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Showing metabocard for PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)) (HMDB0116479)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-09-09 08:15:59 UTC
Update Date2022-11-30 19:26:37 UTC
HMDB IDHMDB0116479
Secondary Accession NumbersNone
Metabolite Identification
Common NamePGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z))
DescriptionPGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)) is a phosphatidylglycerophosphate (PGP). It is a glycerophospholipid in which a phosphoglycerol moiety occupies a glycerol substitution site followed by another phosphate moiety. Phosphatidylglycerolphosphate is present at a level of 1-2% in most animal tissues, but it can be the second most abundant phospholipid in lung surfactant (up to 11% of the total). It is well established that the concentration of phosphatidylglycerolphosphate increases during fetal development. Phosphatidylglycerolphosphate may be present in animal tissues merely as a precursor for cardiolipin synthesis. As is the case with diacylglycerols, phosphatidylglycerophosphates can have many different combinations of fatty acids of varying lengths and saturation attached to the C-1 and C-2 positions. Fatty acids containing 16, 18 and 20 carbons are the most common. PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)), in particular, consists of one chain of docosahexaenoic acid at the C-1 position and one chain of eicosatetraenoic acid at the C-2 position. They are synthesized by the addition of glycerol 3-phosphate to a CDP-diacylglycerol. In turn, PGPs are dephosphorylated to phosphatidylglycerols (PGs). While most phospholipids have a saturated fatty acid on C-1 and an unsaturated fatty acid on C-2 of the glycerol backbone, the fatty acid distribution at the C-1 and C-2 positions of glycerol within phospholipids is continually in flux, owing to phospholipid degradation and the continuous phospholipid remodeling that occurs while these molecules are in membranes.
Structure
Data?1563873721
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0116479 (PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)))

PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z))
  Mrv1652309171703192D          

 65 64  0  0  1  0            999 V2000
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M  END
Download

3D MOL for HMDB0116479 (PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)))

HMDB0116479
     RDKit          3D
PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z))
139138  0  0  0  0  0  0  0  0999 V2000
    3.3252   -3.6264    5.3252 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8219   -4.6896    4.3577 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9017   -5.6880    4.2373 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4934   -5.9858    3.1177 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1749   -5.3778    1.8182 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7712   -6.4257    0.8796 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0116479 (PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)))

PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z))
  Mrv1652309171703192D          

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M  END
> <DATABASE_ID>
HMDB0116479

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CC\C=C/C\C=C/C\C=C/C\C=C/C\C=C/C\C=C/CC)OC(=O)CCCCCC\C=C/C\C=C/C\C=C/C\C=C/CC

> <INCHI_IDENTIFIER>
InChI=1S/C48H76O13P2/c1-3-5-7-9-11-13-15-17-19-21-22-24-25-27-29-31-33-35-37-39-47(50)57-43-46(44-60-63(55,56)59-42-45(49)41-58-62(52,53)54)61-48(51)40-38-36-34-32-30-28-26-23-20-18-16-14-12-10-8-6-4-2/h5-8,11-14,17-20,22,24,26-29,33,35,45-46,49H,3-4,9-10,15-16,21,23,25,30-32,34,36-44H2,1-2H3,(H,55,56)(H2,52,53,54)/b7-5-,8-6-,13-11-,14-12-,19-17-,20-18-,24-22-,28-26-,29-27-,35-33-/t45-,46+/m0/s1

> <INCHI_KEY>
VPSVZPCVXWJWSR-WWRHEWMHSA-N

> <FORMULA>
C48H76O13P2

> <MOLECULAR_WEIGHT>
923.071

> <EXACT_MASS>
922.476116503

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
139

> <JCHEM_AVERAGE_POLARIZABILITY>
99.64810382859002

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2S)-3-({[(2R)-3-[(4Z,7Z,10Z,13Z,16Z,19Z)-docosa-4,7,10,13,16,19-hexaenoyloxy]-2-[(8Z,11Z,14Z,17Z)-icosa-8,11,14,17-tetraenoyloxy]propoxy](hydroxy)phosphoryl}oxy)-2-hydroxypropoxy]phosphonic acid

