Np mrd loader

Showing NP-Card for PGP(16:0/20:4(5Z,8Z,11Z,14Z)) (NP0339275)

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Record Information
Version2.0
Created at2024-09-11 20:49:18 UTC
Updated at2024-09-11 20:49:18 UTC
NP-MRD IDNP0339275
Secondary Accession NumbersNone
Natural Product Identification
Common NamePGP(16:0/20:4(5Z,8Z,11Z,14Z))
DescriptionPGP(16:0/20:4(5Z,8Z,11Z,14Z)), also known as PGP(16:0/20:4) Or PGP(36:4), 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. 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. Phosphatidylglycerol is formed from phosphatidic acid by a sequence of enzymatic reactions that proceeds via the intermediate, cytidine diphosphate diacylglycerol (CDP-diacylglycerol). It is a glycerophospholipid in which a phosphoglycerol moiety occupies a glycerol substitution site followed by another phosphate moiety. PGP(16:0/20:4(5Z,8Z,11Z,14Z)) is an extremely weak basic (essentially neutral) compound (based on its pKa). Within humans, PGP(16:0/20:4(5Z,8Z,11Z,14Z)) participates in a number of enzymatic reactions. In particular, PGP(16:0/20:4(5Z,8Z,11Z,14Z)) and cytidine monophosphate can be biosynthesized from CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)) and glycerol 3-phosphate through the action of the enzyme CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial. In addition, PGP(16:0/20:4(5Z,8Z,11Z,14Z)) can be converted into PG(16:0/20:4(5Z,8Z,11Z,14Z)); which is mediated by the enzyme phosphatidylglycerophosphatase and protein-tyrosine phosphatase 1. 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. In humans, PGP(16:0/20:4(5Z,8Z,11Z,14Z)) is involved in cardiolipin biosynthesis.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0339275 (PGP(16:0/20:4(5Z,8Z,11Z,14Z)))


  Mrv1652303252017072D          

 59 58  0  0  1  0            999 V2000
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   20.6827   -4.3586    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.2349   -3.1893    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   22.8451   -2.5141    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.6247   -3.8644    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 NP0339275 (PGP(16:0/20:4(5Z,8Z,11Z,14Z)))

Download
3D SDF for NP0339275 (PGP(16:0/20:4(5Z,8Z,11Z,14Z)))

  Mrv1652303252017072D          

 59 58  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0339275

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C42H76O13P2/c1-3-5-7-9-11-13-15-17-18-19-20-22-24-26-28-30-32-34-42(45)55-40(38-54-57(49,50)53-36-39(43)35-52-56(46,47)48)37-51-41(44)33-31-29-27-25-23-21-16-14-12-10-8-6-4-2/h11,13,17-18,20,22,26,28,39-40,43H,3-10,12,14-16,19,21,23-25,27,29-38H2,1-2H3,(H,49,50)(H2,46,47,48)/b13-11-,18-17-,22-20-,28-26-/t39-,40+/m0/s1

> <INCHI_KEY>
DPHOYXSTTLCECY-NYWCEQGFSA-N

> <FORMULA>
C42H76O13P2

> <MOLECULAR_WEIGHT>
850.9926

> <EXACT_MASS>
850.476115542

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
133

> <JCHEM_AVERAGE_POLARIZABILITY>
94.95212542079959

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2S)-3-({[(2R)-3-(hexadecanoyloxy)-2-[(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoyloxy]propoxy](hydroxy)phosphoryl}oxy)-2-hydroxypropoxy]phosphonic acid

> <ALOGPS_LOGP>
7.34

> <JCHEM_LOGP>
11.144073521333333

> <ALOGPS_LOGS>
-6.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.040206143698788

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.3548792964147385

> <JCHEM_PKA_STRONGEST_BASIC>
-3.410499386302644

> <JCHEM_POLAR_SURFACE_AREA>
195.35

> <JCHEM_REFRACTIVITY>
229.05220000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
42

