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Showing metabocard for PGP(i-12:0/i-22:0) (HMDB0116546)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-09-09 08:27:22 UTC
Update Date2022-11-30 19:26:39 UTC
HMDB IDHMDB0116546
Secondary Accession NumbersNone
Metabolite Identification
Common NamePGP(i-12:0/i-22:0)
DescriptionPGP(i-12:0/i-22:0) 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(i-12:0/i-22:0), in particular, consists of one chain of isododecanoic acid at the C-1 position and one chain of isodocosanoic 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?1563873729
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0116546 (PGP(i-12:0/i-22:0))

PGP(i-12:0/i-22:0)
  Mrv1652309171703162D          

 57 56  0  0  1  0            999 V2000
    2.7850    0.9634    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3818    0.3608    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0920    0.7696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8022    0.3608    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9714   -0.3495    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7924   -0.3495    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6715    0.7709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9613    0.3608    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7968    0.3437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5071   -0.0665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2174    0.3437    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9276   -0.0665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0493    0.6481    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
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    1.8811    0.9262    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    5.2224    0.3435    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.5123    0.7696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 10  9  1  0  0  0  0
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 55 57  1  0  0  0  0
M  END
Download

3D MOL for HMDB0116546 (PGP(i-12:0/i-22:0))

HMDB0116546
     RDKit          3D
PGP(i-12:0/i-22:0)
135134  0  0  0  0  0  0  0  0999 V2000
   -0.7809   -8.9886   -3.7244 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1684   -7.6999   -4.4895 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7685   -6.7908   -3.5051 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0025   -7.2430   -5.3083 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1752   -6.0137   -6.1114 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3491   -4.7078   -5.4716 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7385   -4.0686   -4.7308 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4143   -4.6763   -3.5825 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4643   -3.6243   -3.1206 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2452   -4.1397   -1.9602 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2421   -3.1031   -1.5349 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6195   -1.8221   -1.0890 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7077   -0.8265   -0.7028 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0906    0.4783   -0.2312 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1859    1.4536    0.1055 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7109    2.7871    0.5893 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7907    3.4159   -0.5028 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4038    4.7559   -0.0309 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6432    5.6652   -0.8562 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3123    5.5251   -1.3807 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8543    4.5408   -2.3326 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7977    3.1187   -2.0949 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6202    2.2995   -2.5915 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.3674    0.5157    3.1612 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.1750   -7.3678   -2.5947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1110   -6.0525   -3.0765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6916   -6.2629   -3.8736 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1336   -8.0854   -6.0965 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9345   -7.3015   -4.7020 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.6279   -5.9432   -6.9243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3390   -4.6778   -4.9496 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5680   -3.9709   -6.3511 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3032   -3.0719   -4.3408 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5483   -3.7823   -5.4758 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0753   -5.5476   -3.8761 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8270   -4.9932   -2.7275 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0631   -3.3932   -3.9983 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8542   -2.7483   -2.8348 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6429   -4.5391   -1.1467 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8595   -5.0092   -2.3422 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9250   -2.8602   -2.3835 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9089   -3.4703   -0.7141 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9521   -1.3639   -1.8384 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0186   -2.0396   -0.1822 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3268   -0.5959   -1.5769 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3247   -1.2169    0.1305 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3971    0.8893   -0.9957 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5017    0.3328    0.6953 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8400    1.5884   -0.7907 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8447    0.9730    0.8694 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5510    3.4920    0.7076 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1679    2.7402    1.5477 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.2486    3.4023   -1.4727 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.0861    6.5618   -1.9032 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0116546 (PGP(i-12:0/i-22:0))

PGP(i-12:0/i-22:0)
  Mrv1652309171703162D          

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M  END
> <DATABASE_ID>
HMDB0116546

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCC(C)C)OC(=O)CCCCCCCCCCCCCCCCCCC(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C40H80O13P2/c1-35(2)27-23-19-15-13-11-9-7-5-6-8-10-12-14-16-22-26-30-40(43)53-38(33-49-39(42)29-25-21-18-17-20-24-28-36(3)4)34-52-55(47,48)51-32-37(41)31-50-54(44,45)46/h35-38,41H,5-34H2,1-4H3,(H,47,48)(H2,44,45,46)/t37-,38+/m0/s1