> <ALOGPS_LOGP>
7.31

> <JCHEM_LOGP>
11.639955571333331

> <ALOGPS_LOGS>
-5.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.040206143696047

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.3548792964042025

> <JCHEM_PKA_STRONGEST_BASIC>
-3.410499386302644

> <JCHEM_POLAR_SURFACE_AREA>
195.34999999999997

> <JCHEM_REFRACTIVITY>
263.35780000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
42

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.07e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-3-{[(2R)-3-[(4Z,7Z,10Z,13Z,16Z,19Z)-docosa-4,7,10,13,16,19-hexaenoyloxy]-2-[(8Z,11Z,14Z,17Z)-icosa-8,11,14,17-tetraenoyloxy]propoxy(hydroxy)phosphoryl]oxy}-2-hydroxypropoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0116479 (PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)))

HMDB0116479
     RDKit          3D
PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z))
139138  0  0  0  0  0  0  0  0999 V2000
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M  END
Download

PDB for HMDB0116479 (PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)))

HEADER    PROTEIN                                 17-SEP-17   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-SEP-17         0                                  
HETATM    1  H   UNK     0       5.199   1.798   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0      -4.446   0.673   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.772   1.437   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -7.097   0.673   0.000  0.00  0.00           O+0
HETATM    5  H   UNK     0      -3.680  -0.652   0.000  0.00  0.00           H+0
HETATM    6  O   UNK     0      -5.212  -0.652   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -3.120   1.439   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.794   0.673   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.487   0.642   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.813  -0.124   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.139   0.642   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.465  -0.124   0.000  0.00  0.00           C+0
HETATM   13  P   UNK     0       0.092   1.210   0.000  0.00  0.00           P+0
HETATM   14  O   UNK     0      -0.583   0.039   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.092   2.605   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       3.511   1.729   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       6.791   0.641   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0       8.269   1.037   0.000  0.00  0.00           P+0
HETATM   19  O   UNK     0       8.269   2.568   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       9.748   0.641   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       7.504  -0.289   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -8.423   1.437   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -8.423   2.877   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -9.756   0.665   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0     -11.089   1.437   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0     -12.422   0.665   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0     -13.962   0.665   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0     -15.295   1.437   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0     -16.628   0.665   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0     -18.168   0.665   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0     -19.501   1.437   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0     -20.834   0.665   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0     -22.374   0.665   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0     -23.707   1.437   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0     -25.040   0.665   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0     -26.580   0.665   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0     -27.913   1.437   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0     -29.246   0.665   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0     -30.786   0.665   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0     -32.119   1.437   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0     -33.452   0.665   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0     -34.992   0.665   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0     -36.325   1.437   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0     -37.658   0.665   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      -6.601  -1.436   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0      -6.601  -2.876   0.000  0.00  0.00           O+0
HETATM   47  C   UNK     0      -7.934  -0.665   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      -9.267  -1.436   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0     -10.600  -0.665   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0     -11.933  -1.436   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0     -13.266  -0.665   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0     -14.599  -1.436   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0     -15.932  -0.665   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0     -17.472  -0.665   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0     -18.805  -1.436   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0     -20.138  -0.665   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0     -21.678  -0.665   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0     -23.011  -1.436   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0     -24.344  -0.665   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0     -25.884  -0.665   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0     -27.217  -1.436   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0     -28.550  -0.665   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0     -30.090  -0.665   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0     -31.423  -1.436   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0     -32.756  -0.665   0.000  0.00  0.00           C+0
CONECT    1   11                                                            
CONECT    2    3    6    5    7                                             
CONECT    3    2    4                                                       
CONECT    4    3   22                                                       
CONECT    5    2                                                            
CONECT    6    2   45                                                       
CONECT    7    2    8                                                       
CONECT    8    7   13                                                       
CONECT    9   10   13                                                       
CONECT   10    9   11                                                       
CONECT   11   10   16    1   12                                             
CONECT   12   11   17                                                       
CONECT   13    9   14   15    8                                             
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   11                                                            
CONECT   17   12   18                                                       
CONECT   18   17   19   20   21                                             
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   18                                                            
CONECT   22    4   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43                                                            
CONECT   45    6   46   47                                                  
CONECT   46   45                                                            
CONECT   47   45   48                                                       
CONECT   48   47   49                                                       
CONECT   49   48   50                                                       
CONECT   50   49   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55                                                       
CONECT   55   54   56                                                       
CONECT   56   55   57                                                       
CONECT   57   56   58                                                       
CONECT   58   57   59                                                       
CONECT   59   58   60                                                       
CONECT   60   59   61                                                       
CONECT   61   60   62                                                       
CONECT   62   61   63                                                       
CONECT   63   62   64                                                       
CONECT   64   63   65                                                       
CONECT   65   64                                                            
MASTER        0    0    0    0    0    0    0    0   65    0  128    0
END
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3D PDB for HMDB0116479 (PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)))

