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Showing metabocard for PGP(a-13:0/i-17:0) (HMDB0116523)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-09-09 08:23:32 UTC
Update Date2022-11-30 19:26:38 UTC
HMDB IDHMDB0116523
Secondary Accession NumbersNone
Metabolite Identification
Common NamePGP(a-13:0/i-17:0)
DescriptionPGP(a-13:0/i-17:0) 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(a-13:0/i-17:0), in particular, consists of one chain of anteisotridecanoic acid at the C-1 position and one chain of isoheptadecanoic 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?1563873727
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0116523 (PGP(a-13:0/i-17:0))

PGP(a-13:0/i-17:0)
  Mrv1652309171703152D          

 53 52  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
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   -0.3125    0.0209    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0493    1.3958    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8811    0.9262    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6379    0.3435    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4301    0.5557    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.4301    1.3759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2224    0.3435    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0200   -0.1546    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5123    0.7696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5123    1.5410    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.9405    0.7696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6546    0.3564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  2  3  1  0  0  0  0
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 50 51  1  0  0  0  0
 51 52  1  0  0  0  0
 51 53  1  0  0  0  0
M  END
Download

3D MOL for HMDB0116523 (PGP(a-13:0/i-17:0))

HMDB0116523
     RDKit          3D
PGP(a-13:0/i-17:0)
123122  0  0  0  0  0  0  0  0999 V2000
    0.5414   -2.7545   -7.8247 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2223   -1.6226   -8.7733 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8327   -0.3253   -8.2494 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4637    0.7402   -9.2595 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2280   -0.0720   -6.9035 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7360    1.1817   -6.2339 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1049    1.3955   -4.8979 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3841    1.5546   -4.9168 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8294    1.7471   -3.4639 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.6498    2.0824   -1.8744 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1230    2.2775   -1.6782 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3860    2.3859   -0.2157 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4732    1.2871    0.4328 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5404    3.5527    0.4833 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.9186    2.9051    4.0730 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.1583    2.0095    6.3087 P   0  0  0  0  0  5  0  0  0  0  0  0
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   -2.7045    1.4956    7.0016 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3733    0.1969    6.5926 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.1995   -4.3869    2.3598 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2639   -5.2342    1.7906 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0116523 (PGP(a-13:0/i-17:0))

PGP(a-13:0/i-17:0)
  Mrv1652309171703152D          

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M  END
> <DATABASE_ID>
HMDB0116523

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C36H72O13P2/c1-5-32(4)24-20-16-13-14-17-21-25-35(38)45-29-34(30-48-51(43,44)47-28-33(37)27-46-50(40,41)42)49-36(39)26-22-18-12-10-8-6-7-9-11-15-19-23-31(2)3/h31-34,37H,5-30H2,1-4H3,(H,43,44)(H2,40,41,42)/t32?,33-,34+/m0/s1

> <INCHI_KEY>
VDPKZTIMPSQGOE-PRIWKQAOSA-N

> <FORMULA>
C36H72O13P2

> <MOLECULAR_WEIGHT>
774.907

> <EXACT_MASS>
774.444816374

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
123

> <JCHEM_AVERAGE_POLARIZABILITY>
88.18614954919651

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2S)-2-hydroxy-3-({hydroxy[(2R)-3-[(10-methyldodecanoyl)oxy]-2-[(15-methylhexadecanoyl)oxy]propoxy]phosphoryl}oxy)propoxy]phosphonic acid

> <ALOGPS_LOGP>
5.65

> <JCHEM_LOGP>
9.609249020666667

> <ALOGPS_LOGS>
-5.77

> <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>
196.875

> <JCHEM_ROTATABLE_BOND_COUNT>
38

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.30e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-hydroxy-3-{[hydroxy((2R)-3-[(10-methyldodecanoyl)oxy]-2-[(15-methylhexadecanoyl)oxy]propoxy)phosphoryl]oxy}propoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0116523 (PGP(a-13:0/i-17:0))

