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Showing NP-Card for PGP(16:1(9Z)/18:1(9Z)) (NP0339284)

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Record Information
Version2.0
Created at2024-09-11 20:52:16 UTC
Updated at2024-09-11 20:52:16 UTC
NP-MRD IDNP0339284
Secondary Accession NumbersNone
Natural Product Identification
Common NamePGP(16:1(9Z)/18:1(9Z))
DescriptionPGP(16:1(9Z)/18:1(9Z)), also known as PGP(16:1/18:1) Or PGP(34:2), 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. 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. PGP(16:1(9Z)/18:1(9Z)) is an extremely weak basic (essentially neutral) compound (based on its pKa). 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. 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). PGP(16:1(9Z)/18:1(9Z)), in particular, consists of one chain of palmitoleic acid at the C-1 position and one chain of oleic acid at the C-2 position. PGP also serves as a precursor for the synthesis of cardiolipin. Bioynthesis proceeds by condensation of phosphatidic acid and cytidine triphosphate with elimination of pyrophosphate via the action of phosphatidate cytidyltransferase (or CDP-synthase). It is well established that the concentration of Phosphatidylglycerolphosphate increases during fetal development. It was first documented in 1995 (PMID: 7834746). Phosphatidylglycerolphosphate may be present in animal tissues merely as a precursor for diphosphatidylglycerol (cardiolipin) (PMID: 11413487) (PMID: 16902246) (PMID: 17374880) (PMID: 20044567).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0339284 (PGP(16:1(9Z)/18:1(9Z)))

PGP(16:1(9Z)/18:1(9Z))
  Mrv1652303252017082D          

 57 56  0  0  1  0            999 V2000
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   -2.3818    0.3608    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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   -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
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    1.8811    0.9262    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D MOL for NP0339284 (PGP(16:1(9Z)/18:1(9Z)))

Download
3D SDF for NP0339284 (PGP(16:1(9Z)/18:1(9Z)))
PGP(16:1(9Z)/18:1(9Z))
  Mrv1652303252017082D          

 57 56  0  0  1  0            999 V2000
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   -2.3818    0.3608    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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    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
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    4.4300    1.3758    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0339284

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C40H76O13P2/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/h14,16-18,37-38,41H,3-13,15,19-36H2,1-2H3,(H,47,48)(H2,44,45,46)/b16-14-,18-17-/t37-,38+/m0/s1

> <INCHI_KEY>
FPBKBTVRSMJESP-GDNUZSQHSA-N

> <FORMULA>
C40H76O13P2

> <MOLECULAR_WEIGHT>
826.983

> <EXACT_MASS>
826.476116503

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
131

> <JCHEM_AVERAGE_POLARIZABILITY>
92.69307906353495

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
7.06

> <JCHEM_LOGP>
10.978779504666665

> <ALOGPS_LOGS>
-6.00

> <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>
217.61700000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
42

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.19e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-3-{[(2R)-3-[(9Z)-hexadec-9-enoyloxy]-2-[(9Z)-octadec-9-enoyloxy]propoxy(hydroxy)phosphoryl]oxy}-2-hydroxypropoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0339284 (PGP(16:1(9Z)/18:1(9Z)))
Download
PDB for NP0339284 (PGP(16:1(9Z)/18:1(9Z)))
HEADER    PROTEIN                                 25-MAR-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: PGP(16:1(9Z)/18:1(9Z))                            
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-MAR-20         0                                  
HETATM    1  H   UNK     0       5.198   1.798   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0      -4.446   0.673   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.772   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      -5.212  -0.652   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -3.120   1.439   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.794   0.673   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.487   0.642   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       8.269   1.037   0.000  0.00  0.00           P+0
HETATM   19  O   UNK     0       8.269   2.568   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       9.748   0.641   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       7.504  -0.289   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -8.423   1.437   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     -20.627   1.437   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0     -21.960   0.665   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0     -23.293   1.437   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0     -24.626   0.665   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0     -25.959   1.437   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0     -27.292   0.665   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0     -28.625   1.437   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -6.601  -1.436   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0      -6.601  -2.876   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0      -7.934  -0.665   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      -9.267  -1.436   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0     -10.600  -0.665   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0     -11.933  -1.436   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0     -13.266  -0.665   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0     -14.599  -1.436   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0     -15.932  -0.665   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0     -17.265  -1.436   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0     -18.805  -1.436   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0     -20.138  -0.665   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 NP0339284 (PGP(16:1(9Z)/18:1(9Z)))
Download
SMILES for NP0339284 (PGP(16:1(9Z)/18:1(9Z)))
[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCC\C=C/CCCCCC)OC(=O)CCCCCCC\C=C/CCCCCCCC
Download
INCHI for NP0339284 (PGP(16:1(9Z)/18:1(9Z)))
InChI=1S/C40H76O13P2/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/h14,16-18,37-38,41H,3-13,15,19-36H2,1-2H3,(H,47,48)(H2,44,45,46)/b16-14-,18-17-/t37-,38+/m0/s1
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View in JSmol
Synonyms
ValueSource
1-Palmitoleoyl-2-oleoyl-sn-glycero-3-phospho-(1'-sn-glycerol-3'-phosphate)HMDB
3-sn-Phosphatidyl-1'-sn-glycerol 3'-phosphoric acidHMDB
PGP(16:1/18:1)HMDB
PGP(16:1n7/18:1n9)HMDB
PGP(16:1W7/18:1W9)HMDB
PGP(34:2)HMDB
1-(9Z-Hexadecenoyl)-2-(9Z-octadecenoyl)-sn-glycero-3-phospho-(1'-sn-glycerol-3'-phosphate)HMDB
PGP(16:1(9Z)/18:1(9Z))Lipid Annotator
Chemical FormulaC40H76O13P2
Average Mass826.9830 Da
Monoisotopic Mass826.47612 Da
IUPAC Name[(2S)-3-({[(2R)-3-[(9Z)-hexadec-9-enoyloxy]-2-[(9Z)-octadec-9-enoyloxy]propoxy](hydroxy)phosphoryl}oxy)-2-hydroxypropoxy]phosphonic acid
Traditional Name(2S)-3-{[(2R)-3-[(9Z)-hexadec-9-enoyloxy]-2-[(9Z)-octadec-9-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)CCCCCCC\C=C/CCCCCC)OC(=O)CCCCCCC\C=C/CCCCCCCC
InChI Identifier
InChI=1S/C40H76O13P2/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/h14,16-18,37-38,41H,3-13,15,19-36H2,1-2H3,(H,47,48)(H2,44,45,46)/b16-14-,18-17-/t37-,38+/m0/s1
InChI KeyFPBKBTVRSMJESP-GDNUZSQHSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
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
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP7.06ALOGPS
logP10.98ChemAxon
logS-6ALOGPS
pKa (Strongest Acidic)1.35ChemAxon
pKa (Strongest Basic)-3.4ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area195.35 ŲChemAxon
Rotatable Bond Count42ChemAxon
Refractivity217.62 m³·mol⁻¹ChemAxon
Polarizability92.69 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0013491  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB029491  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53481811  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
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. doi: 10.1016/0092-8674(95)90409-3. [PubMed:7834746  ]