COMPND    HMDB0116479
HETATM    1  C1  UNL     1       3.325  -3.626   5.325  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.822  -4.690   4.358  1.00  0.00           C  
HETATM    3  C3  UNL     1       3.902  -5.688   4.237  1.00  0.00           C  
HETATM    4  C4  UNL     1       4.493  -5.986   3.118  1.00  0.00           C  
HETATM    5  C5  UNL     1       4.175  -5.378   1.818  1.00  0.00           C  
HETATM    6  C6  UNL     1       3.771  -6.426   0.880  1.00  0.00           C  
HETATM    7  C7  UNL     1       2.621  -6.516   0.278  1.00  0.00           C  
HETATM    8  C8  UNL     1       1.527  -5.537   0.472  1.00  0.00           C  
HETATM    9  C9  UNL     1       0.294  -6.175   0.969  1.00  0.00           C  
HETATM   10  C10 UNL     1      -0.842  -6.151   0.305  1.00  0.00           C  
HETATM   11  C11 UNL     1      -1.026  -5.502  -1.002  1.00  0.00           C  
HETATM   12  C12 UNL     1      -1.542  -6.408  -2.068  1.00  0.00           C  
HETATM   13  C13 UNL     1      -2.683  -6.147  -2.644  1.00  0.00           C  
HETATM   14  C14 UNL     1      -3.498  -4.982  -2.274  1.00  0.00           C  
HETATM   15  C15 UNL     1      -3.655  -4.008  -3.360  1.00  0.00           C  
HETATM   16  C16 UNL     1      -4.760  -3.623  -3.920  1.00  0.00           C  
HETATM   17  C17 UNL     1      -6.053  -4.112  -3.550  1.00  0.00           C  
HETATM   18  C18 UNL     1      -7.093  -3.260  -3.003  1.00  0.00           C  
HETATM   19  C19 UNL     1      -7.042  -2.022  -2.655  1.00  0.00           C  
HETATM   20  C20 UNL     1      -5.911  -1.114  -2.698  1.00  0.00           C  
HETATM   21  C21 UNL     1      -5.643  -0.539  -1.294  1.00  0.00           C  
HETATM   22  C22 UNL     1      -4.451   0.355  -1.284  1.00  0.00           C  
HETATM   23  O1  UNL     1      -3.700   0.406  -2.285  1.00  0.00           O  
HETATM   24  O2  UNL     1      -4.139   1.137  -0.200  1.00  0.00           O  
HETATM   25  C23 UNL     1      -3.031   1.997  -0.070  1.00  0.00           C  
HETATM   26  C24 UNL     1      -1.809   1.092  -0.071  1.00  0.00           C  
HETATM   27  C25 UNL     1      -1.961   0.305   1.258  1.00  0.00           C  
HETATM   28  O3  UNL     1      -0.930  -0.574   1.456  1.00  0.00           O  
HETATM   29  P1  UNL     1      -1.035  -1.437   2.877  1.00  0.00           P  
HETATM   30  O4  UNL     1      -2.423  -2.055   3.002  1.00  0.00           O  
HETATM   31  O5  UNL     1       0.127  -2.666   2.878  1.00  0.00           O  
HETATM   32  O6  UNL     1      -0.783  -0.502   4.247  1.00  0.00           O  
HETATM   33  C26 UNL     1      -1.870  -0.517   5.116  1.00  0.00           C  
HETATM   34  C27 UNL     1      -1.629   0.327   6.334  1.00  0.00           C  
HETATM   35  O7  UNL     1      -2.750   0.265   7.159  1.00  0.00           O  
HETATM   36  C28 UNL     1      -0.428  -0.268   7.069  1.00  0.00           C  
HETATM   37  O8  UNL     1      -0.201   0.464   8.233  1.00  0.00           O  
HETATM   38  P2  UNL     1       1.124  -0.183   9.053  1.00  0.00           P  
HETATM   39  O9  UNL     1       1.938  -1.081   8.170  1.00  0.00           O  