HMDB0116523
     RDKit          3D
PGP(a-13:0/i-17:0)
123122  0  0  0  0  0  0  0  0999 V2000
    0.5414   -2.7545   -7.8247 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.2280   -0.0720   -6.9035 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.7985   -4.8409   -1.1445 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8638   -3.6933   -1.0985 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2195   -4.2769   -1.1251 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5400   -2.5775   -7.3550 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6064   -3.6899   -8.4176 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.0763    4.6184    2.2103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4077    2.0376    2.2221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1259    3.8737    4.5630 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.9288    0.8143    7.1602 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.3928    5.0860    1.1165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6805    4.3050    2.5557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2904    3.2415   -0.3166 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8733    4.1750    0.7593 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2541    1.4386    1.5836 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9808    2.4257    2.3697 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4633    2.3617    0.4446 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2404    1.4952   -0.5095 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5233    0.5038    2.1237 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9640   -0.0801    0.4366 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3013   -0.4742    1.8760 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7098   -0.9415    0.1264 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -1.7211    2.6446 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5793   -2.1201    0.9131 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0391   -2.6978    2.4332 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3419   -3.2031    0.7701 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2276   -4.9895    2.4482 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4011   -4.1918    3.4827 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2460   -6.2440    2.3516 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9597   -5.5322    0.7535 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8154   -3.6674    1.5980 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8889   -4.7096    3.0099 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.7167   -5.2856   -2.1914 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7131   -3.2414   -2.1234 H   0  0  0  0  0  0  0  0  0  0  0  0
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    6.3460   -3.7321   -2.0929 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9839   -5.0511   -1.0876 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2563   -3.5321   -0.3281 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for HMDB0116523 (PGP(a-13:0/i-17:0))

HEADER    PROTEIN                                 17-SEP-17   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: PGP(a-13:0/i-17:0)                                
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-SEP-17         0                                  
HETATM    1  H   UNK     0       5.199   1.798   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0      -4.446   0.673   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.772   1.437   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -7.097   0.673   0.000  0.00  0.00           O+0
HETATM    5  H   UNK     0      -3.680  -0.652   0.000  0.00  0.00           H+0
HETATM    6  O   UNK     0      -5.213  -0.652   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -3.120   1.439   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.794   0.673   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.487   0.642   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.813  -0.124   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.139   0.642   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.465  -0.124   0.000  0.00  0.00           C+0
HETATM   13  P   UNK     0       0.092   1.210   0.000  0.00  0.00           P+0
HETATM   14  O   UNK     0      -0.583   0.039   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.092   2.605   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       3.511   1.729   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       6.791   0.641   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0       8.270   1.037   0.000  0.00  0.00           P+0
HETATM   19  O   UNK     0       8.270   2.568   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       9.748   0.641   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       7.504  -0.289   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -8.423   1.437   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -8.423   2.877   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -9.756   0.665   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0     -11.089   1.437   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0     -12.422   0.665   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0     -13.755   1.437   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   1.437   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   1.437   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   1.437   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0     -21.753  -0.104   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0     -23.086   0.668   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -6.601  -1.436   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      -6.601  -2.876   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      -7.934  -0.665   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -9.267  -1.436   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0     -10.600  -0.665   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0     -11.933  -1.436   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0     -13.266  -0.665   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0     -14.599  -1.436   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0     -15.932  -0.665   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0     -17.265  -1.436   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0     -18.598  -0.665   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0     -19.931  -1.436   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0     -21.265  -0.665   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0     -22.598  -1.436   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0     -23.931  -0.665   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0     -25.264  -1.436   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0     -26.597  -0.665   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0     -26.597  -2.205   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   36                                                       
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   35                                                       
CONECT   35   34                                                            
CONECT   36    6   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   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   53                                                  
CONECT   52   51                                                            
CONECT   53   51                                                            
MASTER        0    0    0    0    0    0    0    0   53    0  104    0
END
Download

