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Showing metabocard for PG(i-12:0/a-13:0) (HMDB0116655)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-09-09 08:56:15 UTC
Update Date2022-11-30 19:26:42 UTC
HMDB IDHMDB0116655
Secondary Accession NumbersNone
Metabolite Identification
Common NamePG(i-12:0/a-13:0)
DescriptionPG(i-12:0/a-13:0) is a phosphatidylglycerol - a glycerophospholipid in which a phosphoglycerol moiety occupies a glycerol substitution site. As is the case with diacylglycerols, phosphatidylglycerols can have many different combinations of fatty acids of varying lengths and saturation attached at the C-1 and C-2 positions. Fatty acids containing 16, 18 and 20 carbons are the most common. PG(i-12:0/a-13:0), in particular, consists of one chain of isododecanoic acid at the C-1 position and one chain of anteisotridecanoic acid at the C-2 position. Phosphatidylglycerol 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 phosphatidylglycerol increases during fetal development. Phosphatidylglycerol may be present in animal tissues merely as a precursor for cardiolipin synthesis.
Structure
Data?1563873742
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0116655 (PG(i-12:0/a-13:0))

PG(i-12:0/a-13:0)
  Mrv1652309181707342D          

 44 43  0  0  1  0            999 V2000
   14.0374  -24.1595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3624  -24.5493    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.6871  -24.1595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7126  -24.5493    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0120  -24.5493    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.8354  -25.3289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.3878  -24.1595    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   14.9979  -23.4844    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.7775  -24.8347    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0628  -23.7697    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.7379  -24.1595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.4131  -23.7697    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.0883  -24.1595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9501  -25.3586    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.7261  -23.7330    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.9894  -23.0847    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.8011  -23.0847    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2975  -24.1369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2975  -23.3654    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.5834  -24.5500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8693  -24.1369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1551  -24.5500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4410  -24.1369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.0127  -24.1369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 10  7  1  0  0  0  0
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 43 44  1  0  0  0  0
M  END
Download

3D MOL for HMDB0116655 (PG(i-12:0/a-13:0))

HMDB0116655
     RDKit          3D
PG(i-12:0/a-13:0)
103102  0  0  0  0  0  0  0  0999 V2000
   -9.0169   -0.9627   -1.2575 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6551   -0.9345    0.1916 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6514   -2.2556    0.8792 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0009   -2.9435    0.8360 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6167   -3.1996    0.3587 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2033   -2.6717    0.4960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8340   -2.3961    1.9162 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4323   -1.8691    2.0728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2049   -0.5864    1.3382 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0116655 (PG(i-12:0/a-13:0))

PG(i-12:0/a-13:0)
  Mrv1652309181707342D          

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M  END
> <DATABASE_ID>
HMDB0116655

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C31H61O10P/c1-5-27(4)19-15-11-7-9-13-17-21-31(35)41-29(25-40-42(36,37)39-23-28(33)22-32)24-38-30(34)20-16-12-8-6-10-14-18-26(2)3/h26-29,32-33H,5-25H2,1-4H3,(H,36,37)/t27?,28-,29+/m0/s1

> <INCHI_KEY>
AYZMSNAQZAYDFX-CVWZLOPKSA-N

> <FORMULA>
C31H61O10P

> <MOLECULAR_WEIGHT>
624.793

> <EXACT_MASS>
624.400235162

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
103

> <JCHEM_AVERAGE_POLARIZABILITY>
72.0360130196399

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2S)-2,3-dihydroxypropoxy][(2R)-2-[(10-methyldodecanoyl)oxy]-3-[(10-methylundecanoyl)oxy]propoxy]phosphinic acid

> <ALOGPS_LOGP>
5.28

> <JCHEM_LOGP>
7.509971727

> <ALOGPS_LOGS>
-5.99

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.641245576372423

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8907737771908404

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9689647678483633

> <JCHEM_POLAR_SURFACE_AREA>
148.82000000000002

> <JCHEM_REFRACTIVITY>
162.99710000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
31