HETATM   40  O10 UNL     1       0.567  -1.032  10.384  1.00  0.00           O  
HETATM   41  O11 UNL     1       2.150   1.057   9.590  1.00  0.00           O  
HETATM   42  O12 UNL     1      -0.595   1.769   0.069  1.00  0.00           O  
HETATM   43  C29 UNL     1       0.521   1.615  -0.713  1.00  0.00           C  
HETATM   44  O13 UNL     1       0.468   0.807  -1.646  1.00  0.00           O  
HETATM   45  C30 UNL     1       1.732   2.450  -0.365  1.00  0.00           C  
HETATM   46  C31 UNL     1       1.335   3.472   0.667  1.00  0.00           C  
HETATM   47  C32 UNL     1       2.543   4.298   1.088  1.00  0.00           C  
HETATM   48  C33 UNL     1       2.063   5.310   2.140  1.00  0.00           C  
HETATM   49  C34 UNL     1       1.106   6.280   1.580  1.00  0.00           C  
HETATM   50  C35 UNL     1       1.707   7.319   0.626  1.00  0.00           C  
HETATM   51  C36 UNL     1       0.534   8.044   0.087  1.00  0.00           C  
HETATM   52  C37 UNL     1       0.368   8.262  -1.175  1.00  0.00           C  
HETATM   53  C38 UNL     1       1.233   7.900  -2.284  1.00  0.00           C  
HETATM   54  C39 UNL     1       0.659   7.002  -3.257  1.00  0.00           C  
HETATM   55  C40 UNL     1       1.250   5.921  -3.701  1.00  0.00           C  
HETATM   56  C41 UNL     1       2.631   5.588  -3.161  1.00  0.00           C  
HETATM   57  C42 UNL     1       3.610   5.774  -4.231  1.00  0.00           C  
HETATM   58  C43 UNL     1       4.442   4.925  -4.706  1.00  0.00           C  
HETATM   59  C44 UNL     1       4.743   3.543  -4.406  1.00  0.00           C  
HETATM   60  C45 UNL     1       4.096   2.814  -3.364  1.00  0.00           C  
HETATM   61  C46 UNL     1       3.368   1.731  -3.553  1.00  0.00           C  
HETATM   62  C47 UNL     1       3.132   1.139  -4.867  1.00  0.00           C  
HETATM   63  C48 UNL     1       1.608   1.154  -5.106  1.00  0.00           C  
HETATM   64  H1  UNL     1       4.090  -4.011   6.023  1.00  0.00           H  
HETATM   65  H2  UNL     1       3.675  -2.727   4.773  1.00  0.00           H  
HETATM   66  H3  UNL     1       2.459  -3.312   5.936  1.00  0.00           H  
HETATM   67  H4  UNL     1       2.484  -4.266   3.421  1.00  0.00           H  
HETATM   68  H5  UNL     1       1.911  -5.200   4.798  1.00  0.00           H  
HETATM   69  H6  UNL     1       4.231  -6.219   5.161  1.00  0.00           H  
HETATM   70  H7  UNL     1       5.290  -6.743   3.134  1.00  0.00           H  
HETATM   71  H8  UNL     1       3.577  -4.491   1.823  1.00  0.00           H  
HETATM   72  H9  UNL     1       5.192  -5.004   1.417  1.00  0.00           H  
HETATM   73  H10 UNL     1       4.516  -7.210   0.664  1.00  0.00           H  
HETATM   74  H11 UNL     1       2.444  -7.352  -0.404  1.00  0.00           H  
HETATM   75  H12 UNL     1       1.891  -4.783   1.237  1.00  0.00           H  
HETATM   76  H13 UNL     1       1.332  -4.910  -0.401  1.00  0.00           H  
HETATM   77  H14 UNL     1       0.352  -6.679   1.927  1.00  0.00           H  
HETATM   78  H15 UNL     1      -1.697  -6.662   0.786  1.00  0.00           H  
HETATM   79  H16 UNL     1       0.054  -5.326  -1.398  1.00  0.00           H  