3D PDB for HMDB0116523 (PGP(a-13:0/i-17:0))

COMPND    HMDB0116523
HETATM    1  C1  UNL     1       0.541  -2.755  -7.825  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.222  -1.623  -8.773  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.833  -0.325  -8.249  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.464   0.740  -9.259  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.228  -0.072  -6.904  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.736   1.182  -6.234  1.00  0.00           C  
HETATM    7  C7  UNL     1       0.105   1.395  -4.898  1.00  0.00           C  
HETATM    8  C8  UNL     1      -1.384   1.555  -4.917  1.00  0.00           C  
HETATM    9  C9  UNL     1      -1.829   1.747  -3.464  1.00  0.00           C  
HETATM   10  C10 UNL     1      -3.307   1.925  -3.359  1.00  0.00           C  
HETATM   11  C11 UNL     1      -3.650   2.082  -1.874  1.00  0.00           C  
HETATM   12  C12 UNL     1      -5.123   2.278  -1.678  1.00  0.00           C  
HETATM   13  C13 UNL     1      -5.386   2.386  -0.216  1.00  0.00           C  
HETATM   14  O1  UNL     1      -5.473   1.287   0.433  1.00  0.00           O  
HETATM   15  O2  UNL     1      -5.540   3.553   0.483  1.00  0.00           O  
HETATM   16  C14 UNL     1      -5.778   3.613   1.855  1.00  0.00           C  
HETATM   17  C15 UNL     1      -4.598   3.058   2.606  1.00  0.00           C  
HETATM   18  C16 UNL     1      -4.919   2.905   4.073  1.00  0.00           C  
HETATM   19  O3  UNL     1      -3.878   2.228   4.670  1.00  0.00           O  
HETATM   20  P1  UNL     1      -4.158   2.009   6.309  1.00  0.00           P  
HETATM   21  O4  UNL     1      -4.583   3.298   6.942  1.00  0.00           O  
HETATM   22  O5  UNL     1      -5.303   0.777   6.590  1.00  0.00           O  
HETATM   23  O6  UNL     1      -2.705   1.496   7.002  1.00  0.00           O  
HETATM   24  C17 UNL     1      -2.373   0.197   6.593  1.00  0.00           C  
HETATM   25  C18 UNL     1      -1.046  -0.108   7.301  1.00  0.00           C  
HETATM   26  O7  UNL     1      -0.576  -1.368   7.001  1.00  0.00           O  
HETATM   27  C19 UNL     1      -0.094   0.981   6.811  1.00  0.00           C  
HETATM   28  O8  UNL     1      -0.630   2.213   7.146  1.00  0.00           O  
HETATM   29  P2  UNL     1       0.403   3.425   6.611  1.00  0.00           P  
HETATM   30  O9  UNL     1       1.501   2.824   5.743  1.00  0.00           O  
HETATM   31  O10 UNL     1       1.073   4.223   7.932  1.00  0.00           O  
HETATM   32  O11 UNL     1      -0.428   4.577   5.677  1.00  0.00           O  
HETATM   33  O12 UNL     1      -3.419   3.781   2.372  1.00  0.00           O  
HETATM   34  C20 UNL     1      -2.288   3.248   1.710  1.00  0.00           C  
