NP-MRD: Showing NP-Card for 12-oxo-PDA (NP0045554)

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Record Information

Version

2.0

Created at

2022-03-17 19:31:45 UTC

Updated at

2022-03-17 19:31:45 UTC

NP-MRD ID

NP0045554

Secondary Accession Numbers

None

Natural Product Identification

Common Name

12-oxo-PDA

Description

12-Oxo-PDA, also known as 12-OPDA, 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. Thus, 12-oxo-pda is considered to be an octadecanoid lipid molecule. 12-oxo-PDA is found in Arabidopsis thaliana, Glycine max and Ipomoea tricolor. 12-Oxo-PDA is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241220592D          

 21 21  0  0  1  0            999 V2000
   -3.0676    2.6690    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2471    2.7552    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8346    3.4697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0277    3.2981    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9414    2.4777    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2269    2.0652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4875    2.4777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2020    2.0652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9165    2.4777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6309    2.0652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3454    2.4777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0599    2.0652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7744    2.4777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4888    2.0652    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7744    3.3027    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6951    2.1421    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8666    1.3351    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6512    1.0802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8228    0.2732    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2097   -0.2788    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4250   -0.0239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  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
  5 16  1  0  0  0  0
  2 16  1  0  0  0  0
 16 17  1  6  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0045554

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC\C=C/C[C@H]1[C@@H](CCCCCCCC(O)=O)C=CC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C18H28O3/c1-2-3-7-11-16-15(13-14-17(16)19)10-8-5-4-6-9-12-18(20)21/h3,7,13-16H,2,4-6,8-12H2,1H3,(H,20,21)/b7-3-/t15-,16-/m0/s1

> <INCHI_KEY>
PMTMAFAPLCGXGK-JMTMCXQRSA-N

> <FORMULA>
C18H28O3

> <MOLECULAR_WEIGHT>
292.4131

> <EXACT_MASS>
292.203844762

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
35.151487478730346

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
8-[(1S,5S)-4-oxo-5-[(2Z)-pent-2-en-1-yl]cyclopent-2-en-1-yl]octanoic acid

> <ALOGPS_LOGP>
5.09

> <JCHEM_LOGP>
5.079546357333333

> <ALOGPS_LOGS>
-4.96

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
18.017647713652938

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.784583565856928

> <JCHEM_PKA_STRONGEST_BASIC>
-4.934463579077429

> <JCHEM_POLAR_SURFACE_AREA>
54.370000000000005

> <JCHEM_REFRACTIVITY>
87.25580000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.22e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
12-oxo-phytodienoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0      -5.726   4.982   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -4.195   5.143   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.425   6.477   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.918   6.156   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.757   4.625   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.424   3.855   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.910   4.625   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.244   3.855   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.577   4.625   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.911   3.855   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.245   4.625   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.578   3.855   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.912   4.625   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      10.246   3.855   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       8.912   6.165   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -3.164   3.999   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -3.484   2.492   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -4.949   2.016   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -5.269   0.510   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -4.125  -0.520   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -2.660  -0.045   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   16                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   16                                                  
CONECT    6    5    7                                                       
CONECT    7    6    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                                                            
CONECT   16    5    2   17                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

View in JSmol

Synonyms

Value	Source
(15Z)-12-Oxophyto-10,15-dienoate	ChEBI
12-OPDA	ChEBI
12-oxo-10,15(Z)-Phytodienoic acid	ChEBI
12-Oxophytodienoic acid	ChEBI
4-oxo-5-(2-Pentenyl)-2-cyclopentene-1-octanoic acid	ChEBI
8-(2-(cis-2'-Pentenyl)-3-oxo-cis-4-cyclopentenyl)octanoic acid	ChEBI
9(S),13(S)-12-oxo-PDA	ChEBI
OPDA	ChEBI
(15Z)-12-Oxophyto-10,15-dienoic acid	Kegg
12-oxo-10,15(Z)-Phytodienoate	Generator
12-Oxophytodienoate	Generator
4-oxo-5-(2-Pentenyl)-2-cyclopentene-1-octanoate	Generator
8-(2-(cis-2'-Pentenyl)-3-oxo-cis-4-cyclopentenyl)octanoate	Generator
OPDA acid	MeSH
12-oxo-cis-10, cis-15-Phytodienoic acid	MeSH

Chemical Formula

C₁₈H₂₈O₃

Average Mass

292.4131 Da

Monoisotopic Mass

292.20384 Da

IUPAC Name

8-[(1S,5S)-4-oxo-5-[(2Z)-pent-2-en-1-yl]cyclopent-2-en-1-yl]octanoic acid

Traditional Name

12-oxo-phytodienoic acid

CAS Registry Number

85551-10-6

SMILES

CC\C=C/C[C@H]1[C@@H](CCCCCCCC(O)=O)C=CC1=O

InChI Identifier

InChI=1S/C18H28O3/c1-2-3-7-11-16-15(13-14-17(16)19)10-8-5-4-6-9-12-18(20)21/h3,7,13-16H,2,4-6,8-12H2,1H3,(H,20,21)/b7-3-/t15-,16-/m0/s1

InChI Key

PMTMAFAPLCGXGK-JMTMCXQRSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Arabidopsis thaliana	Plant	KNApSAcK
Glycine max	Plant	KNApSAcK
Ipomoea tricolor	LOTUS Database	35616633
Zea mays L.	FooDB	KNAPSACK

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
Medium-chain 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

oxo carboxylic acid (CHEBI:15560 )
carbocyclic fatty acid (CHEBI:15560 )
unsaturated fatty acid (CHEBI:15560 )
12-oxophytodienoic acid metabolites (C01226 )
12-oxophytodienoic acid metabolites (LMFA02010001 )

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	5.09	ALOGPS
logP	5.08	ChemAxon
logS	-5	ALOGPS
pKa (Strongest Acidic)	4.78	ChemAxon
pKa (Strongest Basic)	-4.9	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	87.26 m³·mol⁻¹	ChemAxon
Polarizability	35.15 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

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB001432

KNApSAcK ID

C00000365

Chemspider ID

Not Available

KEGG Compound ID

C01226

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5280411

PDB ID

Not Available

ChEBI ID

15560

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 12-oxo-PDA (NP0045554)

MOL for NP0045554 (12-oxo-PDA)

3D MOL for NP0045554 (12-oxo-PDA)

3D SDF for NP0045554 (12-oxo-PDA)

3D-SDF for NP0045554 (12-oxo-PDA)

PDB for NP0045554 (12-oxo-PDA)

3D PDB for NP0045554 (12-oxo-PDA)

SMILES for NP0045554 (12-oxo-PDA)

INCHI for NP0045554 (12-oxo-PDA)

Structure for NP0045554 (12-oxo-PDA)

3D Structure for NP0045554 (12-oxo-PDA)