HETATM   80  H17 UNL     1      -1.415  -4.493  -0.983  1.00  0.00           H  
HETATM   81  H18 UNL     1      -0.941  -7.286  -2.346  1.00  0.00           H  
HETATM   82  H19 UNL     1      -3.046  -6.809  -3.424  1.00  0.00           H  
HETATM   83  H20 UNL     1      -3.132  -4.440  -1.395  1.00  0.00           H  
HETATM   84  H21 UNL     1      -4.484  -5.402  -1.923  1.00  0.00           H  
HETATM   85  H22 UNL     1      -2.701  -3.565  -3.726  1.00  0.00           H  
HETATM   86  H23 UNL     1      -4.630  -2.890  -4.766  1.00  0.00           H  
HETATM   87  H24 UNL     1      -6.049  -5.047  -2.929  1.00  0.00           H  
HETATM   88  H25 UNL     1      -6.503  -4.545  -4.543  1.00  0.00           H  
HETATM   89  H26 UNL     1      -8.117  -3.775  -2.862  1.00  0.00           H  
HETATM   90  H27 UNL     1      -8.018  -1.590  -2.264  1.00  0.00           H  
HETATM   91  H28 UNL     1      -6.196  -0.189  -3.293  1.00  0.00           H  
HETATM   92  H29 UNL     1      -4.977  -1.449  -3.119  1.00  0.00           H  
HETATM   93  H30 UNL     1      -5.402  -1.409  -0.661  1.00  0.00           H  
HETATM   94  H31 UNL     1      -6.556  -0.016  -1.006  1.00  0.00           H  
HETATM   95  H32 UNL     1      -2.980   2.738  -0.899  1.00  0.00           H  
HETATM   96  H33 UNL     1      -3.084   2.590   0.866  1.00  0.00           H  
HETATM   97  H34 UNL     1      -1.856   0.400  -0.905  1.00  0.00           H  
HETATM   98  H35 UNL     1      -1.905   1.117   2.042  1.00  0.00           H  
HETATM   99  H36 UNL     1      -2.951  -0.163   1.204  1.00  0.00           H  
HETATM  100  H37 UNL     1      -0.112  -3.283   3.633  1.00  0.00           H  
HETATM  101  H38 UNL     1      -2.826  -0.291   4.613  1.00  0.00           H  
HETATM  102  H39 UNL     1      -1.956  -1.576   5.472  1.00  0.00           H  
HETATM  103  H40 UNL     1      -1.421   1.373   6.120  1.00  0.00           H  
HETATM  104  H41 UNL     1      -3.457   0.827   6.792  1.00  0.00           H  
HETATM  105  H42 UNL     1      -0.636  -1.312   7.378  1.00  0.00           H  
HETATM  106  H43 UNL     1       0.473  -0.221   6.445  1.00  0.00           H  
HETATM  107  H44 UNL     1       1.128  -1.842  10.491  1.00  0.00           H  
HETATM  108  H45 UNL     1       2.458   1.567   8.802  1.00  0.00           H  
HETATM  109  H46 UNL     1       2.067   2.915  -1.302  1.00  0.00           H  
HETATM  110  H47 UNL     1       2.484   1.751  -0.002  1.00  0.00           H  
HETATM  111  H48 UNL     1       0.492   4.102   0.310  1.00  0.00           H  
HETATM  112  H49 UNL     1       0.921   2.919   1.547  1.00  0.00           H  
HETATM  113  H50 UNL     1       3.254   3.636   1.591  1.00  0.00           H  
HETATM  114  H51 UNL     1       3.027   4.817   0.263  1.00  0.00           H  
HETATM  115  H52 UNL     1       2.968   5.845   2.480  1.00  0.00           H  
HETATM  116  H53 UNL     1       1.609   4.790   2.985  1.00  0.00           H  
HETATM  117  H54 UNL     1       0.744   6.913   2.447  1.00  0.00           H  
HETATM  118  H55 UNL     1       0.213   5.801   1.194  1.00  0.00           H  