HETATM   35  O13 UNL     1      -2.429   2.073   1.338  1.00  0.00           O  
HETATM   36  C21 UNL     1      -1.085   4.096   1.520  1.00  0.00           C  
HETATM   37  C22 UNL     1      -0.007   3.462   0.739  1.00  0.00           C  
HETATM   38  C23 UNL     1       0.502   2.194   1.379  1.00  0.00           C  
HETATM   39  C24 UNL     1       1.624   1.618   0.515  1.00  0.00           C  
HETATM   40  C25 UNL     1       2.171   0.335   1.073  1.00  0.00           C  
HETATM   41  C26 UNL     1       1.079  -0.708   1.140  1.00  0.00           C  
HETATM   42  C27 UNL     1       1.801  -1.984   1.700  1.00  0.00           C  
HETATM   43  C28 UNL     1       0.830  -3.089   1.796  1.00  0.00           C  
HETATM   44  C29 UNL     1       1.199  -4.387   2.360  1.00  0.00           C  
HETATM   45  C30 UNL     1       2.264  -5.234   1.791  1.00  0.00           C  
HETATM   46  C31 UNL     1       3.631  -4.679   1.881  1.00  0.00           C  
HETATM   47  C32 UNL     1       4.677  -5.601   1.286  1.00  0.00           C  
HETATM   48  C33 UNL     1       4.594  -5.903  -0.148  1.00  0.00           C  
HETATM   49  C34 UNL     1       4.798  -4.841  -1.145  1.00  0.00           C  
HETATM   50  C35 UNL     1       3.864  -3.693  -1.098  1.00  0.00           C  
HETATM   51  C36 UNL     1       6.219  -4.277  -1.125  1.00  0.00           C  
HETATM   52  H1  UNL     1       1.540  -2.577  -7.355  1.00  0.00           H  
HETATM   53  H2  UNL     1       0.606  -3.690  -8.418  1.00  0.00           H  
HETATM   54  H3  UNL     1      -0.267  -2.838  -7.079  1.00  0.00           H  
HETATM   55  H4  UNL     1      -0.885  -1.457  -8.846  1.00  0.00           H  
HETATM   56  H5  UNL     1       0.635  -1.798  -9.775  1.00  0.00           H  
HETATM   57  H6  UNL     1       1.912  -0.439  -8.225  1.00  0.00           H  
HETATM   58  H7  UNL     1      -0.522   0.557  -9.731  1.00  0.00           H  
HETATM   59  H8  UNL     1       1.205   0.648 -10.096  1.00  0.00           H  
HETATM   60  H9  UNL     1       0.578   1.766  -8.863  1.00  0.00           H  
HETATM   61  H10 UNL     1      -0.876  -0.045  -6.925  1.00  0.00           H  
HETATM   62  H11 UNL     1       0.542  -0.924  -6.238  1.00  0.00           H  
HETATM   63  H12 UNL     1       0.513   2.081  -6.852  1.00  0.00           H  
HETATM   64  H13 UNL     1       1.830   1.170  -6.090  1.00  0.00           H  
HETATM   65  H14 UNL     1       0.526   2.321  -4.457  1.00  0.00           H  
HETATM   66  H15 UNL     1       0.323   0.499  -4.249  1.00  0.00           H  
HETATM   67  H16 UNL     1      -1.914   0.655  -5.324  1.00  0.00           H  
HETATM   68  H17 UNL     1      -1.698   2.425  -5.531  1.00  0.00           H  
HETATM   69  H18 UNL     1      -1.535   0.838  -2.917  1.00  0.00           H  
