NP-MRD: Showing NP-Card for 15-Deoxy-delta-12,14-prostaglandin J2 (NP0334121)

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Record Information

Version

2.0

Created at

2024-09-09 22:16:54 UTC

Updated at

2024-09-09 22:16:54 UTC

NP-MRD ID

NP0334121

Secondary Accession Numbers

None

Natural Product Identification

Common Name

15-Deoxy-delta-12,14-prostaglandin J2

Description

15-Deoxy-PGJ2 (15d-PGJ2) is a metabolite of the PGJ2 prostanoid family that influences multiple signaling pathways by covalently binding with key signaling molecules. Among them, 15d-PGJ2 has displayed highest potency as an inducer of gene expression. Prostanoids are a subclass of the lipid mediator group known as eicosanoids. They derive from C-20 polyunsaturated fatty acids, mainly dihomo-gamma-linoleic (20:3N-6), arachidonic (20:4N-6), and eicosapentaenoic (20:5N-3) acids, through the action of cyclooxygenases-1 and -2 (COX-1 and COX-2). The reaction product of COX is the unstable endoperoxide prostaglandin H (PGH) that is further transformed into the individual prostanoids by a series of specific prostanoid synthases. Prostanoids are local-acting mediators formed and inactivated within the same or neighbouring cells prior to their release into circulation as inactive metabolites (15-keto- and 13,14-dihydroketo metabolites). Non-enzymatic peroxidation of arachidonic acid and other fatty acids in vivo can result in prostaglandin-like substances isomeric to the COX-derived prostaglandins that are termed isoprostanes. Prostanoids take part in many physiological and pathophysiological processes in practically every organ, tissue and cell, including the vascular, renal, gastrointestinal and reproductive systems. Their activities are mediated through prostanoid-specific receptors and intracellular signalling pathways, whilst their biosynthesis and action are blocked by nonsteroidal antiinflammatory drugs (NSAID). Isoprostanes are considered to be reliable markers of oxidant stress status and have been linked to inflammation, ischaemia-reperfusion, diabetes, cardiovascular disease, reproductive disorders and diabetes. (PMID: 16986207 , 16857669 ) Prostaglandins are eicosanoids. The eicosanoids consist of the prostaglandins (PGs), thromboxanes (TXs), leukotrienes (LTs) and lipoxins (LXs). The PGs and TXs are collectively identified as prostanoids. Prostaglandins were originally shown to be synthesized in the prostate gland, thromboxanes from platelets (thrombocytes) and leukotrienes from leukocytes, hence the derivation of their names. All mammalian cells except erythrocytes synthesize eicosanoids. These molecules are extremely potent, able to cause profound physiological effects at very dilute concentrations. All eicosanoids function locally at the site of synthesis, through receptor-mediated G-protein linked signaling pathways. [HMDB]

Structure

MOL SDF PDB SMILES InChI

PTG
  Mrv0541 02241214052D          

 24 24  0  0  0  0            999 V2000
   -3.9683   -3.3131    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1837   -3.0582    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0122   -2.2512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2275   -1.9963    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0560   -1.1893    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2714   -0.9344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0999   -0.1274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3153    0.1275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1437    0.9345    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6958    1.5476    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5162    1.4614    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2833    2.2621    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5237    2.0905    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6100    1.2701    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3244    0.8576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0389    1.2701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7534    0.8576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4678    1.2701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1823    0.8576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8968    1.2701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6112    0.8576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3257    1.2701    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6112    0.0326    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5794    0.6869    0.0000 H   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
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  9 14  1  0  0  0  0
 10 11  2  0  0  0  0
 12 13  2  0  0  0  0
 12 10  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  6  0  0  0
 14 24  1  1  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0334121

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]1(C\C=C\CCCC(O)=O)C=CC(=O)\C1=C/C=C/CCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C20H28O3/c1-2-3-4-5-6-10-13-18-17(15-16-19(18)21)12-9-7-8-11-14-20(22)23/h6-7,9-10,13,15-17H,2-5,8,11-12,14H2,1H3,(H,22,23)/b9-7+,10-6+,18-13-/t17-/m0/s1

> <INCHI_KEY>
VHRUMKCAEVRUBK-XOVNXQNQSA-N

> <FORMULA>
C20H28O3

> <MOLECULAR_WEIGHT>
316.4345

> <EXACT_MASS>
316.203844762

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
37.87152288302247

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(5E)-7-[(1S,5Z)-5-[(2E)-oct-2-en-1-ylidene]-4-oxocyclopent-2-en-1-yl]hept-5-enoic acid