HETATM  119  H56 UNL     1       2.330   7.992   1.284  1.00  0.00           H  
HETATM  120  H57 UNL     1       2.374   6.902  -0.110  1.00  0.00           H  
HETATM  121  H58 UNL     1      -0.251   8.425   0.785  1.00  0.00           H  
HETATM  122  H59 UNL     1      -0.569   8.806  -1.492  1.00  0.00           H  
HETATM  123  H60 UNL     1       1.392   8.901  -2.867  1.00  0.00           H  
HETATM  124  H61 UNL     1       2.286   7.703  -1.972  1.00  0.00           H  
HETATM  125  H62 UNL     1      -0.357   7.223  -3.675  1.00  0.00           H  
HETATM  126  H63 UNL     1       0.791   5.262  -4.438  1.00  0.00           H  
HETATM  127  H64 UNL     1       2.853   5.962  -2.196  1.00  0.00           H  
HETATM  128  H65 UNL     1       2.530   4.458  -3.034  1.00  0.00           H  
HETATM  129  H66 UNL     1       3.617   6.822  -4.688  1.00  0.00           H  
HETATM  130  H67 UNL     1       5.102   5.361  -5.564  1.00  0.00           H  
HETATM  131  H68 UNL     1       5.895   3.526  -4.129  1.00  0.00           H  
HETATM  132  H69 UNL     1       4.816   2.949  -5.389  1.00  0.00           H  
HETATM  133  H70 UNL     1       4.220   3.143  -2.300  1.00  0.00           H  
HETATM  134  H71 UNL     1       2.906   1.202  -2.697  1.00  0.00           H  
HETATM  135  H72 UNL     1       3.662   1.535  -5.718  1.00  0.00           H  
HETATM  136  H73 UNL     1       3.390   0.033  -4.808  1.00  0.00           H  
HETATM  137  H74 UNL     1       1.149   0.266  -4.667  1.00  0.00           H  
HETATM  138  H75 UNL     1       1.156   2.061  -4.639  1.00  0.00           H  
HETATM  139  H76 UNL     1       1.448   1.140  -6.194  1.00  0.00           H  
CONECT    1    2   64   65   66
CONECT    2    3   67   68
CONECT    3    4    4   69
CONECT    4    5   70
CONECT    5    6   71   72
CONECT    6    7    7   73
CONECT    7    8   74
CONECT    8    9   75   76
CONECT    9   10   10   77
CONECT   10   11   78
CONECT   11   12   79   80
CONECT   12   13   13   81
CONECT   13   14   82
CONECT   14   15   83   84
CONECT   15   16   16   85
CONECT   16   17   86
CONECT   17   18   87   88
CONECT   18   19   19   89
CONECT   19   20   90
CONECT   20   21   91   92
CONECT   21   22   93   94
CONECT   22   23   23   24
CONECT   24   25
CONECT   25   26   95   96
CONECT   26   27   42   97
CONECT   27   28   98   99
CONECT   28   29
CONECT   29   30   30   31   32
CONECT   31  100
CONECT   32   33
CONECT   33   34  101  102
CONECT   34   35   36  103
CONECT   35  104
CONECT   36   37  105  106
CONECT   37   38
CONECT   38   39   39   40   41
CONECT   40  107
CONECT   41  108
CONECT   42   43
CONECT   43   44   44   45
CONECT   45   46  109  110
CONECT   46   47  111  112
CONECT   47   48  113  114
CONECT   48   49  115  116
CONECT   49   50  117  118
CONECT   50   51  119  120
CONECT   51   52   52  121
CONECT   52   53  122
CONECT   53   54  123  124
CONECT   54   55   55  125
CONECT   55   56  126
CONECT   56   57  127  128
CONECT   57   58   58  129
CONECT   58   59  130
CONECT   59   60  131  132
CONECT   60   61   61  133
CONECT   61   62  134
CONECT   62   63  135  136
CONECT   63  137  138  139
END
Download

