Showing metabocard for PGP(25:1(11Z)/25:1(9Z)) (MMDBc0046477)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-19 14:38:43 UTC
Update Date2022-09-01 01:32:12 UTC
Metabolite IDMMDBc0046477
Metabolite Identification
Common NamePGP(25:1(11Z)/25:1(9Z))
DescriptionPGP(25:1(11Z)/25:1(9Z)) belongs to the class of glycerophosphoglycerophosphates, also called phosphatidylglycerophosphates (PGPs). These lipids contain a common glycerophosphate skeleton linked to at least one fatty acyl chain and a glycero-3-phosphate moiety. 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. PGP(25:1(11Z)/25:1(9Z)), in particular, consists of one 11Z-pentacosanoyl chain to the C-1 atom, and one 9Z-pentacosenoyl to the C-2 atom. In E. coli, PGPs can be found in the cytoplasmic membrane. The are synthesized by the addition of glycerol 3-phosphate to a CDP-diacylglycerol. In turn, PGPs are dephosphorylated to Phosphatidylglycerols (PGs) by the enzyme Phosphatidylglycerophosphatase.
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00005634c10d9b88>

PGP(25:1(11Z)/25:1(9Z))
  Mrv1652306231617062D          

 73 72  0  0  1  0            999 V2000
    2.7849    0.9634    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3818    0.3607    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0918    0.7695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8020    0.3607    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9713   -0.3494    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7923   -0.3494    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6715    0.7708    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9613    0.3607    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
    2.9275   -0.0665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0493    0.6480    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3125    0.0209    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
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3D MOL for #<Metabolite:0x00005634c10d9b88>

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3D SDF for #<Metabolite:0x00005634c10d9b88>
PGP(25:1(11Z)/25:1(9Z))
  Mrv1652306231617062D          

 73 72  0  0  1  0            999 V2000
    2.7849    0.9634    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3818    0.3607    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0918    0.7695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
 40 41  1  0  0  0  0
 41 42  1  0  0  0  0
 42 43  1  0  0  0  0
 43 44  1  0  0  0  0
 44 45  1  0  0  0  0
 45 46  1  0  0  0  0
 46 47  1  0  0  0  0
 48  6  1  0  0  0  0
 48 49  2  0  0  0  0
 48 50  1  0  0  0  0
 50 51  1  0  0  0  0
 51 52  1  0  0  0  0
 52 53  1  0  0  0  0
 53 54  1  0  0  0  0
 54 55  1  0  0  0  0
 55 56  1  0  0  0  0
 56 57  1  0  0  0  0
 57 58  2  0  0  0  0
 58 59  1  0  0  0  0
 59 60  1  0  0  0  0
 60 61  1  0  0  0  0
 61 62  1  0  0  0  0
 62 63  1  0  0  0  0
 63 64  1  0  0  0  0
 64 65  1  0  0  0  0
 65 66  1  0  0  0  0
 66 67  1  0  0  0  0
 67 68  1  0  0  0  0
 68 69  1  0  0  0  0
 69 70  1  0  0  0  0
 70 71  1  0  0  0  0
 71 72  1  0  0  0  0
 72 73  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0046477

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCC\C=C/CCCCCCCCCCCCC)OC(=O)CCCCCCC\C=C/CCCCCCCCCCCCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C56H108O13P2/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-35-37-39-41-43-45-47-55(58)65-51-54(52-68-71(63,64)67-50-53(57)49-66-70(60,61)62)69-56(59)48-46-44-42-40-38-36-34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h27,29,32,34,53-54,57H,3-26,28,30-31,33,35-52H2,1-2H3,(H,63,64)(H2,60,61,62)/b29-27-,34-32-/t53-,54+/m0/s1

> <INCHI_KEY>
RCNWSELADYQFJH-VXCZFNEBSA-N

> <FORMULA>
C56H108O13P2

> <MOLECULAR_WEIGHT>
1051.415

> <EXACT_MASS>
1050.726517534

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
179

> <JCHEM_AVERAGE_POLARIZABILITY>
128.11753275532877

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2S)-2-hydroxy-3-({hydroxy[(2R)-3-[(11Z)-pentacos-11-enoyloxy]-2-[(9Z)-pentacos-9-enoyloxy]propoxy]phosphoryl}oxy)propoxy]phosphonic acid