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.44e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2,3-dihydroxypropoxy((2R)-2-[(10-methyldodecanoyl)oxy]-3-[(10-methylundecanoyl)oxy]propoxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0116655 (PG(i-12:0/a-13:0))

HMDB0116655
     RDKit          3D
PG(i-12:0/a-13:0)
103102  0  0  0  0  0  0  0  0999 V2000
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   -2.0952    6.5324    4.1887 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2364    8.2393    3.3181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7103    8.2699    1.5673 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1796    9.4793    2.6010 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  2  0
 19 21  1  0
 21 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  1  0
 27 28  1  0
 28 29  1  0
 29 30  1  0
 29 31  1  0
 16 32  1  0
 32 33  1  0
 33 34  1  0
 34 35  2  0
 34 36  1  0
 34 37  1  0
 37 38  1  0
 38 39  1  0
 39 40  1  0
 39 41  1  0
 41 42  1  0
  1 43  1  0
  1 44  1  0
  1 45  1  0
  2 46  1  0
  2 47  1  0
  3 48  1  0
  4 49  1  0
  4 50  1  0
  4 51  1  0
  5 52  1  0
  5 53  1  0
  6 54  1  0
  6 55  1  0
  7 56  1  0
  7 57  1  0
  8 58  1  0
  8 59  1  0
  9 60  1  0
  9 61  1  0
 10 62  1  0
 10 63  1  0
 11 64  1  0
 11 65  1  0
 12 66  1  0
 12 67  1  0
 16 68  1  6
 17 69  1  0
 17 70  1  0
 21 71  1  0
 21 72  1  0
 22 73  1  0
 22 74  1  0
 23 75  1  0
 23 76  1  0
 24 77  1  0
 24 78  1  0
 25 79  1  0
 25 80  1  0
 26 81  1  0
 26 82  1  0
 27 83  1  0
 27 84  1  0
 28 85  1  0
 28 86  1  0
 29 87  1  0
 30 88  1  0
 30 89  1  0
 30 90  1  0
 31 91  1  0
 31 92  1  0
 31 93  1  0
 32 94  1  0
 32 95  1  0
 36 96  1  0
 38 97  1  0
 38 98  1  0
 39 99  1  6
 40100  1  0
 41101  1  0
 41102  1  0
 42103  1  0
M  END
Download

PDB for HMDB0116655 (PG(i-12:0/a-13:0))

HEADER    PROTEIN                                 18-SEP-17   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: PG(i-12:0/a-13:0)                                 
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   18-SEP-17         0                                  
HETATM    1  C   UNK     0      26.203 -45.098   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      24.943 -45.825   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      23.683 -45.098   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      27.464 -45.825   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      22.422 -45.825   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      23.959 -47.281   0.000  0.00  0.00           O+0
HETATM    7  P   UNK     0      28.724 -45.098   0.000  0.00  0.00           P+0
HETATM    8  O   UNK     0      27.996 -43.837   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      29.451 -46.358   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      29.984 -44.370   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      31.244 -45.098   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      32.504 -44.370   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      33.765 -45.098   0.000  0.00  0.00           C+0
HETATM   14  H   UNK     0      26.040 -47.336   0.000  0.00  0.00           H+0
HETATM   15  O   UNK     0      34.955 -44.302   0.000  0.00  0.00           O+0
HETATM   16  H   UNK     0      33.580 -43.091   0.000  0.00  0.00           H+0
HETATM   17  O   UNK     0      31.362 -43.091   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      21.089 -45.055   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      21.089 -43.615   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      19.756 -45.827   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      18.423 -45.055   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      17.090 -45.827   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      15.756 -45.055   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      14.423 -45.827   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      13.090 -45.055   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      11.757 -45.827   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      10.424 -45.055   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       9.091 -45.827   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       7.758 -45.055   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       7.758 -46.596   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      22.626 -48.051   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      22.626 -49.491   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      21.293 -47.279   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      19.960 -48.051   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      18.627 -47.279   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      17.294 -48.051   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      15.961 -47.279   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      14.628 -48.051   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      13.295 -47.279   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      11.961 -48.051   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      10.628 -47.279   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       9.295 -48.051   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       9.295 -46.511   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       7.962 -47.282   0.000  0.00  0.00           C+0
CONECT    1    2    4                                                       
CONECT    2    1    6   14    3                                             
CONECT    3    2    5                                                       
CONECT    4    1    7                                                       
CONECT    5    3   18                                                       
CONECT    6    2   31                                                       
CONECT    7    4    8    9   10                                             
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    7   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   16   17   13                                             
CONECT   13   12   15                                                       
CONECT   14    2                                                            
CONECT   15   13                                                            
CONECT   16   12                                                            
CONECT   17   12                                                            
CONECT   18    5   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28                                                            
CONECT   31    6   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   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   43                                                  
CONECT   42   41                                                            
CONECT   43   41   44                                                       
CONECT   44   43                                                            
MASTER        0    0    0    0    0    0    0    0   44    0   86    0
END
Download