SMILES for HMDB0116479 (PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)))

[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CC\C=C/C\C=C/C\C=C/C\C=C/C\C=C/C\C=C/CC)OC(=O)CCCCCC\C=C/C\C=C/C\C=C/C\C=C/CC
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INCHI for HMDB0116479 (PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)))

InChI=1S/C48H76O13P2/c1-3-5-7-9-11-13-15-17-19-21-22-24-25-27-29-31-33-35-37-39-47(50)57-43-46(44-60-63(55,56)59-42-45(49)41-58-62(52,53)54)61-48(51)40-38-36-34-32-30-28-26-23-20-18-16-14-12-10-8-6-4-2/h5-8,11-14,17-20,22,24,26-29,33,35,45-46,49H,3-4,9-10,15-16,21,23,25,30-32,34,36-44H2,1-2H3,(H,55,56)(H2,52,53,54)/b7-5-,8-6-,13-11-,14-12-,19-17-,20-18-,24-22-,28-26-,29-27-,35-33-/t45-,46+/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-Docosahexaenoyl-2-eicosatetraenoyl-sn-glycero-3-phospho-(1'-sn-glycerol-3'-phosphate)HMDB
PGP(22:6/20:4)HMDB
PGP(22:6n3/20:4n3)HMDB
PGP(22:6W3/20:4W3)HMDB
PGP(42:10)HMDB
3-sn-Phosphatidyl-1'-sn-glycerol 3'-phosphoric acidHMDB
1-(4Z,7Z,10Z,13Z,16Z,19Z-Docosahexaenoyl)-2-(8Z,11Z,14Z,17Z-eicosapentaenoyl)-sn-glycero-3-phospho-(1'-sn-glycerol-3'-phosphate)HMDB
1-Docosahexaenoyl-2-eicsoatetraenoyl-sn-glycero-3-phospho-(1'-sn-glycerol-3'-phosphate)HMDB
[(2S)-3-({[(2R)-3-[(4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16,19-hexaenoyloxy]-2-[(8Z,11Z,17Z)-icosa-8,11,14,17-tetraenoyloxy]propoxy](hydroxy)phosphoryl}oxy)-2-hydroxypropoxy]phosphonateHMDB
1-docosahexaenoyl-2-eicosatetraenoyl-sn-glycero-3-phospho-(1'-sn-glycerol-3'-phosphate) SMPDB, HMDB
PGP(22:6/20:4) SMPDB, HMDB
PGP(22:6n3/20:4n3) SMPDB, HMDB
PGP(22:6w3/20:4w3) SMPDB, HMDB
PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z))SMPDB
Chemical FormulaC48H76O13P2
Average Molecular Weight923.071
Monoisotopic Molecular Weight922.476116503
IUPAC Name[(2S)-3-({[(2R)-3-[(4Z,7Z,10Z,13Z,16Z,19Z)-docosa-4,7,10,13,16,19-hexaenoyloxy]-2-[(8Z,11Z,14Z,17Z)-icosa-8,11,14,17-tetraenoyloxy]propoxy](hydroxy)phosphoryl}oxy)-2-hydroxypropoxy]phosphonic acid
Traditional Name(2S)-3-{[(2R)-3-[(4Z,7Z,10Z,13Z,16Z,19Z)-docosa-4,7,10,13,16,19-hexaenoyloxy]-2-[(8Z,11Z,14Z,17Z)-icosa-8,11,14,17-tetraenoyloxy]propoxy(hydroxy)phosphoryl]oxy}-2-hydroxypropoxyphosphonic acid
CAS Registry NumberNot Available
SMILES
[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CC\C=C/C\C=C/C\C=C/C\C=C/C\C=C/C\C=C/CC)OC(=O)CCCCCC\C=C/C\C=C/C\C=C/C\C=C/CC
InChI Identifier
InChI=1S/C48H76O13P2/c1-3-5-7-9-11-13-15-17-19-21-22-24-25-27-29-31-33-35-37-39-47(50)57-43-46(44-60-63(55,56)59-42-45(49)41-58-62(52,53)54)61-48(51)40-38-36-34-32-30-28-26-23-20-18-16-14-12-10-8-6-4-2/h5-8,11-14,17-20,22,24,26-29,33,35,45-46,49H,3-4,9-10,15-16,21,23,25,30-32,34,36-44H2,1-2H3,(H,55,56)(H2,52,53,54)/b7-5-,8-6-,13-11-,14-12-,19-17-,20-18-,24-22-,28-26-,29-27-,35-33-/t45-,46+/m0/s1
InChI KeyVPSVZPCVXWJWSR-WWRHEWMHSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as phosphatidylglycerophosphates. These are glycerophosphoglycerophosphates in which two fatty acids are bonded to the 1-glycerol moiety through ester linkages.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassGlycerophospholipids
Sub ClassGlycerophosphoglycerophosphates
Direct ParentPhosphatidylglycerophosphates
Alternative Parents
Substituents
  • Diacylglycerophosphoglycerophosphate
  • Sn-glycerol-3-phosphate
  • Fatty acid ester
  • Monoalkyl phosphate
  • Dialkyl phosphate
  • Dicarboxylic acid or derivatives
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Fatty acyl
  • Secondary alcohol
  • Carboxylic acid ester
  • Carboxylic acid derivative
  • Organooxygen compound
  • Organic oxide
  • Organic oxygen compound