> <INCHI_KEY>
MEZHYUGWUQWXOK-QPPIDDCLSA-N

> <FORMULA>
C40H80O13P2

> <MOLECULAR_WEIGHT>
831.015

> <EXACT_MASS>
830.507416632

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
135

> <JCHEM_AVERAGE_POLARIZABILITY>
97.02110400340021

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2S)-2-hydroxy-3-({hydroxy[(2R)-2-[(20-methylhenicosanoyl)oxy]-3-[(10-methylundecanoyl)oxy]propoxy]phosphoryl}oxy)propoxy]phosphonic acid

> <ALOGPS_LOGP>
6.55

> <JCHEM_LOGP>
11.387523680666664

> <ALOGPS_LOGS>
-6.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.0402061436989327

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.354879296415124

> <JCHEM_PKA_STRONGEST_BASIC>
-3.410499386302644

> <JCHEM_POLAR_SURFACE_AREA>
195.34999999999997

> <JCHEM_REFRACTIVITY>
215.279

> <JCHEM_ROTATABLE_BOND_COUNT>
42

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.95e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-hydroxy-3-{[hydroxy((2R)-2-[(20-methylhenicosanoyl)oxy]-3-[(10-methylundecanoyl)oxy]propoxy)phosphoryl]oxy}propoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0116546 (PGP(i-12:0/i-22:0))

HMDB0116546
     RDKit          3D
PGP(i-12:0/i-22:0)
135134  0  0  0  0  0  0  0  0999 V2000
   -0.7809   -8.9886   -3.7244 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1684   -7.6999   -4.4895 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7685   -6.7908   -3.5051 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0025   -7.2430   -5.3083 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1752   -6.0137   -6.1114 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for HMDB0116546 (PGP(i-12:0/i-22:0))

HEADER    PROTEIN                                 17-SEP-17   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: PGP(i-12:0/i-22:0)                                
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-SEP-17         0                                  
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HETATM   47  C   UNK     0     -21.265  -0.665   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0     -22.598  -1.436   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0     -23.931  -0.665   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0     -25.264  -1.436   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0     -26.597  -0.665   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0     -27.930  -1.436   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0     -29.263  -0.665   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0     -30.596  -1.436   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0     -31.929  -0.665   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0     -33.262  -1.436   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0     -33.262   0.104   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   35                                                       
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   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
CONECT   35    6   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   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   45                                                       
CONECT   45   44   46                                                       
CONECT   46   45   47                                                       
CONECT   47   46   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   57                                                  
CONECT   56   55                                                            
CONECT   57   55                                                            
MASTER        0    0    0    0    0    0    0    0   57    0  112    0
END
Download

3D PDB for HMDB0116546 (PGP(i-12:0/i-22:0))