3D PDB for HMDB0116655 (PG(i-12:0/a-13:0))

COMPND    HMDB0116655
HETATM    1  C1  UNL     1      -9.017  -0.963  -1.257  1.00  0.00           C  
HETATM    2  C2  UNL     1      -8.655  -0.934   0.192  1.00  0.00           C  
HETATM    3  C3  UNL     1      -8.651  -2.256   0.879  1.00  0.00           C  
HETATM    4  C4  UNL     1     -10.001  -2.943   0.836  1.00  0.00           C  
HETATM    5  C5  UNL     1      -7.617  -3.200   0.359  1.00  0.00           C  
HETATM    6  C6  UNL     1      -6.203  -2.672   0.496  1.00  0.00           C  
HETATM    7  C7  UNL     1      -5.834  -2.396   1.916  1.00  0.00           C  
HETATM    8  C8  UNL     1      -4.432  -1.869   2.073  1.00  0.00           C  
HETATM    9  C9  UNL     1      -4.205  -0.586   1.338  1.00  0.00           C  
HETATM   10  C10 UNL     1      -2.798  -0.103   1.564  1.00  0.00           C  
HETATM   11  C11 UNL     1      -1.754  -1.073   1.112  1.00  0.00           C  
HETATM   12  C12 UNL     1      -1.815  -1.419  -0.340  1.00  0.00           C  
HETATM   13  C13 UNL     1      -1.671  -0.213  -1.168  1.00  0.00           C  
HETATM   14  O1  UNL     1      -2.634   0.198  -1.858  1.00  0.00           O  
HETATM   15  O2  UNL     1      -0.484   0.483  -1.200  1.00  0.00           O  
HETATM   16  C14 UNL     1      -0.422   1.641  -2.048  1.00  0.00           C  
HETATM   17  C15 UNL     1       0.696   1.324  -3.034  1.00  0.00           C  
HETATM   18  O3  UNL     1       1.872   1.172  -2.264  1.00  0.00           O  
HETATM   19  C16 UNL     1       3.097   0.818  -2.851  1.00  0.00           C  
HETATM   20  O4  UNL     1       3.095   0.633  -4.086  1.00  0.00           O  
HETATM   21  C17 UNL     1       4.238   0.706  -1.944  1.00  0.00           C  
HETATM   22  C18 UNL     1       5.434   0.135  -2.662  1.00  0.00           C  
HETATM   23  C19 UNL     1       5.156  -1.250  -3.142  1.00  0.00           C  
HETATM   24  C20 UNL     1       6.344  -1.835  -3.860  1.00  0.00           C  
HETATM   25  C21 UNL     1       7.526  -1.860  -2.930  1.00  0.00           C  
HETATM   26  C22 UNL     1       7.259  -2.667  -1.674  1.00  0.00           C  
HETATM   27  C23 UNL     1       8.525  -2.613  -0.806  1.00  0.00           C  
HETATM   28  C24 UNL     1       8.331  -3.384   0.469  1.00  0.00           C  
HETATM   29  C25 UNL     1       9.566  -3.349   1.341  1.00  0.00           C  
HETATM   30  C26 UNL     1       9.885  -1.910   1.694  1.00  0.00           C  
HETATM   31  C27 UNL     1       9.260  -4.079   2.625  1.00  0.00           C  
HETATM   32  C28 UNL     1      -0.033   2.861  -1.235  1.00  0.00           C  
HETATM   33  O5  UNL     1      -0.972   3.096  -0.223  1.00  0.00           O  
HETATM   34  P1  UNL     1      -0.556   4.450   0.681  1.00  0.00           P  
HETATM   35  O6  UNL     1      -0.388   5.654  -0.232  1.00  0.00           O  
HETATM   36  O7  UNL     1       0.830   4.158   1.585  1.00  0.00           O  
HETATM   37  O8  UNL     1      -1.861   4.778   1.731  1.00  0.00           O  
HETATM   38  C29 UNL     1      -2.107   6.154   1.725  1.00  0.00           C  