> <ALOGPS_LOGP>
9.33

> <JCHEM_LOGP>
18.091878144666666

> <ALOGPS_LOGS>
-6.94

> <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>
291.233

> <JCHEM_ROTATABLE_BOND_COUNT>
58

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.19e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-hydroxy-3-{[hydroxy((2R)-3-[(11Z)-pentacos-11-enoyloxy]-2-[(9Z)-pentacos-9-enoyloxy]propoxy)phosphoryl]oxy}propoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for #<Metabolite:0x00005634c10d9b88>
Download
PDB for #<Metabolite:0x00005634c10d9b88>
HEADER    PROTEIN                                 23-JUN-16   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: PGP(25:1(11Z)/25:1(9Z))                           
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-JUN-16         0                                  
HETATM    1  H   UNK     0       5.198   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      -5.771   1.436   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   0.641   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   0.641   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   1.436   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -8.423   2.876   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   1.436   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     -13.755   1.436   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0     -15.088   0.665   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0     -16.421   1.436   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0     -17.754   0.665   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0     -19.087   1.436   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0     -20.420   0.665   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0     -21.753   1.436   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0     -23.293   1.436   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0     -24.626   0.665   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0     -25.959   1.436   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0     -27.292   0.665   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0     -28.625   1.436   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0     -29.958   0.665   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0     -31.291   1.436   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0     -32.624   0.665   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0     -33.957   1.436   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0     -35.290   0.665   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0     -36.623   1.436   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0     -37.956   0.665   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0     -39.289   1.436   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0     -40.622   0.665   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      -6.601  -1.436   0.000  0.00  0.00           C+0
HETATM   49  O   UNK     0      -6.601  -2.876   0.000  0.00  0.00           O+0
HETATM   50  C   UNK     0      -7.934  -0.665   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      -9.267  -1.436   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0     -10.600  -0.665   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0     -11.933  -1.436   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0     -13.266  -0.665   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0     -14.599  -1.436   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0     -15.932  -0.665   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0     -17.265  -1.436   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0     -18.805  -1.436   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0     -20.138  -0.665   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0     -21.471  -1.436   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0     -22.804  -0.665   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0     -24.137  -1.436   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0     -25.470  -0.665   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0     -26.803  -1.436   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0     -28.136  -0.665   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0     -29.469  -1.436   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0     -30.802  -0.665   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0     -32.135  -1.436   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0     -33.468  -0.665   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0     -34.801  -1.436   0.000  0.00  0.00           C+0
HETATM   71  C   UNK     0     -36.134  -0.665   0.000  0.00  0.00           C+0
HETATM   72  C   UNK     0     -37.467  -1.436   0.000  0.00  0.00           C+0
HETATM   73  C   UNK     0     -38.800  -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   48                                                       
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   45                                                       
CONECT   45   44   46                                                       
CONECT   46   45   47                                                       
CONECT   47   46                                                            
CONECT   48    6   49   50                                                  
CONECT   49   48                                                            
CONECT   50   48   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   66                                                       
CONECT   66   65   67                                                       
CONECT   67   66   68                                                       
CONECT   68   67   69                                                       
CONECT   69   68   70                                                       
CONECT   70   69   71                                                       
CONECT   71   70   72                                                       
CONECT   72   71   73                                                       
CONECT   73   72                                                            
MASTER        0    0    0    0    0    0    0    0   73    0  144    0
END

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3D PDB for #<Metabolite:0x00005634c10d9b88>
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SMILES for #<Metabolite:0x00005634c10d9b88>
[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCC\C=C/CCCCCCCCCCCCC)OC(=O)CCCCCCC\C=C/CCCCCCCCCCCCCCC
Download
INCHI for #<Metabolite:0x00005634c10d9b88>
InChI=1S/C56H108O13P2/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-35-37-39-41-43-45-47-55(58)65-51-54(52-68-71(63,64)67-50-53(57)49-66-70(60,61)62)69-56(59)48-46-44-42-40-38-36-34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h27,29,32,34,53-54,57H,3-26,28,30-31,33,35-52H2,1-2H3,(H,63,64)(H2,60,61,62)/b29-27-,34-32-/t53-,54+/m0/s1
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Synonyms
ValueSource
[(2S)-2-Hydroxy-3-({hydroxy[(2R)-3-[(11Z)-pentacos-11-enoyloxy]-2-[(9Z)-pentacos-9-enoyloxy]propoxy]phosphoryl}oxy)propoxy]phosphonateGenerator
Molecular FormulaC56H108O13P2
Average Mass1051.415
Monoisotopic Mass1050.726517534
IUPAC Name[(2S)-2-hydroxy-3-({hydroxy[(2R)-3-[(11Z)-pentacos-11-enoyloxy]-2-[(9Z)-pentacos-9-enoyloxy]propoxy]phosphoryl}oxy)propoxy]phosphonic acid
Traditional Name(2S)-2-hydroxy-3-{[hydroxy((2R)-3-[(11Z)-pentacos-11-enoyloxy]-2-[(9Z)-pentacos-9-enoyloxy]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/CCCCCCCCCCCCC)OC(=O)CCCCCCC\C=C/CCCCCCCCCCCCCCC
InChI Identifier
InChI=1S/C56H108O13P2/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-35-37-39-41-43-45-47-55(58)65-51-54(52-68-71(63,64)67-50-53(57)49-66-70(60,61)62)69-56(59)48-46-44-42-40-38-36-34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h27,29,32,34,53-54,57H,3-26,28,30-31,33,35-52H2,1-2H3,(H,63,64)(H2,60,61,62)/b29-27-,34-32-/t53-,54+/m0/s1
InChI KeyRCNWSELADYQFJH-VXCZFNEBSA-N