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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2022-09-09 20:20:33 UTC

Update Date

2022-09-22 18:34:47 UTC

HMDB ID

HMDB0341312

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Dinor-12-oxophytodienoic Acid

Description

Dinor-12-oxophytodienoic Acid, also known as (S,S,Z)-dinor-12-oxo pda, 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, dinor-12-oxophytodienoic Acid is considered to be an octadecanoid. Based on a literature review very few articles have been published on Dinor-12-oxophytodienoic Acid.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309092222582D          

 23 23  0  0  1  0            999 V2000
    1.8750   -3.8405    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0465   -3.0335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8312   -2.7785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0027   -1.9716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4334   -2.4815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6488   -2.7364    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6050   -1.6745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9919   -1.1225    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7621   -0.8268    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1849   -1.2940    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1507   -2.0477    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2276   -0.5795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3244    0.0336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0781   -0.3020    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0349    0.5219    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7926    0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5070   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2215    0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9360   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6505    0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3649   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0794    0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3649   -1.1270    0.0000 O   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  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  8  7  1  6  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
  8 14  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  6  0  0  0
 16 17  1  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  1  0  0  0  0
 21 23  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341312

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C16H24O3/c1-2-3-5-9-14-13(11-12-15(14)17)8-6-4-7-10-16(18)19/h3,5,11-14H,2,4,6-10H2,1H3,(H,18,19)/b5-3-/t13-,14-/m0/s1

> <INCHI_KEY>
SZVNKXCDJUBPQO-DWMAKUKJSA-N

> <FORMULA>
C16H24O3

> <MOLECULAR_WEIGHT>
264.365

> <EXACT_MASS>
264.172544633

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
30.91719381122295

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
6-[(1S,5S)-4-oxo-5-[(2Z)-pent-2-en-1-yl]cyclopent-2-en-1-yl]hexanoic acid

> <JCHEM_LOGP>
4.190409027333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
18.017840565262134

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.600039097236508

> <JCHEM_PKA_STRONGEST_BASIC>
-4.934463589469639

> <JCHEM_POLAR_SURFACE_AREA>
54.37

> <JCHEM_REFRACTIVITY>
78.05379999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
6-[(1S,5S)-4-oxo-5-[(2Z)-pent-2-en-1-yl]cyclopent-2-en-1-yl]hexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  H   UNK     0       3.500  -7.169   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       3.820  -5.663   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.285  -5.187   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.605  -3.680   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.676  -4.632   0.000  0.00  0.00           C+0
HETATM    6  H   UNK     0       1.211  -5.108   0.000  0.00  0.00           H+0
HETATM    7  C   UNK     0       2.996  -3.126   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.851  -2.095   0.000  0.00  0.00           C+0
HETATM    9  H   UNK     0       3.289  -1.543   0.000  0.00  0.00           H+0
HETATM   10  C   UNK     0       0.345  -2.415   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -0.281  -3.822   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -0.425  -1.082   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.606   0.063   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.012  -0.564   0.000  0.00  0.00           C+0
HETATM   15  H   UNK     0       1.932   0.974   0.000  0.00  0.00           H+0
HETATM   16  C   UNK     0       3.346   0.206   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.680  -0.564   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.013   0.206   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.347  -0.564   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.681   0.206   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.015  -0.564   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      11.348   0.206   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      10.015  -2.104   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    5                                                  
CONECT    3    2    4                                                       
CONECT    4    3                                                            
CONECT    5    2    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   10   14                                             
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13    8   15   16                                             
CONECT   15   14                                                            
CONECT   16   14   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                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   46    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(S,S,Z)-Dinor-12-oxo pda	ChEBI
(S,S,Z)-Dinor-12-oxo-phytodienoic acid	ChEBI
(S,S,Z)-Dinor-opda	ChEBI
4-oxo-5S-(2Z)-2-Penten-1-yl-2-cyclopentene-1S-hexanoic acid	ChEBI
Dinor-12-oxo pda	ChEBI
(S,S,Z)-Dinor-12-oxo-phytodienoate	Generator
4-oxo-5S-(2Z)-2-Penten-1-yl-2-cyclopentene-1S-hexanoate	Generator
Dinor-12-oxophytodienoate	Generator

Chemical Formula

C₁₆H₂₄O₃

Average Molecular Weight

264.365

Monoisotopic Molecular Weight

264.172544633

IUPAC Name

6-[(1S,5S)-4-oxo-5-[(2Z)-pent-2-en-1-yl]cyclopent-2-en-1-yl]hexanoic acid

Traditional Name

6-[(1S,5S)-4-oxo-5-[(2Z)-pent-2-en-1-yl]cyclopent-2-en-1-yl]hexanoic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C16H24O3/c1-2-3-5-9-14-13(11-12-15(14)17)8-6-4-7-10-16(18)19/h3,5,11-14H,2,4,6-10H2,1H3,(H,18,19)/b5-3-/t13-,14-/m0/s1

InChI Key

SZVNKXCDJUBPQO-DWMAKUKJSA-N

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

Not Available

Ontology

Not Available

Physical Properties

State

Not Available

Experimental Molecular 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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	4.19	ChemAxon
pKa (Strongest Acidic)	4.6	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	9	ChemAxon
Refractivity	78.05 m³·mol⁻¹	ChemAxon
Polarizability	30.92 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

Predicted Chromatographic Properties

Predicted Retention Times

Not Available

Predicted Kovats Retention Indices

Not Available

Spectra

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00057209

Chemspider ID

29341845

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

91746127

PDB ID

Not Available

ChEBI ID

138434

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1829631

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Simon-Manso Y, Marupaka R, Yan X, Liang Y, Telu KH, Mirokhin Y, Stein SE: Mass Spectrometry Fingerprints of Small-Molecule Metabolites in Biofluids: Building a Spectral Library of Recurrent Spectra for Urine Analysis. Anal Chem. 2019 Sep 17;91(18):12021-12029. doi: 10.1021/acs.analchem.9b02977. Epub 2019 Aug 30. [PubMed:31424920 ]

Showing metabocard for Dinor-12-oxophytodienoic Acid (HMDB0341312)

MOL for HMDB0341312 (Dinor-12-oxophytodienoic Acid)

3D MOL for HMDB0341312 (Dinor-12-oxophytodienoic Acid)

3D SDF for HMDB0341312 (Dinor-12-oxophytodienoic Acid)

3D-SDF for HMDB0341312 (Dinor-12-oxophytodienoic Acid)

PDB for HMDB0341312 (Dinor-12-oxophytodienoic Acid)

3D PDB for HMDB0341312 (Dinor-12-oxophytodienoic Acid)

SMILES for HMDB0341312 (Dinor-12-oxophytodienoic Acid)

INCHI for HMDB0341312 (Dinor-12-oxophytodienoic Acid)

Structure for HMDB0341312 (Dinor-12-oxophytodienoic Acid)

3D Structure for HMDB0341312 (Dinor-12-oxophytodienoic Acid)

Predicted Retention Times

Predicted Kovats Retention Indices