HETATM   39  C30 UNL     1      -3.261   6.468   2.648  1.00  0.00           C  
HETATM   40  O9  UNL     1      -2.913   6.051   3.923  1.00  0.00           O  
HETATM   41  C31 UNL     1      -3.468   7.972   2.590  1.00  0.00           C  
HETATM   42  O10 UNL     1      -2.266   8.565   2.966  1.00  0.00           O  
HETATM   43  H1  UNL     1     -10.100  -1.163  -1.417  1.00  0.00           H  
HETATM   44  H2  UNL     1      -8.426  -1.639  -1.874  1.00  0.00           H  
HETATM   45  H3  UNL     1      -8.828   0.071  -1.675  1.00  0.00           H  
HETATM   46  H4  UNL     1      -7.629  -0.490   0.313  1.00  0.00           H  
HETATM   47  H5  UNL     1      -9.322  -0.199   0.707  1.00  0.00           H  
HETATM   48  H6  UNL     1      -8.444  -2.077   1.959  1.00  0.00           H  
HETATM   49  H7  UNL     1     -10.827  -2.241   0.607  1.00  0.00           H  
HETATM   50  H8  UNL     1     -10.184  -3.551   1.754  1.00  0.00           H  
HETATM   51  H9  UNL     1      -9.973  -3.658  -0.012  1.00  0.00           H  
HETATM   52  H10 UNL     1      -7.797  -3.309  -0.745  1.00  0.00           H  
HETATM   53  H11 UNL     1      -7.676  -4.172   0.877  1.00  0.00           H  
HETATM   54  H12 UNL     1      -5.532  -3.475   0.110  1.00  0.00           H  
HETATM   55  H13 UNL     1      -6.058  -1.769  -0.126  1.00  0.00           H  
HETATM   56  H14 UNL     1      -5.912  -3.304   2.559  1.00  0.00           H  
HETATM   57  H15 UNL     1      -6.538  -1.626   2.359  1.00  0.00           H  
HETATM   58  H16 UNL     1      -3.743  -2.687   1.737  1.00  0.00           H  
HETATM   59  H17 UNL     1      -4.251  -1.662   3.155  1.00  0.00           H  
HETATM   60  H18 UNL     1      -4.446  -0.638   0.252  1.00  0.00           H  
HETATM   61  H19 UNL     1      -4.880   0.177   1.772  1.00  0.00           H  
HETATM   62  H20 UNL     1      -2.617   0.885   1.074  1.00  0.00           H  
HETATM   63  H21 UNL     1      -2.661   0.006   2.676  1.00  0.00           H  
HETATM   64  H22 UNL     1      -1.817  -1.999   1.745  1.00  0.00           H  
HETATM   65  H23 UNL     1      -0.764  -0.623   1.340  1.00  0.00           H  
HETATM   66  H24 UNL     1      -0.996  -2.151  -0.547  1.00  0.00           H  
HETATM   67  H25 UNL     1      -2.761  -1.931  -0.621  1.00  0.00           H  
HETATM   68  H26 UNL     1      -1.352   1.774  -2.587  1.00  0.00           H  
HETATM   69  H27 UNL     1       0.828   2.184  -3.732  1.00  0.00           H  
HETATM   70  H28 UNL     1       0.490   0.398  -3.605  1.00  0.00           H  
HETATM   71  H29 UNL     1       4.528   1.706  -1.520  1.00  0.00           H  
HETATM   72  H30 UNL     1       3.970   0.049  -1.064  1.00  0.00           H  
HETATM   73  H31 UNL     1       5.636   0.819  -3.518  1.00  0.00           H  
HETATM   74  H32 UNL     1       6.343   0.176  -1.996  1.00  0.00           H  
HETATM   75  H33 UNL     1       4.864  -1.939  -2.305  1.00  0.00           H  
HETATM   76  H34 UNL     1       4.293  -1.276  -3.846  1.00  0.00           H  
HETATM   77  H35 UNL     1       6.576  -1.137  -4.708  1.00  0.00           H  