HETATM   70  H19 UNL     1      -1.268   2.614  -3.050  1.00  0.00           H  
HETATM   71  H20 UNL     1      -3.800   1.020  -3.775  1.00  0.00           H  
HETATM   72  H21 UNL     1      -3.600   2.852  -3.887  1.00  0.00           H  
HETATM   73  H22 UNL     1      -3.152   3.014  -1.516  1.00  0.00           H  
HETATM   74  H23 UNL     1      -3.332   1.198  -1.301  1.00  0.00           H  
HETATM   75  H24 UNL     1      -5.410   3.224  -2.169  1.00  0.00           H  
HETATM   76  H25 UNL     1      -5.710   1.465  -2.150  1.00  0.00           H  
HETATM   77  H26 UNL     1      -6.632   2.905   2.068  1.00  0.00           H  
HETATM   78  H27 UNL     1      -6.076   4.618   2.210  1.00  0.00           H  
HETATM   79  H28 UNL     1      -4.408   2.038   2.222  1.00  0.00           H  
HETATM   80  H29 UNL     1      -5.126   3.874   4.563  1.00  0.00           H  
HETATM   81  H30 UNL     1      -5.830   2.280   4.150  1.00  0.00           H  
HETATM   82  H31 UNL     1      -5.352   0.164   5.794  1.00  0.00           H  
HETATM   83  H32 UNL     1      -3.171  -0.485   6.895  1.00  0.00           H  
HETATM   84  H33 UNL     1      -2.209   0.242   5.506  1.00  0.00           H  
HETATM   85  H34 UNL     1      -1.232   0.069   8.380  1.00  0.00           H  
HETATM   86  H35 UNL     1      -1.241  -1.792   6.400  1.00  0.00           H  
HETATM   87  H36 UNL     1       0.929   0.814   7.160  1.00  0.00           H  
HETATM   88  H37 UNL     1      -0.106   0.922   5.687  1.00  0.00           H  
HETATM   89  H38 UNL     1       0.489   4.087   8.717  1.00  0.00           H  
HETATM   90  H39 UNL     1       0.236   4.957   5.055  1.00  0.00           H  
HETATM   91  H40 UNL     1      -1.393   5.086   1.117  1.00  0.00           H  
HETATM   92  H41 UNL     1      -0.680   4.305   2.556  1.00  0.00           H  
HETATM   93  H42 UNL     1      -0.290   3.242  -0.317  1.00  0.00           H  
HETATM   94  H43 UNL     1       0.873   4.175   0.759  1.00  0.00           H  
HETATM   95  H44 UNL     1      -0.254   1.439   1.584  1.00  0.00           H  
HETATM   96  H45 UNL     1       0.981   2.426   2.370  1.00  0.00           H  
HETATM   97  H46 UNL     1       2.463   2.362   0.445  1.00  0.00           H  
HETATM   98  H47 UNL     1       1.240   1.495  -0.510  1.00  0.00           H  
HETATM   99  H48 UNL     1       2.523   0.504   2.124  1.00  0.00           H  
HETATM  100  H49 UNL     1       2.964  -0.080   0.437  1.00  0.00           H  
HETATM  101  H50 UNL     1       0.301  -0.474   1.876  1.00  0.00           H  
HETATM  102  H51 UNL     1       0.710  -0.941   0.126  1.00  0.00           H  
HETATM  103  H52 UNL     1       2.254  -1.721   2.645  1.00  0.00           H  
HETATM  104  H53 UNL     1       2.579  -2.120   0.913  1.00  0.00           H  
HETATM  105  H54 UNL     1      -0.039  -2.698   2.433  1.00  0.00           H  
HETATM  106  H55 UNL     1       0.342  -3.203   0.770  1.00  0.00           H  
HETATM  107  H56 UNL     1       0.228  -4.989   2.448  1.00  0.00           H  
HETATM  108  H57 UNL     1       1.401  -4.192   3.483  1.00  0.00           H  
HETATM  109  H58 UNL     1       2.246  -6.244   2.352  1.00  0.00           H  
HETATM  110  H59 UNL     1       1.960  -5.532   0.754  1.00  0.00           H  
HETATM  111  H60 UNL     1       3.815  -3.667   1.598  1.00  0.00           H  
HETATM  112  H61 UNL     1       3.889  -4.710   3.010  1.00  0.00           H  
HETATM  113  H62 UNL     1       5.660  -5.109   1.547  1.00  0.00           H  
HETATM  114  H63 UNL     1       4.694  -6.540   1.920  1.00  0.00           H  
HETATM  115  H64 UNL     1       5.388  -6.700  -0.358  1.00  0.00           H  
HETATM  116  H65 UNL     1       3.644  -6.439  -0.431  1.00  0.00           H  
HETATM  117  H66 UNL     1       4.717  -5.286  -2.191  1.00  0.00           H  
HETATM  118  H67 UNL     1       3.713  -3.241  -2.123  1.00  0.00           H  
HETATM  119  H68 UNL     1       4.353  -2.853  -0.534  1.00  0.00           H  
HETATM  120  H69 UNL     1       2.921  -3.930  -0.630  1.00  0.00           H  
HETATM  121  H70 UNL     1       6.346  -3.732  -2.093  1.00  0.00           H  
HETATM  122  H71 UNL     1       6.984  -5.051  -1.088  1.00  0.00           H  
HETATM  123  H72 UNL     1       6.256  -3.532  -0.328  1.00  0.00           H  
CONECT    1    2   52   53   54
CONECT    2    3   55   56
CONECT    3    4    5   57
CONECT    4   58   59   60
CONECT    5    6   61   62
CONECT    6    7   63   64
CONECT    7    8   65   66
CONECT    8    9   67   68
CONECT    9   10   69   70
CONECT   10   11   71   72
CONECT   11   12   73   74
CONECT   12   13   75   76
CONECT   13   14   14   15
CONECT   15   16
CONECT   16   17   77   78
CONECT   17   18   33   79
CONECT   18   19   80   81
CONECT   19   20
CONECT   20   21   21   22   23
CONECT   22   82
CONECT   23   24
CONECT   24   25   83   84
CONECT   25   26   27   85
CONECT   26   86
CONECT   27   28   87   88
CONECT   28   29
CONECT   29   30   30   31   32
CONECT   31   89
CONECT   32   90
CONECT   33   34
CONECT   34   35   35   36
CONECT   36   37   91   92
CONECT   37   38   93   94
CONECT   38   39   95   96
CONECT   39   40   97   98
CONECT   40   41   99  100
CONECT   41   42  101  102
CONECT   42   43  103  104
CONECT   43   44  105  106
CONECT   44   45  107  108
CONECT   45   46  109  110
CONECT   46   47  111  112
CONECT   47   48  113  114
CONECT   48   49  115  116
CONECT   49   50   51  117
CONECT   50  118  119  120
CONECT   51  121  122  123
END
Download

SMILES for HMDB0116523 (PGP(a-13:0/i-17:0))

[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCC(C)CC)OC(=O)CCCCCCCCCCCCCC(C)C
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INCHI for HMDB0116523 (PGP(a-13:0/i-17:0))

InChI=1S/C36H72O13P2/c1-5-32(4)24-20-16-13-14-17-21-25-35(38)45-29-34(30-48-51(43,44)47-28-33(37)27-46-50(40,41)42)49-36(39)26-22-18-12-10-8-6-7-9-11-15-19-23-31(2)3/h31-34,37H,5-30H2,1-4H3,(H,43,44)(H2,40,41,42)/t32?,33-,34+/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-anteisotridecanoyl-2-isoheptadecanoyl-sn-glycero-3-phospho-(1'-sn-glycerol-3'-phosphate)SMPDB, HMDB
PGP(a-13:0/i-17:0)SMPDB
PGP(30:0)SMPDB, HMDB
3-sn-phosphatidyl-1'-sn-glycerol 3'-phosphoric acidLipid Annotator, HMDB
[(2S)-2-Hydroxy-3-({hydroxy[(2R)-3-[(10-methyldodecanoyl)oxy]-2-[(15-methylhexadecanoyl)oxy]propoxy]phosphoryl}oxy)propoxy]phosphonateGenerator, HMDB
Chemical FormulaC36H72O13P2
Average Molecular Weight774.907
Monoisotopic Molecular Weight774.444816374
IUPAC Name[(2S)-2-hydroxy-3-({hydroxy[(2R)-3-[(10-methyldodecanoyl)oxy]-2-[(15-methylhexadecanoyl)oxy]propoxy]phosphoryl}oxy)propoxy]phosphonic acid
Traditional Name(2S)-2-hydroxy-3-{[hydroxy((2R)-3-[(10-methyldodecanoyl)oxy]-2-[(15-methylhexadecanoyl)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)CC)OC(=O)CCCCCCCCCCCCCC(C)C
InChI Identifier
InChI=1S/C36H72O13P2/c1-5-32(4)24-20-16-13-14-17-21-25-35(38)45-29-34(30-48-51(43,44)47-28-33(37)27-46-50(40,41)42)49-36(39)26-22-18-12-10-8-6-7-9-11-15-19-23-31(2)3/h31-34,37H,5-30H2,1-4H3,(H,43,44)(H2,40,41,42)/t32?,33-,34+/m0/s1
InChI KeyVDPKZTIMPSQGOE-PRIWKQAOSA-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
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
logP5.65ALOGPS
logP9.61ChemAxon
logS-5.8ALOGPS
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 Count38ChemAxon
Refractivity196.88 m³·mol⁻¹ChemAxon
Polarizability88.19 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]+285.3431661259
DarkChem[M-H]-271.60531661259
DeepCCS[M+H]+267.31530932474
DeepCCS[M-H]-265.41930932474
DeepCCS[M-2H]-298.6630932474
DeepCCS[M+Na]+272.95630932474
AllCCS[M+H]+281.232859911
AllCCS[M+H-H2O]+281.132859911
AllCCS[M+NH4]+281.232859911
AllCCS[M+Na]+281.232859911
AllCCS[M-H]-272.932859911
AllCCS[M+Na-2H]-279.032859911
AllCCS[M+HCOO]-285.832859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
PGP(a-13:0/i-17:0)[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCC(C)CC)OC(=O)CCCCCCCCCCCCCC(C)C4736.2Standard polar33892256
PGP(a-13:0/i-17:0)[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCC(C)CC)OC(=O)CCCCCCCCCCCCCC(C)C4420.7Standard non polar33892256
PGP(a-13:0/i-17:0)[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCC(C)CC)OC(=O)CCCCCCCCCCCCCC(C)C5161.9Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - PGP(a-13:0/i-17:0) GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-13Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PGP(a-13:0/i-17:0) GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PGP(a-13:0/i-17:0) GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PGP(a-13:0/i-17:0) GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PGP(a-13:0/i-17:0) GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PGP(a-13:0/i-17:0) GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PGP(a-13:0/i-17:0) GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(a-13:0/i-17:0) 10V, Positive-QTOFsplash10-0a4i-1890082700-9803ded29042c118a7d52019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(a-13:0/i-17:0) 20V, Positive-QTOFsplash10-0pba-5981043400-a0f1da6e30b078a6049b2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(a-13:0/i-17:0) 40V, Positive-QTOFsplash10-0a4i-9761130100-96832f6c09f961ffb21b2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(a-13:0/i-17:0) 10V, Negative-QTOFsplash10-01xt-4490031300-bd467b35290377894d432019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(a-13:0/i-17:0) 20V, Negative-QTOFsplash10-004j-9140000000-88b763dcf30de803e3c92019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(a-13:0/i-17:0) 40V, Negative-QTOFsplash10-004i-9010000000-95776e9a2cb728312b912019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(a-13:0/i-17:0) 10V, Positive-QTOFsplash10-004i-3100154900-dbe6a502cd1b004646172021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(a-13:0/i-17:0) 20V, Positive-QTOFsplash10-0ab9-3400159000-6f570a258837b7299b7f2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(a-13:0/i-17:0) 40V, Positive-QTOFsplash10-0zfr-8686910000-2d16312f98cd69bf9c682021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(a-13:0/i-17:0) 10V, Negative-QTOFsplash10-00di-0010000900-7b179ae20ab1cfe6ca4e2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(a-13:0/i-17:0) 20V, Negative-QTOFsplash10-0fk9-3090031700-50d3b905155b19abaae72021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(a-13:0/i-17:0) 40V, Negative-QTOFsplash10-0ftk-4092422100-7a82f68d652bef75db722021-09-25Wishart 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131823178
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.