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.81e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-3-{[(2R)-3-(hexadecanoyloxy)-2-[(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoyloxy]propoxy(hydroxy)phosphoryl]oxy}-2-hydroxypropoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0339275 (PGP(16:0/20:4(5Z,8Z,11Z,14Z)))
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PDB for NP0339275 (PGP(16:0/20:4(5Z,8Z,11Z,14Z)))
HEADER    PROTEIN                                 25-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-MAR-20         0                                  
HETATM    1  C   UNK     0      40.851  -5.953   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      39.591  -6.681   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      38.331  -5.953   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      42.112  -6.681   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      37.071  -6.681   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      38.608  -8.136   0.000  0.00  0.00           O+0
HETATM    7  P   UNK     0      43.372  -5.953   0.000  0.00  0.00           P+0
HETATM    8  O   UNK     0      42.644  -4.693   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      44.099  -7.214   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      44.632  -5.226   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      45.892  -5.953   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      47.152  -5.226   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      48.413  -5.953   0.000  0.00  0.00           C+0
HETATM   14  H   UNK     0      40.688  -8.192   0.000  0.00  0.00           H+0
HETATM   15  O   UNK     0      49.603  -5.157   0.000  0.00  0.00           O+0
HETATM   16  H   UNK     0      48.228  -3.947   0.000  0.00  0.00           H+0
HETATM   17  O   UNK     0      46.010  -3.947   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      15.732  -6.681   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      17.065  -5.911   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      18.399  -6.681   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      19.733  -5.911   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      21.066  -6.681   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      22.400  -5.911   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      23.734  -6.681   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      25.067  -5.911   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      26.401  -6.681   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      27.735  -5.911   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      29.068  -6.681   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      30.402  -5.911   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      31.736  -6.681   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      33.069  -5.911   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      34.403  -6.681   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      35.737  -5.911   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      35.737  -4.371   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      11.934  -8.130   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      13.267  -8.900   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      14.601  -8.131   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      15.935  -8.901   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      17.269  -8.131   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      18.602  -8.902   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      19.936  -8.899   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      21.269  -8.129   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      22.603  -8.899   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      23.937  -8.903   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      25.271  -8.133   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      26.604  -8.903   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      27.938  -8.898   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      29.272  -8.128   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      30.605  -8.898   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      31.939  -8.904   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      33.273  -8.135   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      34.607  -8.905   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      35.940  -8.135   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      37.274  -8.906   0.000  0.00  0.00           C+0
HETATM   55  O   UNK     0      37.274 -10.446   0.000  0.00  0.00           O+0
HETATM   56  P   UNK     0      50.985  -5.838   0.000  0.00  0.00           P+0
HETATM   57  O   UNK     0      52.366  -6.518   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      51.665  -4.456   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0      50.304  -7.219   0.000  0.00  0.00           O+0
CONECT    1    2    4                                                       
CONECT    2    1    3    6   14                                             
CONECT    3    2    5                                                       
CONECT    4    1    7                                                       
CONECT    5    3   33                                                       
CONECT    6    2   54                                                       
CONECT    7    4    8    9   10                                             
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    7   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   16   17                                             
CONECT   13   12   15                                                       
CONECT   14    2                                                            
CONECT   15   13   56                                                       
CONECT   16   12                                                            
CONECT   17   12                                                            
CONECT   18   19                                                            
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32    5   34                                                  
CONECT   34   33                                                            
CONECT   35   36                                                            
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44   46                                                       
CONECT   46   45   47                                                       
CONECT   47   46   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    6   55                                                  
CONECT   55   54                                                            
CONECT   56   57   58   59   15                                             
CONECT   57   56                                                            
CONECT   58   56                                                            
CONECT   59   56                                                            
MASTER        0    0    0    0    0    0    0    0   59    0  116    0
END

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3D PDB for NP0339275 (PGP(16:0/20:4(5Z,8Z,11Z,14Z)))
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SMILES for NP0339275 (PGP(16:0/20:4(5Z,8Z,11Z,14Z)))
[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCCCCCCCC)OC(=O)CCC\C=C/C\C=C/C\C=C/C\C=C/CCCCC
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INCHI for NP0339275 (PGP(16:0/20:4(5Z,8Z,11Z,14Z)))
InChI=1S/C42H76O13P2/c1-3-5-7-9-11-13-15-17-18-19-20-22-24-26-28-30-32-34-42(45)55-40(38-54-57(49,50)53-36-39(43)35-52-56(46,47)48)37-51-41(44)33-31-29-27-25-23-21-16-14-12-10-8-6-4-2/h11,13,17-18,20,22,26,28,39-40,43H,3-10,12,14-16,19,21,23-25,27,29-38H2,1-2H3,(H,49,50)(H2,46,47,48)/b13-11-,18-17-,22-20-,28-26-/t39-,40+/m0/s1
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Synonyms
ValueSource
1-Palmitoyl-2-arachidonoyl-sn-glycero-3-phospho-(1'-sn-glycerol-3'-phosphate)HMDB
3-sn-Phosphatidyl-1'-sn-glycerol 3'-phosphoric acidHMDB
PGP(16:0/20:4)HMDB
PGP(16:0/20:4n6)HMDB
PGP(16:0/20:4W6)HMDB
PGP(36:4)HMDB
1-Hexadecanoyl-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phospho-(1'-sn-glycerol-3'-phosphate)HMDB
PGP(16:0/20:4(5Z,8Z,11Z,14Z))Lipid Annotator
Chemical FormulaC42H76O13P2
Average Mass850.9926 Da
Monoisotopic Mass850.47612 Da
IUPAC Name[(2S)-3-({[(2R)-3-(hexadecanoyloxy)-2-[(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoyloxy]propoxy](hydroxy)phosphoryl}oxy)-2-hydroxypropoxy]phosphonic acid
Traditional Name(2S)-3-{[(2R)-3-(hexadecanoyloxy)-2-[(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoyloxy]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)CCC\C=C/C\C=C/C\C=C/C\C=C/CCCCC
InChI Identifier
InChI=1S/C42H76O13P2/c1-3-5-7-9-11-13-15-17-18-19-20-22-24-26-28-30-32-34-42(45)55-40(38-54-57(49,50)53-36-39(43)35-52-56(46,47)48)37-51-41(44)33-31-29-27-25-23-21-16-14-12-10-8-6-4-2/h11,13,17-18,20,22,26,28,39-40,43H,3-10,12,14-16,19,21,23-25,27,29-38H2,1-2H3,(H,49,50)(H2,46,47,48)/b13-11-,18-17-,22-20-,28-26-/t39-,40+/m0/s1
InChI KeyDPHOYXSTTLCECY-NYWCEQGFSA-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
logP7.34ALOGPS
logP11.14ChemAxon
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 Count42ChemAxon
Refractivity229.05 m³·mol⁻¹ChemAxon
Polarizability94.95 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0013482  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB029482  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53481802  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References