HETATM   78  H36 UNL     1       6.116  -2.854  -4.250  1.00  0.00           H  
HETATM   79  H37 UNL     1       7.870  -0.860  -2.674  1.00  0.00           H  
HETATM   80  H38 UNL     1       8.373  -2.342  -3.497  1.00  0.00           H  
HETATM   81  H39 UNL     1       6.437  -2.245  -1.098  1.00  0.00           H  
HETATM   82  H40 UNL     1       7.053  -3.714  -1.948  1.00  0.00           H  
HETATM   83  H41 UNL     1       8.683  -1.537  -0.542  1.00  0.00           H  
HETATM   84  H42 UNL     1       9.352  -2.996  -1.409  1.00  0.00           H  
HETATM   85  H43 UNL     1       8.132  -4.460   0.252  1.00  0.00           H  
HETATM   86  H44 UNL     1       7.502  -2.957   1.051  1.00  0.00           H  
HETATM   87  H45 UNL     1      10.442  -3.804   0.825  1.00  0.00           H  
HETATM   88  H46 UNL     1       8.996  -1.411   2.126  1.00  0.00           H  
HETATM   89  H47 UNL     1      10.236  -1.408   0.756  1.00  0.00           H  
HETATM   90  H48 UNL     1      10.727  -1.861   2.439  1.00  0.00           H  
HETATM   91  H49 UNL     1       8.533  -4.913   2.397  1.00  0.00           H  
HETATM   92  H50 UNL     1       8.798  -3.324   3.321  1.00  0.00           H  
HETATM   93  H51 UNL     1      10.168  -4.497   3.086  1.00  0.00           H  
HETATM   94  H52 UNL     1       0.927   2.694  -0.724  1.00  0.00           H  
HETATM   95  H53 UNL     1      -0.049   3.739  -1.903  1.00  0.00           H  
HETATM   96  H54 UNL     1       0.553   3.935   2.512  1.00  0.00           H  
HETATM   97  H55 UNL     1      -1.214   6.693   2.037  1.00  0.00           H  
HETATM   98  H56 UNL     1      -2.355   6.416   0.668  1.00  0.00           H  
HETATM   99  H57 UNL     1      -4.149   5.912   2.269  1.00  0.00           H  
HETATM  100  H58 UNL     1      -2.095   6.532   4.189  1.00  0.00           H  
HETATM  101  H59 UNL     1      -4.236   8.239   3.318  1.00  0.00           H  
HETATM  102  H60 UNL     1      -3.710   8.270   1.567  1.00  0.00           H  
HETATM  103  H61 UNL     1      -2.180   9.479   2.601  1.00  0.00           H  
CONECT    1    2   43   44   45
CONECT    2    3   46   47
CONECT    3    4    5   48
CONECT    4   49   50   51
CONECT    5    6   52   53
CONECT    6    7   54   55
CONECT    7    8   56   57
CONECT    8    9   58   59
CONECT    9   10   60   61
CONECT   10   11   62   63
CONECT   11   12   64   65
CONECT   12   13   66   67
CONECT   13   14   14   15
CONECT   15   16
CONECT   16   17   32   68
CONECT   17   18   69   70
CONECT   18   19
CONECT   19   20   20   21
CONECT   21   22   71   72
CONECT   22   23   73   74
CONECT   23   24   75   76
CONECT   24   25   77   78
CONECT   25   26   79   80
CONECT   26   27   81   82
CONECT   27   28   83   84
CONECT   28   29   85   86
CONECT   29   30   31   87
CONECT   30   88   89   90
CONECT   31   91   92   93
CONECT   32   33   94   95
CONECT   33   34
CONECT   34   35   35   36   37
CONECT   36   96
CONECT   37   38
CONECT   38   39   97   98
CONECT   39   40   41   99
CONECT   40  100
CONECT   41   42  101  102
CONECT   42  103
END
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SMILES for HMDB0116655 (PG(i-12:0/a-13:0))

