NP-MRD: Showing NP-Card for Prostaglandin D2-1-glyceryl ester (NP0339386)

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Record Information

Version

2.0

Created at

2024-09-11 21:34:29 UTC

Updated at

2024-09-11 21:34:29 UTC

NP-MRD ID

NP0339386

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Prostaglandin D2-1-glyceryl ester

Description

Prostaglandin D2-1-glyceryl ester, also known as PGD2-1-glyceryl ester, belongs to the class of organic compounds known as prostaglandins and related compounds. These are unsaturated carboxylic acids consisting of a 20 carbon skeleton that also contains a five member ring, and are based upon the fatty acid arachidonic acid. It was first documented in 2000 (PMID: 11413487). Prostaglandin D2-1-glyceryl ester is an extremely weak basic (essentially neutral) compound (based on its pKa) (PMID: 16902246) (PMID: 17374880) (PMID: 20044567).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02271200292D          

 30 30  0  0  1  0            999 V2000
    7.5129   -9.1629    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1808   -8.6786    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.7672   -9.9478    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8478   -9.1641    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.5923   -9.9485    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.1816   -7.8536    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.6327   -8.9098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2453   -9.4623    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0302   -9.2080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2024   -8.4012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9872   -8.1469    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1594   -7.3401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9442   -7.0858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1164   -6.2790    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5568   -7.6384    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.9012   -6.0247    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0735   -5.2179    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8583   -4.9636    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0305   -4.1568    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.4608   -4.6653    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2818  -10.6148    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0767  -10.6163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7405  -11.3697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2249  -12.0375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.8888  -12.7909    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3731  -13.4588    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0370  -14.2122    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5213  -14.8800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1851  -15.6334    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0454  -11.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  2  6  1  6  0  0  0
  4  7  1  6  0  0  0
  8  7  1  0  0  0  0
  9  8  2  0  0  0  0
 10  9  1  0  0  0  0
 11 10  1  0  0  0  0
 12 11  1  0  0  0  0
 13 12  1  0  0  0  0
 14 13  1  0  0  0  0
 15 13  2  0  0  0  0
 16 14  1  0  0  0  0
 17 16  1  0  0  0  0
 18 17  1  0  0  0  0
 19 18  1  0  0  0  0
 20 17  1  0  0  0  0
 21  3  2  0  0  0  0
  5 22  1  1  0  0  0
 22 23  2  0  0  0  0
 24 23  1  0  0  0  0
 25 24  1  0  0  0  0
 26 25  1  0  0  0  0
 27 26  1  0  0  0  0
 28 27  1  0  0  0  0
 29 28  1  0  0  0  0
 24 30  1  6  0  0  0
M  END


  Mrv0541 02271200292D          

 30 30  0  0  1  0            999 V2000
    7.5129   -9.1629    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1808   -8.6786    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.7672   -9.9478    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8478   -9.1641    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.5923   -9.9485    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.1816   -7.8536    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.6327   -8.9098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2453   -9.4623    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0302   -9.2080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2024   -8.4012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9872   -8.1469    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1594   -7.3401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9442   -7.0858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1164   -6.2790    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5568   -7.6384    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.9012   -6.0247    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0735   -5.2179    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8583   -4.9636    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0305   -4.1568    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.4608   -4.6653    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2818  -10.6148    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0767  -10.6163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7405  -11.3697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2249  -12.0375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.8888  -12.7909    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3731  -13.4588    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0370  -14.2122    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5213  -14.8800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1851  -15.6334    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0454  -11.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  2  6  1  6  0  0  0
  4  7  1  6  0  0  0
  8  7  1  0  0  0  0
  9  8  2  0  0  0  0
 10  9  1  0  0  0  0
 11 10  1  0  0  0  0
 12 11  1  0  0  0  0
 13 12  1  0  0  0  0
 14 13  1  0  0  0  0
 15 13  2  0  0  0  0
 16 14  1  0  0  0  0
 17 16  1  0  0  0  0
 18 17  1  0  0  0  0
 19 18  1  0  0  0  0
 20 17  1  0  0  0  0
 21  3  2  0  0  0  0
  5 22  1  1  0  0  0
 22 23  2  0  0  0  0
 24 23  1  0  0  0  0
 25 24  1  0  0  0  0
 26 25  1  0  0  0  0
 27 26  1  0  0  0  0
 28 27  1  0  0  0  0
 29 28  1  0  0  0  0
 24 30  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0339386

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCC[C@@H](O)\C=C\[C@@H]1[C@@H](C\C=C/CCCC(=O)OCC(O)CO)[C@@H](O)CC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C23H38O7/c1-2-3-6-9-17(25)12-13-20-19(21(27)14-22(20)28)10-7-4-5-8-11-23(29)30-16-18(26)15-24/h4,7,12-13,17-21,24-27H,2-3,5-6,8-11,14-16H2,1H3/b7-4-,13-12+/t17-,18?,19-,20-,21+/m1/s1

> <INCHI_KEY>
AWSHXGOINMVSGP-CDCWMRKJSA-N

> <FORMULA>
C23H38O7

> <MOLECULAR_WEIGHT>
426.5436

> <EXACT_MASS>
426.26175357

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
48.71584973615388

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2,3-dihydroxypropyl (5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3R)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]hept-5-enoate

> <ALOGPS_LOGP>
2.31

> <JCHEM_LOGP>
2.050727238999999

> <ALOGPS_LOGS>
-3.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.11698057891612

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.463053368729145

> <JCHEM_PKA_STRONGEST_BASIC>
-1.5973959065529568

> <JCHEM_POLAR_SURFACE_AREA>
124.29

> <JCHEM_REFRACTIVITY>
116.459

> <JCHEM_ROTATABLE_BOND_COUNT>
16

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.46e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3-dihydroxypropyl (5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3R)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]hept-5-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 27-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-FEB-12         0                                  
HETATM    1  C   UNK     0      14.024 -17.104   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      15.271 -16.200   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      14.499 -18.569   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      16.516 -17.106   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      16.039 -18.571   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      15.272 -14.660   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      17.981 -16.632   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      19.125 -17.663   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      20.590 -17.188   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      20.911 -15.682   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      22.376 -15.208   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      22.698 -13.702   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      24.163 -13.227   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      24.484 -11.721   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      25.306 -14.258   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      25.949 -11.246   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      26.271  -9.740   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      27.735  -9.265   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      28.057  -7.759   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      25.127  -8.709   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      13.593 -19.814   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      16.943 -19.817   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      16.316 -21.223   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      17.220 -22.470   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      16.592 -23.876   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      17.496 -25.123   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      16.869 -26.529   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      17.773 -27.776   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      17.146 -29.182   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      18.751 -22.310   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4    6                                                  
CONECT    3    1    5   21                                                  
CONECT    4    2    5    7                                                  
CONECT    5    3    4   22                                                  
CONECT    6    2                                                            
CONECT    7    4    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13   16                                                       
CONECT   15   13                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18   20                                                  
CONECT   18   17   19                                                       
CONECT   19   18                                                            
CONECT   20   17                                                            
CONECT   21    3                                                            
CONECT   22    5   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   30                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28                                                            
CONECT   30   24                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   60    0
END

View in JSmol

Synonyms

Value	Source
PGD2-1-Glyceryl ester	HMDB
2,3-Dihydroxypropyl (5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3R)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]hept-5-enoic acid	Generator

Chemical Formula

C₂₃H₃₈O₇

Average Mass

426.5436 Da

Monoisotopic Mass

426.26175 Da

IUPAC Name

2,3-dihydroxypropyl (5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3R)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]hept-5-enoate

Traditional Name

2,3-dihydroxypropyl (5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3R)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]hept-5-enoate

CAS Registry Number

Not Available

SMILES

CCCCC[C@@H](O)\C=C\[C@@H]1[C@@H](C\C=C/CCCC(=O)OCC(O)CO)[C@@H](O)CC1=O

InChI Identifier

InChI=1S/C23H38O7/c1-2-3-6-9-17(25)12-13-20-19(21(27)14-22(20)28)10-7-4-5-8-11-23(29)30-16-18(26)15-24/h4,7,12-13,17-21,24-27H,2-3,5-6,8-11,14-16H2,1H3/b7-4-,13-12+/t17-,18?,19-,20-,21+/m1/s1

InChI Key

AWSHXGOINMVSGP-CDCWMRKJSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as prostaglandins and related compounds. These are unsaturated carboxylic acids consisting of a 20 carbon skeleton that also contains a five member ring, and are based upon the fatty acid arachidonic acid.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Eicosanoids

Direct Parent

Prostaglandins and related compounds

Alternative Parents

Substituents

Prostaglandin skeleton
Fatty alcohol
1-acyl-sn-glycerol
Monoradylglycerol
Monoacylglycerol
Glycerolipid
Fatty acid ester
Cyclopentanol
Cyclic alcohol
Carboxylic acid ester
Cyclic ketone
Secondary alcohol
Ketone
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Alcohol
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Carbonyl group
Primary alcohol
Organooxygen compound
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	2.31	ALOGPS
logP	2.05	ChemAxon
logS	-3.5	ALOGPS
pKa (Strongest Acidic)	13.46	ChemAxon
pKa (Strongest Basic)	-1.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	124.29 Å²	ChemAxon
Rotatable Bond Count	16	ChemAxon
Refractivity	116.46 m³·mol⁻¹	ChemAxon
Polarizability	48.72 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0013653

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB029623

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

53481917

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
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 ]
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 ]
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 ]

Showing NP-Card for Prostaglandin D2-1-glyceryl ester (NP0339386)

MOL for NP0339386 (Prostaglandin D2-1-glyceryl ester)

3D MOL for NP0339386 (Prostaglandin D2-1-glyceryl ester)

3D SDF for NP0339386 (Prostaglandin D2-1-glyceryl ester)

3D-SDF for NP0339386 (Prostaglandin D2-1-glyceryl ester)

PDB for NP0339386 (Prostaglandin D2-1-glyceryl ester)

3D PDB for NP0339386 (Prostaglandin D2-1-glyceryl ester)

SMILES for NP0339386 (Prostaglandin D2-1-glyceryl ester)

INCHI for NP0339386 (Prostaglandin D2-1-glyceryl ester)

Structure for NP0339386 (Prostaglandin D2-1-glyceryl ester)

3D Structure for NP0339386 (Prostaglandin D2-1-glyceryl ester)