Showing NP-Card for PGD2 ethanolamide (NP0340004)

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Record Information
Version2.0
Created at2024-09-12 00:52:28 UTC
Updated at2024-09-12 00:52:28 UTC
NP-MRD IDNP0340004
Secondary Accession NumbersNone
Natural Product Identification
Common NamePGD2 ethanolamide
DescriptionPGD2 ethanolamide 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. Based on a literature review very few articles have been published on PGD2 ethanolamide.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0340004 (PGD2 ethanolamide)

      
  Mrv2104 05272303242D          

 28 28  0  0  0  0            999 V2000
   -2.9241    0.3669    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5915   -0.1180    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3366   -0.9026    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5116   -0.9026    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3760    0.1368    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0266   -1.5700    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9241    1.1919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2096    1.6044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3846    1.6044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6701    1.1919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0443    1.6044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7587    1.1919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4732    1.6044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4732    2.4293    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1877    1.1919    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9021    1.6044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6166    1.1919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3311    1.6044    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2567   -0.1180    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5422    0.2944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8276   -0.1180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1131    0.2944    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1131    1.1194    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6011   -0.1180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3156    0.2944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0301   -0.1180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7445    0.2944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4590   -0.1180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  1  6  0  0  0
  4  6  2  0  0  0  0
  1  7  1  6  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 19 20  1  1  0  0  0
 20 21  2  0  0  0  0
  1 19  1  0  0  0  0
  4 19  1  0  0  0  0
 21 22  1  0  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 22 23  1  1  0  0  0
M  END
Download

3D MOL for NP0340004 (PGD2 ethanolamide)

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3D SDF for NP0340004 (PGD2 ethanolamide)
      
  Mrv2104 05272303242D          

 28 28  0  0  0  0            999 V2000
   -2.9241    0.3669    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5915   -0.1180    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3366   -0.9026    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5116   -0.9026    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3760    0.1368    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0266   -1.5700    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9241    1.1919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2096    1.6044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3846    1.6044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6701    1.1919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0443    1.6044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7587    1.1919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4732    1.6044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4732    2.4293    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1877    1.1919    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9021    1.6044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6166    1.1919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3311    1.6044    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2567   -0.1180    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5422    0.2944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8276   -0.1180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1131    0.2944    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1131    1.1194    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6011   -0.1180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3156    0.2944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0301   -0.1180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7445    0.2944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4590   -0.1180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  1  6  0  0  0
  4  6  2  0  0  0  0
  1  7  1  6  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 19 20  1  1  0  0  0
 20 21  2  0  0  0  0
  1 19  1  0  0  0  0
  4 19  1  0  0  0  0
 21 22  1  0  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 22 23  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0340004

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1/C22H37NO5/c1-2-3-6-9-17(25)12-13-19-18(20(26)16-21(19)27)10-7-4-5-8-11-22(28)23-14-15-24/h4,7,12-13,17-20,24-26H,2-3,5-6,8-11,14-16H2,1H3,(H,23,28)/b7-4-,13-12+/t17-,18+,19+,20-/s2

> <INCHI_KEY>
KEYDJKSQFDUAGF-VVEBQAJGNA-N

> <FORMULA>
C22H37NO5

> <MOLECULAR_WEIGHT>
395.54

> <EXACT_MASS>
395.267173295

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
46.39156399087395

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <JCHEM_LOGP>
1.9519015769999997

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.370815396065804

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.586322214796525

> <JCHEM_PKA_STRONGEST_BASIC>
-1.1327989773442306

> <JCHEM_POLAR_SURFACE_AREA>
106.86

> <JCHEM_REFRACTIVITY>
112.44630000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
14

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
PGD2-EA

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0340004 (PGD2 ethanolamide)
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PDB for NP0340004 (PGD2 ethanolamide)
HEADER    PROTEIN                                 27-MAY-23   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-23         0                                  
HETATM    1  C   UNK     0      -5.458   0.685   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.704  -0.220   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -6.228  -1.685   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.688  -1.685   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -8.169   0.255   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      -3.783  -2.931   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -5.458   2.225   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.125   2.995   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.585   2.995   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.251   2.225   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.083   2.995   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.416   2.225   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.750   2.995   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.750   4.535   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0       4.084   2.225   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       5.417   2.995   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.751   2.225   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       8.085   2.995   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -4.213  -0.220   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -2.879   0.550   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.545  -0.220   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -0.211   0.550   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -0.211   2.090   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       1.122  -0.220   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.456   0.550   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.790  -0.220   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       5.123   0.550   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       6.457  -0.220   0.000  0.00  0.00           C+0
CONECT    1    2    7   19                                                  
CONECT    2    1    3    5                                                  
CONECT    3    2    4                                                       
CONECT    4    3    6   19                                                  
CONECT    5    2                                                            
CONECT    6    4                                                            
CONECT    7    1    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                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17                                                            
CONECT   19   20    1    4                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   24   23                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27                                                            
MASTER        0    0    0    0    0    0    0    0   28    0   56    0
END

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3D PDB for NP0340004 (PGD2 ethanolamide)
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SMILES for NP0340004 (PGD2 ethanolamide)
CCCCC[C@H](O)\C=C\[C@@H]1[C@@H](C\C=C/CCCC(=O)NCCO)[C@@H](O)CC1=O
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INCHI for NP0340004 (PGD2 ethanolamide)
InChI=1/C22H37NO5/c1-2-3-6-9-17(25)12-13-19-18(20(26)16-21(19)27)10-7-4-5-8-11-22(28)23-14-15-24/h4,7,12-13,17-20,24-26H,2-3,5-6,8-11,14-16H2,1H3,(H,23,28)/b7-4-,13-12+/t17-,18+,19+,20-/s2
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View in JSmol
SynonymsNot Available
Chemical FormulaC22H37NO5
Average Mass395.5400 Da
Monoisotopic Mass395.26717 Da
IUPAC Name(5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]-N-(2-hydroxyethyl)hept-5-enamide
Traditional NamePGD2-EA
CAS Registry NumberNot Available
SMILES
CCCCC[C@H](O)\C=C\[C@@H]1[C@@H](C\C=C/CCCC(=O)NCCO)[C@@H](O)CC1=O
InChI Identifier
InChI=1/C22H37NO5/c1-2-3-6-9-17(25)12-13-19-18(20(26)16-21(19)27)10-7-4-5-8-11-22(28)23-14-15-24/h4,7,12-13,17-20,24-26H,2-3,5-6,8-11,14-16H2,1H3,(H,23,28)/b7-4-,13-12+/t17-,18+,19+,20-/s2
InChI KeyKEYDJKSQFDUAGF-VVEBQAJGNA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
DescriptionThis compound 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.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassFatty Acyls  
Sub ClassEicosanoids  
Direct ParentProstaglandins and related compounds  
Alternative Parents
Substituents
  • Prostaglandin skeleton
    • 

  • N-acylethanolamine
    • 

  • Cyclopentanol
    • 

  • Fatty amide
    • 

  • N-acyl-amine
    • 

  • Cyclic alcohol
    • 

  • Carboxamide group
    • 

  • Ketone
    • 

  • Cyclic ketone
    • 

  • Secondary alcohol
    • 

  • Secondary carboxylic acid amide
    • 

  • Carboxylic acid derivative
    • 

  • Alkanolamine
    • 

  • Organonitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Organic nitrogen compound
    • 

  • Organooxygen compound
    • 

  • Primary alcohol
    • 

  • Carbonyl group
    • 

  • Alcohol
    • 

  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External Descriptors
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
logP1.95ChemAxon
pKa (Strongest Acidic)14.59ChemAxon
pKa (Strongest Basic)-1.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area106.86 ŲChemAxon
Rotatable Bond Count14ChemAxon
Refractivity112.45 m³·mol⁻¹ChemAxon
Polarizability46.39 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References