[H][C@](O)(CO)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCC(C)C)OC(=O)CCCCCCCCC(C)CC
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INCHI for HMDB0116655 (PG(i-12:0/a-13:0))

InChI=1S/C31H61O10P/c1-5-27(4)19-15-11-7-9-13-17-21-31(35)41-29(25-40-42(36,37)39-23-28(33)22-32)24-38-30(34)20-16-12-8-6-10-14-18-26(2)3/h26-29,32-33H,5-25H2,1-4H3,(H,36,37)/t27?,28-,29+/m0/s1
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Synonyms
ValueSource
1-isododecanoyl-2-anteisotridecanoyl-sn-glycero-3-phospho-(1'-glycerol)SMPDB, HMDB
1-isododecanoyl-2-anteisotridecanoyl-sn-glycero-3-phosphoglycerolSMPDB, HMDB
PG(i-12:0/a-13:0)SMPDB
PG(25:0)SMPDB, HMDB
Phosphatidylglycerol(i-12:0/a-13:0)SMPDB, HMDB
Phosphatidylglycerol(25:0)SMPDB, HMDB
GPG(i-12:0/a-13:0)Lipid Annotator, HMDB
GPG(25:0)Lipid Annotator, HMDB
[(2S)-2,3-Dihydroxypropoxy][(2R)-2-[(10-methyldodecanoyl)oxy]-3-[(10-methylundecanoyl)oxy]propoxy]phosphinateGenerator, HMDB
Chemical FormulaC31H61O10P
Average Molecular Weight624.793
Monoisotopic Molecular Weight624.400235162
IUPAC Name[(2S)-2,3-dihydroxypropoxy][(2R)-2-[(10-methyldodecanoyl)oxy]-3-[(10-methylundecanoyl)oxy]propoxy]phosphinic acid
Traditional Name(2S)-2,3-dihydroxypropoxy((2R)-2-[(10-methyldodecanoyl)oxy]-3-[(10-methylundecanoyl)oxy]propoxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
[H][C@](O)(CO)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCC(C)C)OC(=O)CCCCCCCCC(C)CC
InChI Identifier
InChI=1S/C31H61O10P/c1-5-27(4)19-15-11-7-9-13-17-21-31(35)41-29(25-40-42(36,37)39-23-28(33)22-32)24-38-30(34)20-16-12-8-6-10-14-18-26(2)3/h26-29,32-33H,5-25H2,1-4H3,(H,36,37)/t27?,28-,29+/m0/s1
InChI KeyAYZMSNAQZAYDFX-CVWZLOPKSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as phosphatidylglycerols. These are glycerophosphoglycerols in which two fatty acids are bonded to the 1-glycerol moiety through ester linkages. As is the case with diacylglycerols, phosphatidylglycerols can have many different combinations of fatty acids of varying lengths and saturation attached to the C-1 and C-2 positions.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassGlycerophospholipids
Sub ClassGlycerophosphoglycerols
Direct ParentPhosphatidylglycerols
Alternative Parents
Substituents
  • 1,2-diacylglycerophosphoglycerol
  • Fatty acid ester
  • Dialkyl phosphate
  • Dicarboxylic acid or derivatives
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Fatty acyl
  • 1,2-diol
  • Carboxylic acid ester
  • Secondary alcohol
  • Carboxylic acid derivative
  • Organic oxide
  • Organooxygen compound
  • Alcohol
  • Organic oxygen compound
  • Primary alcohol
  • Carbonyl group
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
DispositionNot Available
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
logP5.28ALOGPS
logP7.51ChemAxon
logS-6ALOGPS
pKa (Strongest Acidic)1.89ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area148.82 ŲChemAxon
Rotatable Bond Count31ChemAxon
Refractivity163 m³·mol⁻¹ChemAxon
Polarizability72.04 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]+244.31631661259