COMPND    HMDB0116546
HETATM    1  C1  UNL     1      -0.781  -8.989  -3.724  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.168  -7.700  -4.489  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.768  -6.791  -3.505  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.003  -7.243  -5.308  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.175  -6.014  -6.111  1.00  0.00           C  
HETATM    6  C6  UNL     1      -0.349  -4.708  -5.472  1.00  0.00           C  
HETATM    7  C7  UNL     1       0.738  -4.069  -4.731  1.00  0.00           C  
HETATM    8  C8  UNL     1       1.414  -4.676  -3.582  1.00  0.00           C  
HETATM    9  C9  UNL     1       2.464  -3.624  -3.121  1.00  0.00           C  
HETATM   10  C10 UNL     1       3.245  -4.140  -1.960  1.00  0.00           C  
HETATM   11  C11 UNL     1       4.242  -3.103  -1.535  1.00  0.00           C  
HETATM   12  C12 UNL     1       3.619  -1.822  -1.089  1.00  0.00           C  
HETATM   13  C13 UNL     1       4.708  -0.826  -0.703  1.00  0.00           C  
HETATM   14  C14 UNL     1       4.091   0.478  -0.231  1.00  0.00           C  
HETATM   15  C15 UNL     1       5.186   1.454   0.106  1.00  0.00           C  
HETATM   16  C16 UNL     1       4.711   2.787   0.589  1.00  0.00           C  
HETATM   17  C17 UNL     1       3.791   3.416  -0.503  1.00  0.00           C  
HETATM   18  C18 UNL     1       3.404   4.756  -0.031  1.00  0.00           C  
HETATM   19  C19 UNL     1       2.643   5.665  -0.856  1.00  0.00           C  
HETATM   20  C20 UNL     1       1.312   5.525  -1.381  1.00  0.00           C  
HETATM   21  C21 UNL     1       0.854   4.541  -2.333  1.00  0.00           C  
HETATM   22  C22 UNL     1       0.798   3.119  -2.095  1.00  0.00           C  
HETATM   23  O1  UNL     1       1.620   2.300  -2.592  1.00  0.00           O  
HETATM   24  O2  UNL     1      -0.196   2.530  -1.277  1.00  0.00           O  
HETATM   25  C23 UNL     1      -0.317   1.186  -0.981  1.00  0.00           C  
HETATM   26  C24 UNL     1      -1.467   0.538  -1.677  1.00  0.00           C  
HETATM   27  O3  UNL     1      -2.728   1.160  -1.465  1.00  0.00           O  
HETATM   28  C25 UNL     1      -3.860   0.587  -2.001  1.00  0.00           C  
HETATM   29  O4  UNL     1      -3.582  -0.531  -2.644  1.00  0.00           O  
HETATM   30  C26 UNL     1      -5.232   0.975  -1.993  1.00  0.00           C  
HETATM   31  C27 UNL     1      -5.710   2.196  -1.353  1.00  0.00           C  
HETATM   32  C28 UNL     1      -5.640   2.313   0.109  1.00  0.00           C  
HETATM   33  C29 UNL     1      -4.325   2.285   0.807  1.00  0.00           C  
HETATM   34  C30 UNL     1      -4.654   2.520   2.291  1.00  0.00           C  
HETATM   35  C31 UNL     1      -3.481   2.636   3.165  1.00  0.00           C  
HETATM   36  C32 UNL     1      -2.520   3.735   2.970  1.00  0.00           C  
HETATM   37  C33 UNL     1      -2.926   5.133   3.166  1.00  0.00           C  
HETATM   38  C34 UNL     1      -3.995   5.745   2.355  1.00  0.00           C  
HETATM   39  C35 UNL     1      -3.758   5.767   0.870  1.00  0.00           C  
HETATM   40  C36 UNL     1      -4.014   7.251   2.797  1.00  0.00           C  
HETATM   41  C37 UNL     1      -0.269   0.771   0.444  1.00  0.00           C  
HETATM   42  O5  UNL     1       0.903   1.081   1.089  1.00  0.00           O  
HETATM   43  P1  UNL     1       0.907   0.537   2.683  1.00  0.00           P  
HETATM   44  O6  UNL     1       2.367   0.516   3.161  1.00  0.00           O  
HETATM   45  O7  UNL     1       0.088   1.544   3.736  1.00  0.00           O  
HETATM   46  O8  UNL     1       0.368  -1.071   2.812  1.00  0.00           O  
HETATM   47  C38 UNL     1      -0.760  -1.133   3.662  1.00  0.00           C  
HETATM   48  C39 UNL     1      -1.162  -2.588   3.725  1.00  0.00           C  
HETATM   49  O9  UNL     1      -0.074  -3.295   4.251  1.00  0.00           O  
HETATM   50  C40 UNL     1      -2.380  -2.799   4.590  1.00  0.00           C  
