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Showing NP-Card for Phosphatidylglycerol (NP0046497)

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Record Information
Version2.0
Created at2022-03-17 20:04:13 UTC
Updated at2022-03-17 20:04:13 UTC
NP-MRD IDNP0046497
Secondary Accession NumbersNone
Natural Product Identification
Common NamePhosphatidylglycerol
DescriptionPhosphatidylglycerol belongs to the class of organic compounds known as glycerophosphates. Glycerophosphates are compounds containing a glycerol linked to a phosphate group. Phosphatidylglycerol is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0046497 (Phosphatidylglycerol)


  Mrv1533007131513362D          

 16 13  0  0  0  0            999 V2000
    1.3200   -1.0003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0825   -0.2858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9075   -0.2858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1450   -1.0003    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3200    0.4287    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9800    0.4287    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1550    1.2537    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1550   -0.3963    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3300    0.4287    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1550    0.4287    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.5021    0.1375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9311    0.1375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2166   -0.2750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.6503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -3.0628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.6503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  3  1  0  0  0  0
  9  2  1  0  0  0  0
 10  6  1  0  0  0  0
 10  7  1  0  0  0  0
 10  8  2  0  0  0  0
 10  9  1  0  0  0  0
 13 11  1  0  0  0  0
 13 12  1  0  0  0  0
 15 14  1  0  0  0  0
 16 15  1  0  0  0  0
M  END
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3D MOL for NP0046497 (Phosphatidylglycerol)

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3D SDF for NP0046497 (Phosphatidylglycerol)

  Mrv1533007131513362D          

 16 13  0  0  0  0            999 V2000
    1.3200   -1.0003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0825   -0.2858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9075   -0.2858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1450   -1.0003    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3200    0.4287    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9800    0.4287    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1550    1.2537    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1550   -0.3963    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3300    0.4287    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1550    0.4287    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.5021    0.1375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9311    0.1375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2166   -0.2750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.6503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -3.0628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.6503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  3  1  0  0  0  0
  9  2  1  0  0  0  0
 10  6  1  0  0  0  0
 10  7  1  0  0  0  0
 10  8  2  0  0  0  0
 10  9  1  0  0  0  0
 13 11  1  0  0  0  0
 13 12  1  0  0  0  0
 15 14  1  0  0  0  0
 16 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0046497

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC.CCO.OCC(O)COP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C3H9O6P.C3H8.C2H6O/c4-1-3(5)2-9-10(6,7)8;1-3-2;1-2-3/h3-5H,1-2H2,(H2,6,7,8);3H2,1-2H3;3H,2H2,1H3

> <INCHI_KEY>
GDQGIGPGALPYCN-UHFFFAOYSA-N

> <FORMULA>
C8H23O7P

> <MOLECULAR_WEIGHT>
262.239

> <EXACT_MASS>
262.118140079

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
13.450137666564107

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2,3-dihydroxypropoxy)phosphonic acid; ethanol; propane

> <ALOGPS_LOGP>
-1.84

> <JCHEM_LOGP>
-1.9625800539999998

> <ALOGPS_LOGS>
-0.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.533552281214722

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.5077547010974532

> <JCHEM_PKA_STRONGEST_BASIC>
-2.968964717967575

> <JCHEM_POLAR_SURFACE_AREA>
107.22000000000001

> <JCHEM_REFRACTIVITY>
31.389

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.06e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ethyl alcohol propane α-glycerophosphate

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0046497 (Phosphatidylglycerol)
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PDB for NP0046497 (Phosphatidylglycerol)
HEADER    PROTEIN                                 13-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-JUL-15         0                                  
HETATM    1  C   UNK     0       2.464  -1.867   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.154  -0.533   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.694  -0.533   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.004  -1.867   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       2.464   0.800   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      -3.696   0.800   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -2.156   2.340   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -2.156  -0.740   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -0.616   0.800   0.000  0.00  0.00           O+0
HETATM   10  P   UNK     0      -2.156   0.800   0.000  0.00  0.00           P+0
HETATM   11  C   UNK     0       8.404   0.257   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      11.071   0.257   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.738  -0.513   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.334  -4.947   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000  -5.717   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.334  -4.947   0.000  0.00  0.00           O+0
CONECT    1    3    4                                                       
CONECT    2    3    9                                                       
CONECT    3    1    2    5                                                  
CONECT    4    1                                                            
CONECT    5    3                                                            
CONECT    6   10                                                            
CONECT    7   10                                                            
CONECT    8   10                                                            
CONECT    9    2   10                                                       
CONECT   10    6    7    8    9                                             
CONECT   11   13                                                            
CONECT   12   13                                                            
CONECT   13   11   12                                                       
CONECT   14   15                                                            
CONECT   15   14   16                                                       
CONECT   16   15                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   26    0
END

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3D PDB for NP0046497 (Phosphatidylglycerol)
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SMILES for NP0046497 (Phosphatidylglycerol)
CCC.CCO.OCC(O)COP(O)(O)=O
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INCHI for NP0046497 (Phosphatidylglycerol)
InChI=1S/C3H9O6P.C3H8.C2H6O/c4-1-3(5)2-9-10(6,7)8;1-3-2;1-2-3/h3-5H,1-2H2,(H2,6,7,8);3H2,1-2H3;3H,2H2,1H3
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View in JSmol
SynonymsNot Available
Chemical FormulaC8H23O7P
Average Mass262.2390 Da
Monoisotopic Mass262.11814 Da
IUPAC Name(2,3-dihydroxypropoxy)phosphonic acid; ethanol; propane
Traditional Nameethyl alcohol propane α-glycerophosphate
CAS Registry NumberNot Available
SMILES
CCC.CCO.OCC(O)COP(O)(O)=O
InChI Identifier
InChI=1S/C3H9O6P.C3H8.C2H6O/c4-1-3(5)2-9-10(6,7)8;1-3-2;1-2-3/h3-5H,1-2H2,(H2,6,7,8);3H2,1-2H3;3H,2H2,1H3
InChI KeyGDQGIGPGALPYCN-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Capsicum annuumFooDB
Carica papaya L.FooDB
Cucumis sativus L.FooDB
Daucus carotaFooDB
Daucus carota ssp. sativusFooDB
Ficus caricaFooDB
Glycine maxFooDB
Malus pumilaFooDB
Portulaca oleraceaFooDB
Solanum lycopersicum var. lycopersicumFooDB
Spinacia oleraceaFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as glycerophosphates. Glycerophosphates are compounds containing a glycerol linked to a phosphate group.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassGlycerophospholipids  
Sub ClassGlycerophosphates  
Direct ParentGlycerophosphates  
Alternative Parents
Substituents
  • Sn-glycerol-3-phosphate
    • 

  • Monoalkyl phosphate
    • 

  • Alkyl phosphate
    • 

  • Phosphoric acid ester
    • 

  • Organic phosphoric acid derivative
    • 

  • Secondary alcohol
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • Aliphatic acyclic compound
Molecular FrameworkNot Available
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
logP-1.8ALOGPS
logP-2ChemAxon
logS-0.75ALOGPS
pKa (Strongest Acidic)1.51ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area107.22 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity31.39 m³·mol⁻¹ChemAxon
Polarizability13.45 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB004686  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPhosphatidylglycerol  
METLIN IDNot Available
PubChem Compound45109789  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available