DarkChem[M-H]-238.45431661259
DeepCCS[M+H]+251.44630932474
DeepCCS[M-H]-249.24130932474
DeepCCS[M-2H]-282.48130932474
DeepCCS[M+Na]+257.3630932474
AllCCS[M+H]+256.032859911
AllCCS[M+H-H2O]+255.532859911
AllCCS[M+NH4]+256.532859911
AllCCS[M+Na]+256.732859911
AllCCS[M-H]-238.232859911
AllCCS[M+Na-2H]-242.832859911
AllCCS[M+HCOO]-248.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
PG(i-12:0/a-13:0)[H][C@](O)(CO)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCC(C)C)OC(=O)CCCCCCCCC(C)CC4105.4Standard polar33892256
PG(i-12:0/a-13:0)[H][C@](O)(CO)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCC(C)C)OC(=O)CCCCCCCCC(C)CC3755.6Standard non polar33892256
PG(i-12:0/a-13:0)[H][C@](O)(CO)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCC(C)C)OC(=O)CCCCCCCCC(C)CC4184.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
PG(i-12:0/a-13:0),1TMS,isomer #1CCC(C)CCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC(C)C)COP(=O)(O)OC[C@H](CO)O[Si](C)(C)C4215.6Semi standard non polar33892256
PG(i-12:0/a-13:0),1TMS,isomer #2CCC(C)CCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC(C)C)COP(=O)(O)OC[C@@H](O)CO[Si](C)(C)C4196.7Semi standard non polar33892256
PG(i-12:0/a-13:0),1TMS,isomer #3CCC(C)CCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC(C)C)COP(=O)(OC[C@@H](O)CO)O[Si](C)(C)C4190.4Semi standard non polar33892256
PG(i-12:0/a-13:0),2TMS,isomer #1CCC(C)CCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC(C)C)COP(=O)(O)OC[C@H](CO[Si](C)(C)C)O[Si](C)(C)C4192.9Semi standard non polar33892256
PG(i-12:0/a-13:0),2TMS,isomer #2CCC(C)CCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC(C)C)COP(=O)(OC[C@H](CO)O[Si](C)(C)C)O[Si](C)(C)C4196.0Semi standard non polar33892256
PG(i-12:0/a-13:0),2TMS,isomer #3CCC(C)CCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC(C)C)COP(=O)(OC[C@@H](O)CO[Si](C)(C)C)O[Si](C)(C)C4180.6Semi standard non polar33892256
PG(i-12:0/a-13:0),3TMS,isomer #1CCC(C)CCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC(C)C)COP(=O)(OC[C@H](CO[Si](C)(C)C)O[Si](C)(C)C)O[Si](C)(C)C4166.8Semi standard non polar33892256
PG(i-12:0/a-13:0),3TMS,isomer #1CCC(C)CCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC(C)C)COP(=O)(OC[C@H](CO[Si](C)(C)C)O[Si](C)(C)C)O[Si](C)(C)C3672.8Standard non polar33892256
PG(i-12:0/a-13:0),3TMS,isomer #1CCC(C)CCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC(C)C)COP(=O)(OC[C@H](CO[Si](C)(C)C)O[Si](C)(C)C)O[Si](C)(C)C4551.8Standard polar33892256
PG(i-12:0/a-13:0),1TBDMS,isomer #1CCC(C)CCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC(C)C)COP(=O)(O)OC[C@H](CO)O[Si](C)(C)C(C)(C)C4440.1Semi standard non polar33892256
PG(i-12:0/a-13:0),1TBDMS,isomer #2CCC(C)CCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC(C)C)COP(=O)(O)OC[C@@H](O)CO[Si](C)(C)C(C)(C)C4434.7Semi standard non polar33892256
PG(i-12:0/a-13:0),1TBDMS,isomer #3CCC(C)CCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC(C)C)COP(=O)(OC[C@@H](O)CO)O[Si](C)(C)C(C)(C)C4420.4Semi standard non polar33892256