> <ALOGPS_LOGP>
5.39

> <JCHEM_LOGP>
5.457149731333333

> <ALOGPS_LOGS>
-5.02

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
17.786482545828832

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.658500253952263

> <JCHEM_PKA_STRONGEST_BASIC>
-5.001707861342161

> <JCHEM_POLAR_SURFACE_AREA>
54.370000000000005

> <JCHEM_REFRACTIVITY>
98.4503

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.00e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(5E)-7-[(1S,5Z)-5-[(2E)-oct-2-en-1-ylidene]-4-oxocyclopent-2-en-1-yl]hept-5-enoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: PTG                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -7.407  -6.184   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.943  -5.709   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.623  -4.202   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.158  -3.726   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.838  -2.220   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.373  -1.744   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.053  -0.238   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.589   0.238   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.268   1.744   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.299   2.889   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -2.830   2.728   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -0.529   4.223   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.978   3.902   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.139   2.371   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.472   1.601   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.806   2.371   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.140   1.601   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.473   2.371   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.807   1.601   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.141   2.371   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.474   1.601   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      11.808   2.371   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      10.474   0.061   0.000  0.00  0.00           O+0
HETATM   24  H   UNK     0       1.082   1.282   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   14                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   13   10                                                       
CONECT   13   12   14                                                       
CONECT   14    9   13   15   24                                             
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   14                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   48    0
END

View in JSmol

Synonyms

Value	Source
(5E,14E)-11-Oxoprosta-5,9,12,14-tetraen-1-Oate	Generator

Chemical Formula

C₂₀H₂₈O₃

Average Mass

316.4345 Da

Monoisotopic Mass

316.20384 Da

IUPAC Name

(5E)-7-[(1S,5Z)-5-[(2E)-oct-2-en-1-ylidene]-4-oxocyclopent-2-en-1-yl]hept-5-enoic acid

Traditional Name

(5E)-7-[(1S,5Z)-5-[(2E)-oct-2-en-1-ylidene]-4-oxocyclopent-2-en-1-yl]hept-5-enoic acid

CAS Registry Number

Not Available

SMILES

[H][C@]1(C\C=C\CCCC(O)=O)C=CC(=O)\C1=C/C=C/CCCCC

InChI Identifier

InChI=1S/C20H28O3/c1-2-3-4-5-6-10-13-18-17(15-16-19(18)21)12-9-7-8-11-14-20(22)23/h6-7,9-10,13,15-17H,2-5,8,11-12,14H2,1H3,(H,22,23)/b9-7+,10-6+,18-13-/t17-/m0/s1

InChI Key

VHRUMKCAEVRUBK-XOVNXQNQSA-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
Long-chain fatty acid
Fatty acid
Unsaturated fatty acid
Cyclic ketone
Ketone
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
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	5.39	ALOGPS
logP	5.46	ChemAxon
logS	-5	ALOGPS
pKa (Strongest Acidic)	4.66	ChemAxon
pKa (Strongest Basic)	-5	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	54.37 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	98.45 m³·mol⁻¹	ChemAxon
Polarizability	37.87 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

DB08435

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

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

23654841

PDB ID

PTG

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for 15-Deoxy-delta-12,14-prostaglandin J2 (NP0334121)

MOL for NP0334121 (15-Deoxy-delta-12,14-prostaglandin J2)

3D MOL for NP0334121 (15-Deoxy-delta-12,14-prostaglandin J2)

3D SDF for NP0334121 (15-Deoxy-delta-12,14-prostaglandin J2)

3D-SDF for NP0334121 (15-Deoxy-delta-12,14-prostaglandin J2)

PDB for NP0334121 (15-Deoxy-delta-12,14-prostaglandin J2)

3D PDB for NP0334121 (15-Deoxy-delta-12,14-prostaglandin J2)

SMILES for NP0334121 (15-Deoxy-delta-12,14-prostaglandin J2)

INCHI for NP0334121 (15-Deoxy-delta-12,14-prostaglandin J2)

Structure for NP0334121 (15-Deoxy-delta-12,14-prostaglandin J2)

3D Structure for NP0334121 (15-Deoxy-delta-12,14-prostaglandin J2)