  • Alcohol
  • Carbonyl group
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
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
logP7.31ALOGPS
logP11.64ChemAxon
logS-5.9ALOGPS
pKa (Strongest Acidic)1.35ChemAxon
pKa (Strongest Basic)-3.4ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area195.35 ŲChemAxon
Rotatable Bond Count42ChemAxon
Refractivity263.36 m³·mol⁻¹ChemAxon
Polarizability99.65 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+285.68930932474
DeepCCS[M-H]-283.55330932474
DeepCCS[M-2H]-316.89730932474
DeepCCS[M+Na]+291.60230932474
AllCCS[M+H]+307.032859911
AllCCS[M+H-H2O]+307.032859911
AllCCS[M+NH4]+306.932859911
AllCCS[M+Na]+306.932859911
AllCCS[M-H]-313.532859911
AllCCS[M+Na-2H]-320.632859911
AllCCS[M+HCOO]-328.432859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022.2.94 minutes32390414
Predicted by Siyang on May 30, 202232.365 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.53 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid5719.5 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid280.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid313.7 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid292.4 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid902.4 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1844.0 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid992.6 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)267.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid3244.9 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid1384.3 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid2622.1 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1331.7 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid744.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate314.8 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA500.2 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water12.4 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)) 10V, Positive-QTOFsplash10-0ab9-1386037129-966b22730539e279482c2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)) 20V, Positive-QTOFsplash10-0aor-3394003113-3ae47f0d14201a6105232019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)) 40V, Positive-QTOFsplash10-0a4r-9378014221-4ac046771e9f238dfd242019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)) 10V, Negative-QTOFsplash10-004i-4029002002-2fe0edf5f18afa572a362019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)) 20V, Negative-QTOFsplash10-004i-9023000000-fe42e2fee2e94a93ae1c2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)) 40V, Negative-QTOFsplash10-004i-9001000000-1f9fc7c351e54feae7172019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)) 10V, Positive-QTOFsplash10-00di-0000002092-7da1c88e821e906b51902021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)) 20V, Positive-QTOFsplash10-0pk9-1200001950-d9d30f0fb6403f12eb422021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)) 40V, Positive-QTOFsplash10-0w4i-0096010010-71d8b6e81a9882a8af632021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)) 10V, Negative-QTOFsplash10-00di-0010000009-91a6a29734b0ac83d0832021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)) 20V, Negative-QTOFsplash10-0ffw-5095048004-423ef4c0da701be1c4d12021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:4(8Z,11Z,14Z,17Z)) 40V, Negative-QTOFsplash10-0ufs-3092122000-747167a6db3677a61e5d2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
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 ID74878191
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131823134
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 ReferencesNot Available