HETATM   51  O10 UNL     1      -2.663  -4.167   4.610  1.00  0.00           O  
HETATM   52  P2  UNL     1      -4.025  -4.497   5.558  1.00  0.00           P  
HETATM   53  O11 UNL     1      -3.619  -4.639   7.025  1.00  0.00           O  
HETATM   54  O12 UNL     1      -5.110  -3.224   5.483  1.00  0.00           O  
HETATM   55  O13 UNL     1      -4.776  -5.922   5.106  1.00  0.00           O  
HETATM   56  H1  UNL     1      -0.484  -9.790  -4.417  1.00  0.00           H  
HETATM   57  H2  UNL     1      -1.736  -9.291  -3.204  1.00  0.00           H  
HETATM   58  H3  UNL     1      -0.043  -8.767  -2.944  1.00  0.00           H  
HETATM   59  H4  UNL     1      -1.990  -8.055  -5.209  1.00  0.00           H  
HETATM   60  H5  UNL     1      -2.175  -7.368  -2.595  1.00  0.00           H  
HETATM   61  H6  UNL     1      -1.111  -6.053  -3.077  1.00  0.00           H  
HETATM   62  H7  UNL     1      -2.692  -6.263  -3.874  1.00  0.00           H  
HETATM   63  H8  UNL     1       0.134  -8.085  -6.097  1.00  0.00           H  
HETATM   64  H9  UNL     1       0.934  -7.302  -4.702  1.00  0.00           H  
HETATM   65  H10 UNL     1      -1.102  -6.216  -6.766  1.00  0.00           H  
HETATM   66  H11 UNL     1       0.628  -5.943  -6.924  1.00  0.00           H  
HETATM   67  H12 UNL     1      -1.339  -4.678  -4.950  1.00  0.00           H  
HETATM   68  H13 UNL     1      -0.568  -3.971  -6.351  1.00  0.00           H  
HETATM   69  H14 UNL     1       0.303  -3.072  -4.341  1.00  0.00           H  
HETATM   70  H15 UNL     1       1.548  -3.782  -5.476  1.00  0.00           H  
HETATM   71  H16 UNL     1       2.075  -5.548  -3.876  1.00  0.00           H  
HETATM   72  H17 UNL     1       0.827  -4.993  -2.727  1.00  0.00           H  
HETATM   73  H18 UNL     1       3.063  -3.393  -3.998  1.00  0.00           H  
HETATM   74  H19 UNL     1       1.854  -2.748  -2.835  1.00  0.00           H  
HETATM   75  H20 UNL     1       2.643  -4.539  -1.147  1.00  0.00           H  
HETATM   76  H21 UNL     1       3.859  -5.009  -2.342  1.00  0.00           H  
HETATM   77  H22 UNL     1       4.925  -2.860  -2.384  1.00  0.00           H  
HETATM   78  H23 UNL     1       4.909  -3.470  -0.714  1.00  0.00           H  
HETATM   79  H24 UNL     1       2.952  -1.364  -1.838  1.00  0.00           H  
HETATM   80  H25 UNL     1       3.019  -2.040  -0.182  1.00  0.00           H  
HETATM   81  H26 UNL     1       5.327  -0.596  -1.577  1.00  0.00           H  
HETATM   82  H27 UNL     1       5.325  -1.217   0.130  1.00  0.00           H  
HETATM   83  H28 UNL     1       3.397   0.889  -0.996  1.00  0.00           H  
HETATM   84  H29 UNL     1       3.502   0.333   0.695  1.00  0.00           H  
HETATM   85  H30 UNL     1       5.840   1.588  -0.791  1.00  0.00           H  
HETATM   86  H31 UNL     1       5.845   0.973   0.869  1.00  0.00           H  
HETATM   87  H32 UNL     1       5.551   3.492   0.708  1.00  0.00           H  
HETATM   88  H33 UNL     1       4.168   2.740   1.548  1.00  0.00           H  
HETATM   89  H34 UNL     1       2.864   2.748  -0.433  1.00  0.00           H  
HETATM   90  H35 UNL     1       4.249   3.402  -1.473  1.00  0.00           H  
HETATM   91  H36 UNL     1       4.338   5.343   0.325  1.00  0.00           H  
HETATM   92  H37 UNL     1       2.836   4.564   0.962  1.00  0.00           H  
HETATM   93  H38 UNL     1       3.315   5.957  -1.789  1.00  0.00           H  
HETATM   94  H39 UNL     1       2.697   6.752  -0.366  1.00  0.00           H  
HETATM   95  H40 UNL     1       1.086   6.562  -1.903  1.00  0.00           H  
HETATM   96  H41 UNL     1       0.519   5.655  -0.522  1.00  0.00           H  
HETATM   97  H42 UNL     1       1.497   4.671  -3.278  1.00  0.00           H  
HETATM   98  H43 UNL     1      -0.162   4.907  -2.775  1.00  0.00           H  
HETATM   99  H44 UNL     1       0.606   0.667  -1.457  1.00  0.00           H  
HETATM  100  H45 UNL     1      -1.534  -0.516  -1.308  1.00  0.00           H  
HETATM  101  H46 UNL     1      -1.257   0.568  -2.768  1.00  0.00           H  
