and characterization of the urinary aglycones of vitamin K1 (phylloquinone in man. Biochem Med. 1980 Dec;24(3):250-67. [PubMed:7306367 ]

Showing metabocard for 5C-aglycone (HMDB0004810)

MOL for HMDB0004810 (5C-aglycone)

3D MOL for HMDB0004810 (5C-aglycone)

3D SDF for HMDB0004810 (5C-aglycone)

3D-SDF for HMDB0004810 (5C-aglycone)

PDB for HMDB0004810 (5C-aglycone)

3D PDB for HMDB0004810 (5C-aglycone)

SMILES for HMDB0004810 (5C-aglycone)

INCHI for HMDB0004810 (5C-aglycone)

Structure for HMDB0004810 (5C-aglycone)

3D Structure for HMDB0004810 (5C-aglycone)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra