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Showing metabocard for PGP(16:0/18:1(11Z)) (HMDB0013475)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2010-05-13 16:08:39 UTC
Update Date2022-11-30 19:04:11 UTC
HMDB IDHMDB0013475
Secondary Accession Numbers
  • HMDB13475
Metabolite Identification
Common NamePGP(16:0/18:1(11Z))
DescriptionPGP(16:0/18:1(11Z)) is a phosphatidylglycerolphosphate or glycerophospholipid (PGP or GP). It is a glycerophospholipid in which a phosphoglycerol moiety occupies a glycerol substitution site followed by another phosphate moiety. 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. PGP(16:0/18:1(11Z)), in particular, consists of one chain of palmitic acid at the C-1 position and one chain of vaccenic acid at the C-2 position. The palmitic acid moiety is derived from fish oils, milk fats, vegetable oils and animal fats, while the vaccenic acid moiety is derived from butter fat and animal fat. 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 at 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 diphosphatidylglycerol (cardiolipin). Phosphatidylglycerol is formed from phosphatidic acid by a sequence of enzymatic reactions that proceeds via the intermediate, cytidine diphosphate diacylglycerol (CDP-diacylglycerol). Bioynthesis proceeds by condensation of phosphatidic acid and cytidine triphosphate with elimination of pyrophosphate via the action of phosphatidate cytidyltransferase (or CDP-synthase). CDP-diacylglycerol then reacts with glycerol-3-phosphate via phosphatidylglycerophosphate synthase to form 3-sn-phosphatidyl-1'-sn-glycerol 3'-phosphoric acid, with the release of cytidine monophosphate (CMP). Finally, phosphatidylglycerol is formed by the action of specific phosphatases. 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. PGPs have a net charge of -1 at physiological pH and are found in high concentration in mitochondrial membranes and as components of pulmonary surfactant. PGP also serves as a precursor for the synthesis of cardiolipin. PGP is synthesized from CDP-diacylglycerol and glycerol-3-phosphate.
Structure
Data?1582753121
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0013475 (PGP(16:0/18:1(11Z)))

m282
  Mrv1652303302020122D          

 57 56  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    0.3608    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0919    0.7696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8021    0.3608    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
   -2.7924   -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    0.3608    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
    2.9275   -0.0665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0493    0.6481    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -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
    3.6378    0.3434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4300    0.5557    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.4300    1.3758    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2223    0.3434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0199   -0.1546    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D MOL for HMDB0013475 (PGP(16:0/18:1(11Z)))

HMDB0013475
     RDKit          3D
PGP(16:0/18:1(11Z))
133132  0  0  0  0  0  0  0  0999 V2000
    2.5280    0.0443   -3.1540 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3573    0.3887   -1.9773 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6748    1.1057   -0.8367 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0114    2.3569   -1.3159 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4878    3.3203   -0.3860 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4941    3.1848    0.6652 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7328    2.2774    1.7660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1348    1.4040    2.2410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4733    1.1042    1.8483 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8601   -0.3839    1.6391 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6610   -1.0663    2.9365 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0089   -2.4451    3.2202 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3967   -2.9239    3.1701 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1360   -2.9762    1.8947 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5341   -3.9100    0.8994 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2049   -3.9423   -0.4209 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4768   -4.9705   -1.3361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0343   -4.6158   -1.3295 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3254   -5.3544   -0.5499 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4077   -3.6235   -2.0309 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0189   -3.4505   -1.8565 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2546   -2.1102   -1.1770 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1996   -0.9987   -1.8172 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4456   -0.5803   -2.1240 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4056   -1.2886   -1.7394 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7390    0.6724   -2.9129 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1638    0.6231   -3.3000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2477    0.8722   -2.3336 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.7576    3.2445    1.1956 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.3979    3.8761    5.1501 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1027    4.0107    5.1271 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6368    5.0823    6.0301 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7963   -3.6680   -3.0967 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1286   -3.5467   -2.7744 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1397   -3.7382   -4.1203 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.0843   -5.1319   -4.6935 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5142   -2.6895   -5.3258 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7021   -3.2513   -3.7904 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6484   -3.8916   -4.5486 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0262   -3.4198   -4.2083 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.0314   -4.0399   -4.9442 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1816   -1.9189   -4.4915 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4463   -1.5001   -4.0765 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7110    0.1233   -4.3451 P   0  0  0  0  0  5  0  0  0  0  0  0
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    7.6465    0.8250   -5.4403 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.2933    0.3061   -4.9652 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7181    0.7781   -3.3846 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0570   -0.9516   -3.1494 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2051   -0.0116   -4.0878 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7154   -0.5868   -1.5224 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3070    0.9101   -2.2691 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9403    0.3593   -0.4156 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4489    1.3220   -0.0853 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1784    2.1057   -2.0534 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7788    2.8261   -2.0324 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3949    3.9331    0.0553 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0536    4.1825   -1.0695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5005    2.9793    0.1505 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3185    4.2514    1.0761 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7430    2.3411    2.2347 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2755    0.8135    3.1112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7786    1.6700    0.9260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1764    1.4673    2.6325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9777   -0.2957    1.4602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4448   -0.7988    0.7530 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0607   -0.4140    3.7759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5123   -1.0015    3.1098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2952   -3.1040    2.6394 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6532   -2.6560    4.2936 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9983   -2.2614    3.8667 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5175   -3.9416    3.6644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4486   -1.9986    1.5231 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1429   -3.4731    2.1585 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6310   -4.9523    1.3326 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4495   -3.7706    0.7383 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2964   -3.0299   -0.9777 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2494   -4.3737   -0.3578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9040   -4.8123   -2.3374 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6833   -5.9836   -0.9903 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3307   -4.2155   -1.1305 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0189   -2.2765   -0.1207 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0013475 (PGP(16:0/18:1(11Z)))

m282
  Mrv1652303302020122D          

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M  END
> <DATABASE_ID>
HMDB0013475

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C40H78O13P2/c1-3-5-7-9-11-13-15-17-18-20-22-24-26-28-30-32-40(43)53-38(36-52-55(47,48)51-34-37(41)33-50-54(44,45)46)35-49-39(42)31-29-27-25-23-21-19-16-14-12-10-8-6-4-2/h13,15,37-38,41H,3-12,14,16-36H2,1-2H3,(H,47,48)(H2,44,45,46)/b15-13-/t37-,38+/m0/s1

> <INCHI_KEY>
BMNRKKFJIDDAOJ-GPJPVTGXSA-N

> <FORMULA>
C40H78O13P2

> <MOLECULAR_WEIGHT>
828.999

> <EXACT_MASS>
828.491766568

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
133

> <JCHEM_AVERAGE_POLARIZABILITY>
94.22864438238935

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
7.11

> <JCHEM_LOGP>
11.340701161333332

> <ALOGPS_LOGS>
-6.07

> <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>
195.35

> <JCHEM_REFRACTIVITY>
216.50040000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
43

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.08e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-3-{[(2R)-3-(hexadecanoyloxy)-2-[(11Z)-octadec-11-enoyloxy]propoxy(hydroxy)phosphoryl]oxy}-2-hydroxypropoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0013475 (PGP(16:0/18:1(11Z)))

HMDB0013475
     RDKit          3D
PGP(16:0/18:1(11Z))
133132  0  0  0  0  0  0  0  0999 V2000
    2.5280    0.0443   -3.1540 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3573    0.3887   -1.9773 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6748    1.1057   -0.8367 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0114    2.3569   -1.3159 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4878    3.3203   -0.3860 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4941    3.1848    0.6652 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for HMDB0013475 (PGP(16:0/18:1(11Z)))

HEADER    PROTEIN                                 30-MAR-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: m282                                              
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-MAR-20         0                                  
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HETATM   48  C   UNK     0     -17.265  -1.436   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0     -18.598  -0.665   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0     -19.931  -1.436   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0     -21.471  -1.436   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0     -22.804  -0.665   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0     -24.137  -1.436   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0     -25.470  -0.665   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0     -26.803  -1.436   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0     -28.136  -0.665   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0     -29.469  -1.436   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   39                                                       
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                                                            
CONECT   39    6   40   41                                                  
CONECT   40   39                                                            
CONECT   41   39   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44   46                                                       
CONECT   46   45   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47   49                                                       
CONECT   49   48   50                                                       
CONECT   50   49   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55                                                       
CONECT   55   54   56                                                       
CONECT   56   55   57                                                       
CONECT   57   56                                                            
MASTER        0    0    0    0    0    0    0    0   57    0  112    0
END
Download

3D PDB for HMDB0013475 (PGP(16:0/18:1(11Z)))

COMPND    HMDB0013475
HETATM    1  C1  UNL     1       2.528   0.044  -3.154  1.00  0.00           C  
HETATM    2  C2  UNL     1       3.357   0.389  -1.977  1.00  0.00           C  
HETATM    3  C3  UNL     1       2.675   1.106  -0.837  1.00  0.00           C  
HETATM    4  C4  UNL     1       2.011   2.357  -1.316  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.488   3.320  -0.386  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.494   3.185   0.665  1.00  0.00           C  
HETATM    7  C7  UNL     1       0.733   2.277   1.766  1.00  0.00           C  
HETATM    8  C8  UNL     1      -0.135   1.404   2.241  1.00  0.00           C  
HETATM    9  C9  UNL     1      -1.473   1.104   1.848  1.00  0.00           C  
HETATM   10  C10 UNL     1      -1.860  -0.384   1.639  1.00  0.00           C  
HETATM   11  C11 UNL     1      -1.661  -1.066   2.937  1.00  0.00           C  
HETATM   12  C12 UNL     1      -2.009  -2.445   3.220  1.00  0.00           C  
HETATM   13  C13 UNL     1      -3.397  -2.924   3.170  1.00  0.00           C  
HETATM   14  C14 UNL     1      -4.136  -2.976   1.895  1.00  0.00           C  
HETATM   15  C15 UNL     1      -3.534  -3.910   0.899  1.00  0.00           C  
HETATM   16  C16 UNL     1      -4.205  -3.942  -0.421  1.00  0.00           C  
HETATM   17  C17 UNL     1      -3.477  -4.971  -1.336  1.00  0.00           C  
HETATM   18  C18 UNL     1      -2.034  -4.616  -1.329  1.00  0.00           C  
HETATM   19  O1  UNL     1      -1.325  -5.354  -0.550  1.00  0.00           O  
HETATM   20  O2  UNL     1      -1.408  -3.624  -2.031  1.00  0.00           O  
HETATM   21  C19 UNL     1      -0.019  -3.450  -1.857  1.00  0.00           C  
HETATM   22  C20 UNL     1       0.255  -2.110  -1.177  1.00  0.00           C  
HETATM   23  O3  UNL     1      -0.200  -0.999  -1.817  1.00  0.00           O  
HETATM   24  C21 UNL     1      -1.446  -0.580  -2.124  1.00  0.00           C  
HETATM   25  O4  UNL     1      -2.406  -1.289  -1.739  1.00  0.00           O  
HETATM   26  C22 UNL     1      -1.739   0.672  -2.913  1.00  0.00           C  
HETATM   27  C23 UNL     1      -3.164   0.623  -3.300  1.00  0.00           C  
HETATM   28  C24 UNL     1      -4.248   0.872  -2.334  1.00  0.00           C  
HETATM   29  C25 UNL     1      -4.373   2.345  -1.949  1.00  0.00           C  
HETATM   30  C26 UNL     1      -5.538   2.661  -1.104  1.00  0.00           C  
HETATM   31  C27 UNL     1      -5.650   2.339   0.318  1.00  0.00           C  
HETATM   32  C28 UNL     1      -4.758   3.245   1.196  1.00  0.00           C  
HETATM   33  C29 UNL     1      -5.070   2.910   2.643  1.00  0.00           C  
HETATM   34  C30 UNL     1      -4.476   3.833   3.638  1.00  0.00           C  
HETATM   35  C31 UNL     1      -3.002   3.964   3.705  1.00  0.00           C  
HETATM   36  C32 UNL     1      -2.594   5.037   4.727  1.00  0.00           C  
HETATM   37  C33 UNL     1      -1.096   5.128   4.739  1.00  0.00           C  
HETATM   38  C34 UNL     1      -0.398   3.876   5.150  1.00  0.00           C  
HETATM   39  C35 UNL     1       1.103   4.011   5.127  1.00  0.00           C  
HETATM   40  C36 UNL     1       1.637   5.082   6.030  1.00  0.00           C  
HETATM   41  C37 UNL     1       0.796  -3.668  -3.097  1.00  0.00           C  
HETATM   42  O5  UNL     1       2.129  -3.547  -2.774  1.00  0.00           O  
HETATM   43  P1  UNL     1       3.140  -3.738  -4.120  1.00  0.00           P  
HETATM   44  O6  UNL     1       3.084  -5.132  -4.694  1.00  0.00           O  
HETATM   45  O7  UNL     1       2.514  -2.690  -5.326  1.00  0.00           O  
HETATM   46  O8  UNL     1       4.702  -3.251  -3.790  1.00  0.00           O  
HETATM   47  C38 UNL     1       5.648  -3.892  -4.549  1.00  0.00           C  
HETATM   48  C39 UNL     1       7.026  -3.420  -4.208  1.00  0.00           C  
HETATM   49  O9  UNL     1       8.031  -4.040  -4.944  1.00  0.00           O  
HETATM   50  C40 UNL     1       7.182  -1.919  -4.491  1.00  0.00           C  
HETATM   51  O10 UNL     1       8.446  -1.500  -4.077  1.00  0.00           O  
HETATM   52  P2  UNL     1       8.711   0.123  -4.345  1.00  0.00           P  
HETATM   53  O11 UNL     1       8.575   0.895  -3.038  1.00  0.00           O  
HETATM   54  O12 UNL     1       7.647   0.825  -5.440  1.00  0.00           O  
HETATM   55  O13 UNL     1      10.293   0.306  -4.965  1.00  0.00           O  
HETATM   56  H1  UNL     1       1.718   0.778  -3.385  1.00  0.00           H  
HETATM   57  H2  UNL     1       2.057  -0.952  -3.149  1.00  0.00           H  
HETATM   58  H3  UNL     1       3.205  -0.012  -4.088  1.00  0.00           H  
HETATM   59  H4  UNL     1       3.715  -0.587  -1.522  1.00  0.00           H  
HETATM   60  H5  UNL     1       4.307   0.910  -2.269  1.00  0.00           H  
HETATM   61  H6  UNL     1       1.940   0.359  -0.416  1.00  0.00           H  
HETATM   62  H7  UNL     1       3.449   1.322  -0.085  1.00  0.00           H  
HETATM   63  H8  UNL     1       1.178   2.106  -2.053  1.00  0.00           H  
HETATM   64  H9  UNL     1       2.779   2.826  -2.032  1.00  0.00           H  
HETATM   65  H10 UNL     1       2.395   3.933   0.055  1.00  0.00           H  
HETATM   66  H11 UNL     1       1.054   4.183  -1.069  1.00  0.00           H  
HETATM   67  H12 UNL     1      -0.501   2.979   0.151  1.00  0.00           H  
HETATM   68  H13 UNL     1       0.318   4.251   1.076  1.00  0.00           H  
HETATM   69  H14 UNL     1       1.743   2.341   2.235  1.00  0.00           H  
HETATM   70  H15 UNL     1       0.276   0.814   3.111  1.00  0.00           H  
HETATM   71  H16 UNL     1      -1.779   1.670   0.926  1.00  0.00           H  
HETATM   72  H17 UNL     1      -2.176   1.467   2.633  1.00  0.00           H  
HETATM   73  H18 UNL     1      -2.978  -0.296   1.460  1.00  0.00           H  
HETATM   74  H19 UNL     1      -1.445  -0.799   0.753  1.00  0.00           H  
HETATM   75  H20 UNL     1      -2.061  -0.414   3.776  1.00  0.00           H  
HETATM   76  H21 UNL     1      -0.512  -1.002   3.110  1.00  0.00           H  
HETATM   77  H22 UNL     1      -1.295  -3.104   2.639  1.00  0.00           H  
HETATM   78  H23 UNL     1      -1.653  -2.656   4.294  1.00  0.00           H  
HETATM   79  H24 UNL     1      -3.998  -2.261   3.867  1.00  0.00           H  
HETATM   80  H25 UNL     1      -3.518  -3.942   3.664  1.00  0.00           H  
HETATM   81  H26 UNL     1      -4.449  -1.999   1.523  1.00  0.00           H  
HETATM   82  H27 UNL     1      -5.143  -3.473   2.159  1.00  0.00           H  
HETATM   83  H28 UNL     1      -3.631  -4.952   1.333  1.00  0.00           H  
HETATM   84  H29 UNL     1      -2.450  -3.771   0.738  1.00  0.00           H  
HETATM   85  H30 UNL     1      -4.296  -3.030  -0.978  1.00  0.00           H  
HETATM   86  H31 UNL     1      -5.249  -4.374  -0.358  1.00  0.00           H  
HETATM   87  H32 UNL     1      -3.904  -4.812  -2.337  1.00  0.00           H  
HETATM   88  H33 UNL     1      -3.683  -5.984  -0.990  1.00  0.00           H  
HETATM   89  H34 UNL     1       0.331  -4.215  -1.131  1.00  0.00           H  
HETATM   90  H35 UNL     1      -0.019  -2.276  -0.121  1.00  0.00           H  
HETATM   91  H36 UNL     1       1.393  -2.017  -1.124  1.00  0.00           H  
HETATM   92  H37 UNL     1      -1.564   1.572  -2.288  1.00  0.00           H  
HETATM   93  H38 UNL     1      -1.083   0.762  -3.789  1.00  0.00           H  
HETATM   94  H39 UNL     1      -3.413  -0.415  -3.750  1.00  0.00           H  
HETATM   95  H40 UNL     1      -3.353   1.273  -4.217  1.00  0.00           H  
HETATM   96  H41 UNL     1      -5.208   0.605  -2.821  1.00  0.00           H  
HETATM   97  H42 UNL     1      -4.189   0.286  -1.407  1.00  0.00           H  
HETATM   98  H43 UNL     1      -4.254   3.014  -2.820  1.00  0.00           H  
HETATM   99  H44 UNL     1      -3.448   2.540  -1.325  1.00  0.00           H  
HETATM  100  H45 UNL     1      -6.513   2.380  -1.651  1.00  0.00           H  
HETATM  101  H46 UNL     1      -5.629   3.819  -1.160  1.00  0.00           H  
HETATM  102  H47 UNL     1      -6.689   2.548   0.659  1.00  0.00           H  
HETATM  103  H48 UNL     1      -5.467   1.274   0.581  1.00  0.00           H  
HETATM  104  H49 UNL     1      -3.698   3.096   0.995  1.00  0.00           H  
HETATM  105  H50 UNL     1      -5.105   4.284   1.034  1.00  0.00           H  
HETATM  106  H51 UNL     1      -4.581   1.902   2.805  1.00  0.00           H  
HETATM  107  H52 UNL     1      -6.151   2.779   2.731  1.00  0.00           H  
HETATM  108  H53 UNL     1      -4.936   4.868   3.565  1.00  0.00           H  
HETATM  109  H54 UNL     1      -4.807   3.446   4.658  1.00  0.00           H  
HETATM  110  H55 UNL     1      -2.631   3.015   4.208  1.00  0.00           H  
HETATM  111  H56 UNL     1      -2.499   4.127   2.756  1.00  0.00           H  
HETATM  112  H57 UNL     1      -2.936   4.692   5.721  1.00  0.00           H  
HETATM  113  H58 UNL     1      -3.053   6.009   4.469  1.00  0.00           H  
HETATM  114  H59 UNL     1      -0.774   5.923   5.471  1.00  0.00           H  
HETATM  115  H60 UNL     1      -0.686   5.474   3.768  1.00  0.00           H  
HETATM  116  H61 UNL     1      -0.653   2.972   4.570  1.00  0.00           H  
HETATM  117  H62 UNL     1      -0.656   3.615   6.215  1.00  0.00           H  
HETATM  118  H63 UNL     1       1.475   4.231   4.104  1.00  0.00           H  
HETATM  119  H64 UNL     1       1.526   3.045   5.423  1.00  0.00           H  
HETATM  120  H65 UNL     1       1.033   5.213   6.936  1.00  0.00           H  
HETATM  121  H66 UNL     1       1.786   6.040   5.495  1.00  0.00           H  
HETATM  122  H67 UNL     1       2.658   4.750   6.364  1.00  0.00           H  
HETATM  123  H68 UNL     1       0.632  -4.718  -3.410  1.00  0.00           H  
HETATM  124  H69 UNL     1       0.490  -3.024  -3.945  1.00  0.00           H  
HETATM  125  H70 UNL     1       2.918  -2.978  -6.172  1.00  0.00           H  
HETATM  126  H71 UNL     1       5.592  -4.990  -4.468  1.00  0.00           H  
HETATM  127  H72 UNL     1       5.447  -3.613  -5.620  1.00  0.00           H  
HETATM  128  H73 UNL     1       7.257  -3.619  -3.134  1.00  0.00           H  
HETATM  129  H74 UNL     1       8.893  -3.849  -4.470  1.00  0.00           H  
HETATM  130  H75 UNL     1       7.038  -1.763  -5.574  1.00  0.00           H  
HETATM  131  H76 UNL     1       6.439  -1.400  -3.857  1.00  0.00           H  
HETATM  132  H77 UNL     1       6.841   0.297  -5.602  1.00  0.00           H  
HETATM  133  H78 UNL     1      10.244  -0.062  -5.900  1.00  0.00           H  
CONECT    1    2   56   57   58
CONECT    2    3   59   60
CONECT    3    4   61   62
CONECT    4    5   63   64
CONECT    5    6   65   66
CONECT    6    7   67   68
CONECT    7    8    8   69
CONECT    8    9   70
CONECT    9   10   71   72
CONECT   10   11   73   74
CONECT   11   12   75   76
CONECT   12   13   77   78
CONECT   13   14   79   80
CONECT   14   15   81   82
CONECT   15   16   83   84
CONECT   16   17   85   86
CONECT   17   18   87   88
CONECT   18   19   19   20
CONECT   20   21
CONECT   21   22   41   89
CONECT   22   23   90   91
CONECT   23   24
CONECT   24   25   25   26
CONECT   26   27   92   93
CONECT   27   28   94   95
CONECT   28   29   96   97
CONECT   29   30   98   99
CONECT   30   31  100  101
CONECT   31   32  102  103
CONECT   32   33  104  105
CONECT   33   34  106  107
CONECT   34   35  108  109
CONECT   35   36  110  111
CONECT   36   37  112  113
CONECT   37   38  114  115
CONECT   38   39  116  117
CONECT   39   40  118  119
CONECT   40  120  121  122
CONECT   41   42  123  124
CONECT   42   43
CONECT   43   44   44   45   46
CONECT   45  125
CONECT   46   47
CONECT   47   48  126  127
CONECT   48   49   50  128
CONECT   49  129
CONECT   50   51  130  131
CONECT   51   52
CONECT   52   53   53   54   55
CONECT   54  132
CONECT   55  133
END
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SMILES for HMDB0013475 (PGP(16:0/18:1(11Z)))

[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCCCCCCCC)OC(=O)CCCCCCCCC\C=C/CCCCCC
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INCHI for HMDB0013475 (PGP(16:0/18:1(11Z)))

InChI=1S/C40H78O13P2/c1-3-5-7-9-11-13-15-17-18-20-22-24-26-28-30-32-40(43)53-38(36-52-55(47,48)51-34-37(41)33-50-54(44,45)46)35-49-39(42)31-29-27-25-23-21-19-16-14-12-10-8-6-4-2/h13,15,37-38,41H,3-12,14,16-36H2,1-2H3,(H,47,48)(H2,44,45,46)/b15-13-/t37-,38+/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-Palmitoyl-2-vaccenoyl-sn-glycero-3-phospho-(1'-sn-glycerol-3'-phosphate)HMDB
3-sn-Phosphatidyl-1'-sn-glycerol 3'-phosphoric acidHMDB
PGP(16:0/18:1)HMDB
PGP(16:0/18:1n7)HMDB
PGP(16:0/18:1W7)HMDB
PGP(34:1)HMDB
1-Hexadecanoyl-2-(11Z-octadecenoyl)-sn-glycero-3-phospho-(1'-sn-glycerol-3'-phosphate)HMDB
PGP(16:0/18:1(11Z))Lipid Annotator
Chemical FormulaC40H78O13P2
Average Molecular Weight828.999
Monoisotopic Molecular Weight828.491766568
IUPAC Name[(2S)-3-({[(2R)-3-(hexadecanoyloxy)-2-[(11Z)-octadec-11-enoyloxy]propoxy](hydroxy)phosphoryl}oxy)-2-hydroxypropoxy]phosphonic acid
Traditional Name(2S)-3-{[(2R)-3-(hexadecanoyloxy)-2-[(11Z)-octadec-11-enoyloxy]propoxy(hydroxy)phosphoryl]oxy}-2-hydroxypropoxyphosphonic acid
CAS Registry NumberNot Available
SMILES
[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCCCCCCCC)OC(=O)CCCCCCCCC\C=C/CCCCCC
InChI Identifier
InChI=1S/C40H78O13P2/c1-3-5-7-9-11-13-15-17-18-20-22-24-26-28-30-32-40(43)53-38(36-52-55(47,48)51-34-37(41)33-50-54(44,45)46)35-49-39(42)31-29-27-25-23-21-19-16-14-12-10-8-6-4-2/h13,15,37-38,41H,3-12,14,16-36H2,1-2H3,(H,47,48)(H2,44,45,46)/b15-13-/t37-,38+/m0/s1
InChI KeyBMNRKKFJIDDAOJ-GPJPVTGXSA-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 Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
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
Water Solubility0.00071 g/LALOGPS
logP7.11ALOGPS
logP11.34ChemAxon
logS-6.1ALOGPS
pKa (Strongest Acidic)1.35ChemAxon
pKa (Strongest Basic)-3.4ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area195.35 ŲChemAxon
Rotatable Bond Count43ChemAxon
Refractivity216.5 m³·mol⁻¹ChemAxon
Polarizability94.23 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]+301.61131661259
DarkChem[M-H]-287.30531661259
DeepCCS[M+H]+279.02930932474
DeepCCS[M-H]-277.13330932474
DeepCCS[M-2H]-310.37330932474
DeepCCS[M+Na]+284.83230932474
AllCCS[M+H]+294.532859911
AllCCS[M+H-H2O]+294.632859911
AllCCS[M+NH4]+294.432859911
AllCCS[M+Na]+294.432859911
AllCCS[M-H]-288.432859911
AllCCS[M+Na-2H]-294.532859911
AllCCS[M+HCOO]-301.232859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
PGP(16:0/18:1(11Z))[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCCCCCCCC)OC(=O)CCCCCCCCC\C=C/CCCCCC5069.3Standard polar33892256
PGP(16:0/18:1(11Z))[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCCCCCCCC)OC(=O)CCCCCCCCC\C=C/CCCCCC4781.0Standard non polar33892256
PGP(16:0/18:1(11Z))[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCCCCCCCC)OC(=O)CCCCCCCCC\C=C/CCCCCC5748.5Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(16:0/18:1(11Z)) 10V, Positive-QTOFsplash10-07gs-0290050140-148fec6eb4e24653d8cb2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(16:0/18:1(11Z)) 20V, Positive-QTOFsplash10-0ap1-1391021010-efd28ea9fb049e8d76652015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(16:0/18:1(11Z)) 40V, Positive-QTOFsplash10-0cdr-3693120100-4fdd0f0ad588f3b3e14f2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(16:0/18:1(11Z)) 10V, Negative-QTOFsplash10-057r-2090020010-b11d66a904bbae3ec6b72015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(16:0/18:1(11Z)) 20V, Negative-QTOFsplash10-004i-9060000000-40e0bb1c56654c9797702015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(16:0/18:1(11Z)) 40V, Negative-QTOFsplash10-004i-9010000000-aff4a02985fce2b7bf172015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(16:0/18:1(11Z)) 10V, Positive-QTOFsplash10-004i-2100060690-32bb83a9b1be9f764a2d2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(16:0/18:1(11Z)) 20V, Positive-QTOFsplash10-0560-5700069600-27f97883562b1ae9b8032021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(16:0/18:1(11Z)) 40V, Positive-QTOFsplash10-0zfs-5473910000-f55edef154f852be162f2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(16:0/18:1(11Z)) 10V, Negative-QTOFsplash10-004i-0010000090-7f4e07b96246f1c72f892021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(16:0/18:1(11Z)) 20V, Negative-QTOFsplash10-0fb9-2090040040-18bedf9abdee3a8df0cb2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(16:0/18:1(11Z)) 40V, Negative-QTOFsplash10-0fba-3092051000-8b66f3689b7055103bda2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen LocationsNot Available
Tissue Locations
  • All Tissues
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 IDFDB029475
KNApSAcK IDNot Available
Chemspider ID7826086
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound9547136
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.