HETATM  102  H47 UNL     1      -5.825   0.083  -1.512  1.00  0.00           H  
HETATM  103  H48 UNL     1      -5.661   0.946  -3.070  1.00  0.00           H  
HETATM  104  H49 UNL     1      -6.803   2.408  -1.688  1.00  0.00           H  
HETATM  105  H50 UNL     1      -5.191   3.124  -1.807  1.00  0.00           H  
HETATM  106  H51 UNL     1      -6.370   1.589   0.606  1.00  0.00           H  
HETATM  107  H52 UNL     1      -6.132   3.331   0.354  1.00  0.00           H  
HETATM  108  H53 UNL     1      -3.975   1.197   0.728  1.00  0.00           H  
HETATM  109  H54 UNL     1      -3.631   2.973   0.378  1.00  0.00           H  
HETATM  110  H55 UNL     1      -5.149   1.521   2.581  1.00  0.00           H  
HETATM  111  H56 UNL     1      -5.447   3.235   2.395  1.00  0.00           H  
HETATM  112  H57 UNL     1      -2.915   1.668   3.234  1.00  0.00           H  
HETATM  113  H58 UNL     1      -3.883   2.747   4.225  1.00  0.00           H  
HETATM  114  H59 UNL     1      -1.946   3.649   2.007  1.00  0.00           H  
HETATM  115  H60 UNL     1      -1.690   3.551   3.740  1.00  0.00           H  
HETATM  116  H61 UNL     1      -3.217   5.253   4.253  1.00  0.00           H  
HETATM  117  H62 UNL     1      -2.030   5.840   3.092  1.00  0.00           H  
HETATM  118  H63 UNL     1      -4.987   5.405   2.646  1.00  0.00           H  
HETATM  119  H64 UNL     1      -2.800   5.336   0.561  1.00  0.00           H  
HETATM  120  H65 UNL     1      -4.631   5.226   0.415  1.00  0.00           H  
HETATM  121  H66 UNL     1      -3.807   6.795   0.460  1.00  0.00           H  
HETATM  122  H67 UNL     1      -4.256   7.324   3.858  1.00  0.00           H  
HETATM  123  H68 UNL     1      -4.703   7.807   2.139  1.00  0.00           H  
HETATM  124  H69 UNL     1      -2.995   7.654   2.625  1.00  0.00           H  
HETATM  125  H70 UNL     1      -0.387  -0.334   0.470  1.00  0.00           H  
HETATM  126  H71 UNL     1      -1.171   1.177   0.951  1.00  0.00           H  
HETATM  127  H72 UNL     1       0.541   2.392   3.895  1.00  0.00           H  
HETATM  128  H73 UNL     1      -1.574  -0.482   3.298  1.00  0.00           H  
HETATM  129  H74 UNL     1      -0.505  -0.758   4.682  1.00  0.00           H  
HETATM  130  H75 UNL     1      -1.359  -2.919   2.698  1.00  0.00           H  
HETATM  131  H76 UNL     1      -0.373  -4.117   4.735  1.00  0.00           H  
HETATM  132  H77 UNL     1      -2.171  -2.502   5.639  1.00  0.00           H  
HETATM  133  H78 UNL     1      -3.236  -2.260   4.164  1.00  0.00           H  
HETATM  134  H79 UNL     1      -5.319  -2.999   4.525  1.00  0.00           H  
HETATM  135  H80 UNL     1      -4.970  -6.009   4.156  1.00  0.00           H  
CONECT    1    2   56   57   58
CONECT    2    3    4   59
CONECT    3   60   61   62
CONECT    4    5   63   64
CONECT    5    6   65   66
CONECT    6    7   67   68
CONECT    7    8   69   70
CONECT    8    9   71   72
CONECT    9   10   73   74
CONECT   10   11   75   76
CONECT   11   12   77   78
CONECT   12   13   79   80
CONECT   13   14   81   82
CONECT   14   15   83   84
CONECT   15   16   85   86
CONECT   16   17   87   88
CONECT   17   18   89   90
CONECT   18   19   91   92
CONECT   19   20   93   94
CONECT   20   21   95   96
CONECT   21   22   97   98
CONECT   22   23   23   24
CONECT   24   25
CONECT   25   26   41   99
CONECT   26   27  100  101
CONECT   27   28
CONECT   28   29   29   30
CONECT   30   31  102  103
CONECT   31   32  104  105
CONECT   32   33  106  107
CONECT   33   34  108  109
CONECT   34   35  110  111
CONECT   35   36  112  113
CONECT   36   37  114  115
CONECT   37   38  116  117
CONECT   38   39   40  118
CONECT   39  119  120  121
CONECT   40  122  123  124
CONECT   41   42  125  126
CONECT   42   43
CONECT   43   44   44   45   46
CONECT   45  127
CONECT   46   47
CONECT   47   48  128  129
CONECT   48   49   50  130
CONECT   49  131
CONECT   50   51  132  133
CONECT   51   52
CONECT   52   53   53   54   55
CONECT   54  134
CONECT   55  135
END
Download

SMILES for HMDB0116546 (PGP(i-12:0/i-22:0))

[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCC(C)C)OC(=O)CCCCCCCCCCCCCCCCCCC(C)C
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INCHI for HMDB0116546 (PGP(i-12:0/i-22:0))

InChI=1S/C40H80O13P2/c1-35(2)27-23-19-15-13-11-9-7-5-6-8-10-12-14-16-22-26-30-40(43)53-38(33-49-39(42)29-25-21-18-17-20-24-28-36(3)4)34-52-55(47,48)51-32-37(41)31-50-54(44,45)46/h35-38,41H,5-34H2,1-4H3,(H,47,48)(H2,44,45,46)/t37-,38+/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-Isododecanoyl-2-isodocosanoyl-sn-glycero-3-phospho-(1'-sn-glycerol-3'-phosphate)HMDB
PGP(34:0)HMDB
3-sn-Phosphatidyl-1'-sn-glycerol 3'-phosphoric acidHMDB
[(2S)-2-Hydroxy-3-({hydroxy[(2R)-2-[(20-methylhenicosanoyl)oxy]-3-[(10-methylundecanoyl)oxy]propoxy]phosphoryl}oxy)propoxy]phosphonateHMDB
PGP(i-12:0/i-22:0)SMPDB
Chemical FormulaC40H80O13P2
Average Molecular Weight831.015
Monoisotopic Molecular Weight830.507416632
IUPAC Name[(2S)-2-hydroxy-3-({hydroxy[(2R)-2-[(20-methylhenicosanoyl)oxy]-3-[(10-methylundecanoyl)oxy]propoxy]phosphoryl}oxy)propoxy]phosphonic acid
Traditional Name(2S)-2-hydroxy-3-{[hydroxy((2R)-2-[(20-methylhenicosanoyl)oxy]-3-[(10-methylundecanoyl)oxy]propoxy)phosphoryl]oxy}propoxyphosphonic acid
CAS Registry NumberNot Available
SMILES
[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCC(C)C)OC(=O)CCCCCCCCCCCCCCCCCCC(C)C
InChI Identifier
InChI=1S/C40H80O13P2/c1-35(2)27-23-19-15-13-11-9-7-5-6-8-10-12-14-16-22-26-30-40(43)53-38(33-49-39(42)29-25-21-18-17-20-24-28-36(3)4)34-52-55(47,48)51-32-37(41)31-50-54(44,45)46/h35-38,41H,5-34H2,1-4H3,(H,47,48)(H2,44,45,46)/t37-,38+/m0/s1
InChI KeyMEZHYUGWUQWXOK-QPPIDDCLSA-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
logP6.55ALOGPS
logP11.39ChemAxon
logS-6.1ALOGPS
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
Refractivity215.28 m³·mol⁻¹ChemAxon
Polarizability97.02 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
DarkChem[M+H]+289.72931661259
DarkChem[M-H]-252.54531661259
DeepCCS[M+H]+287.84330932474
DeepCCS[M-H]-285.94730932474
DeepCCS[M-2H]-319.18830932474
DeepCCS[M+Na]+293.62230932474
AllCCS[M+H]+291.432859911
AllCCS[M+H-H2O]+291.432859911
AllCCS[M+NH4]+291.532859911
AllCCS[M+Na]+291.532859911
AllCCS[M-H]-288.032859911
AllCCS[M+Na-2H]-294.832859911
AllCCS[M+HCOO]-302.432859911

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. Predicted by Afia on May 17, 2022.10.78 minutes32390414
Predicted by Siyang on May 30, 202223.6497 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.1 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid4650.8 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid186.9 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid312.2 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid166.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid909.7 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1419.5 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 Acid1256.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)272.2 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid2438.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid1052.2 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid2295.0 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1013.3 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid646.0 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate258.6 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA341.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water12.6 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
PGP(i-12:0/i-22:0)[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCC(C)C)OC(=O)CCCCCCCCCCCCCCCCCCC(C)C4977.5Standard polar33892256
PGP(i-12:0/i-22:0)[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCC(C)C)OC(=O)CCCCCCCCCCCCCCCCCCC(C)C4730.8Standard non polar33892256
PGP(i-12:0/i-22:0)[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCC(C)C)OC(=O)CCCCCCCCCCCCCCCCCCC(C)C5557.5Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-12:0/i-22:0) 10V, Positive-QTOFsplash10-001i-1847332490-c1fc3c6081326bde5a0f2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-12:0/i-22:0) 20V, Positive-QTOFsplash10-06z9-4945113230-18c90c06bcb850cc46682019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-12:0/i-22:0) 40V, Positive-QTOFsplash10-0a4i-9566030200-060ffff04b197fbc75842019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-12:0/i-22:0) 10V, Negative-QTOFsplash10-005j-4913101030-7ed3d158bac8a5345e342019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-12:0/i-22:0) 20V, Negative-QTOFsplash10-004j-9410000000-6a77a9a50b1279807d0a2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-12:0/i-22:0) 40V, Negative-QTOFsplash10-004i-9000000000-e587a74af29e14e300432019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-12:0/i-22:0) 10V, Negative-QTOFsplash10-004i-0010000090-2093caa6e7cc2a2ef55a2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-12:0/i-22:0) 20V, Negative-QTOFsplash10-004i-4282204090-05e00303e0fee5e285fa2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-12:0/i-22:0) 40V, Negative-QTOFsplash10-0fia-7097814100-8c0534178c165c83d55a2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-12:0/i-22:0) 10V, Positive-QTOFsplash10-001i-1100060490-fe4930a268e59dae477d2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-12:0/i-22:0) 20V, Positive-QTOFsplash10-057i-2600089700-b6b88b9fe7c48d27d9162021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-12:0/i-22:0) 40V, Positive-QTOFsplash10-0f6t-9687561000-233a4a6291e2c4c2a6222021-09-25Wishart 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 ID74878258
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131823201
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 References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  3. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  4. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  5. Divecha N, Irvine RF: Phospholipid signaling. Cell. 1995 Jan 27;80(2):269-78. [PubMed:7834746 ]
  6. Cevc, Gregor (1993). Phospholipids Handbook. Marcel Dekker.
  7. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.