PG(i-12:0/a-13:0),2TBDMS,isomer #1CCC(C)CCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC(C)C)COP(=O)(O)OC[C@H](CO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C4656.2Semi standard non polar33892256
PG(i-12:0/a-13:0),2TBDMS,isomer #2CCC(C)CCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC(C)C)COP(=O)(OC[C@H](CO)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C4638.5Semi standard non polar33892256
PG(i-12:0/a-13:0),2TBDMS,isomer #3CCC(C)CCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC(C)C)COP(=O)(OC[C@@H](O)CO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C4637.6Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - PG(i-12:0/a-13:0) GC-MS (1 TMS) - 70eV, Positivesplash10-0a5a-7900222000-c9cc307a2b93feaf09932017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PG(i-12:0/a-13:0) GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PG(i-12:0/a-13:0) GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PG(i-12:0/a-13:0) GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PG(i-12:0/a-13:0) GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PG(i-12:0/a-13:0) GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PG(i-12:0/a-13:0) GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PG(i-12:0/a-13:0) GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PG(i-12:0/a-13:0) GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PG(i-12:0/a-13:0) GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PG(i-12:0/a-13:0) GC-MS (TBDMS_2_2) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PG(i-12:0/a-13:0) GC-MS (TBDMS_2_3) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PG(i-12:0/a-13:0) GC-MS ("PG(i-12:0/a-13:0),1TMS,#1" TMS) - 70eV, PositiveNot Available2021-11-02Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PG(i-12:0/a-13:0) 10V, Positive-QTOFsplash10-056r-5931806000-a9f6b0b0e6393380961d2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PG(i-12:0/a-13:0) 20V, Positive-QTOFsplash10-0a6r-6920511000-8ede100ece55eab9a0d12019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PG(i-12:0/a-13:0) 40V, Positive-QTOFsplash10-0a4i-9620300000-f188fe4cceb7e33b49ea2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PG(i-12:0/a-13:0) 10V, Negative-QTOFsplash10-059t-0920212000-3d14ea8aa28e20e5e2d32019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PG(i-12:0/a-13:0) 20V, Negative-QTOFsplash10-002b-4901100000-2b1768c35dc445af95c02019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PG(i-12:0/a-13:0) 40V, Negative-QTOFsplash10-004i-9200000000-5b656744f19f94a917f12019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PG(i-12:0/a-13:0) 10V, Negative-QTOFsplash10-00di-0000009000-b4973e056004dd645cde2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PG(i-12:0/a-13:0) 20V, Negative-QTOFsplash10-022b-0972507000-a2aa15f57098821481422021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PG(i-12:0/a-13:0) 40V, Negative-QTOFsplash10-022a-0962406000-93de501599cf730f67e22021-09-23Wishart 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131823288
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.