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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-09-22 21:14:46 UTC

Update Date

2021-09-22 21:14:46 UTC

HMDB ID

HMDB0301804

Secondary Accession Numbers

None

Metabolite Identification

Common Name

12-oxo-PDA

Description

12-oxo-pda, also known as (15z)-12-oxophyto-10,15-dienoate or 12-oxo-10,15(Z)-phytodienoic acid, is a member of the class of compounds known as prostaglandins and related compounds. Prostaglandins and related compounds 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 practically insoluble (in water) and a weakly acidic compound (based on its pKa). 12-oxo-pda can be found in corn, which makes 12-oxo-pda a potential biomarker for the consumption of this food product.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0301804
     RDKit          3D
12-oxo-PDA
 49 49  0  0  0  0  0  0  0  0999 V2000
   -6.6219   -0.7043    1.1099 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2618    0.4786    0.1881 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9870    1.0037    0.6436 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8477    1.1021   -0.0316 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7666    0.6554   -1.4069 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8688   -0.4023   -1.8142 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0311   -1.7381   -1.1720 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7942   -2.1627   -0.2953 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9998   -2.5119   -1.8638 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0370   -1.7005   -2.2730 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4122   -0.2937   -1.8434 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6915   -0.1535   -0.5229 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8212   -0.0779   -0.8314 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6211    0.0625    0.4214 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0814    0.1287    0.0287 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9886    0.2713    1.2151 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4108    0.3306    0.7591 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3832    0.4750    1.9110 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7669    0.5267    1.3825 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0253    0.4560    0.1508 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.8301    0.6578    2.2639 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6653   -1.1552    1.4438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1099   -0.3232    2.0415 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2132   -1.4605    0.5959 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0896    1.2194    0.3981 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3456    0.0723   -0.8076 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9482    1.3723    1.6867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9809    1.5385    0.4699 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7724    0.4650   -1.8862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4448    1.5866   -2.0046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1523   -0.6503   -2.9181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9668   -3.5959   -2.0445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1372   -1.9546   -2.8141 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0116    0.4290   -2.5994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9129   -1.0114    0.1109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8893    0.7693    0.0200 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1434   -0.9721   -1.3791 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0299    0.8007   -1.4739 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3664    0.9702    1.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5169   -0.7914    1.1138 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2794    1.0123   -0.6342 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3956   -0.7613   -0.5506 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7762    1.2084    1.7744 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8991   -0.5874    1.9189 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5800    1.2133    0.0918 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7281   -0.5520    0.1775 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3383   -0.4093    2.5888 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2181    1.3799    2.5011 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7595    1.1117    3.1592 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  2  0
 19 21  1  0
 11  6  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  2 26  1  0
  3 27  1  0
  4 28  1  0
  5 29  1  0
  5 30  1  0
  6 31  1  6
  9 32  1  0
 10 33  1  0
 11 34  1  6
 12 35  1  0
 12 36  1  0
 13 37  1  0
 13 38  1  0
 14 39  1  0
 14 40  1  0
 15 41  1  0
 15 42  1  0
 16 43  1  0
 16 44  1  0
 17 45  1  0
 17 46  1  0
 18 47  1  0
 18 48  1  0
 21 49  1  0
M  END


  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>
HMDB0301804

> <DATABASE_NAME>
hmdb

> <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

$$$$

HMDB0301804
     RDKit          3D
12-oxo-PDA
 49 49  0  0  0  0  0  0  0  0999 V2000
   -6.6219   -0.7043    1.1099 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2618    0.4786    0.1881 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9870    1.0037    0.6436 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8477    1.1021   -0.0316 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7666    0.6554   -1.4069 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8688   -0.4023   -1.8142 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0311   -1.7381   -1.1720 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7942   -2.1627   -0.2953 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9998   -2.5119   -1.8638 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0370   -1.7005   -2.2730 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4122   -0.2937   -1.8434 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6915   -0.1535   -0.5229 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8212   -0.0779   -0.8314 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6211    0.0625    0.4214 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0814    0.1287    0.0287 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9886    0.2713    1.2151 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4108    0.3306    0.7591 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3832    0.4750    1.9110 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7669    0.5267    1.3825 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0253    0.4560    0.1508 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.8301    0.6578    2.2639 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6653   -1.1552    1.4438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1099   -0.3232    2.0415 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2132   -1.4605    0.5959 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0896    1.2194    0.3981 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3456    0.0723   -0.8076 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9482    1.3723    1.6867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9809    1.5385    0.4699 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7724    0.4650   -1.8862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4448    1.5866   -2.0046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1523   -0.6503   -2.9181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9668   -3.5959   -2.0445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1372   -1.9546   -2.8141 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0116    0.4290   -2.5994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9129   -1.0114    0.1109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8893    0.7693    0.0200 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1434   -0.9721   -1.3791 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0299    0.8007   -1.4739 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3664    0.9702    1.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5169   -0.7914    1.1138 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2794    1.0123   -0.6342 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3956   -0.7613   -0.5506 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7762    1.2084    1.7744 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8991   -0.5874    1.9189 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5800    1.2133    0.0918 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7281   -0.5520    0.1775 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3383   -0.4093    2.5888 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2181    1.3799    2.5011 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7595    1.1117    3.1592 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  2  0
 19 21  1  0
 11  6  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  2 26  1  0
  3 27  1  0
  4 28  1  0
  5 29  1  0
  5 30  1  0
  6 31  1  6
  9 32  1  0
 10 33  1  0
 11 34  1  6
 12 35  1  0
 12 36  1  0
 13 37  1  0
 13 38  1  0
 14 39  1  0
 14 40  1  0
 15 41  1  0
 15 42  1  0
 16 43  1  0
 16 44  1  0
 17 45  1  0
 17 46  1  0
 18 47  1  0
 18 48  1  0
 21 49  1  0
M  END

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

COMPND    HMDB0301804
HETATM    1  C1  UNL     1      -6.622  -0.704   1.110  1.00  0.00           C  
HETATM    2  C2  UNL     1      -6.262   0.479   0.188  1.00  0.00           C  
HETATM    3  C3  UNL     1      -4.987   1.004   0.644  1.00  0.00           C  
HETATM    4  C4  UNL     1      -3.848   1.102  -0.032  1.00  0.00           C  
HETATM    5  C5  UNL     1      -3.767   0.655  -1.407  1.00  0.00           C  
HETATM    6  C6  UNL     1      -2.869  -0.402  -1.814  1.00  0.00           C  
HETATM    7  C7  UNL     1      -3.031  -1.738  -1.172  1.00  0.00           C  
HETATM    8  O1  UNL     1      -3.794  -2.163  -0.295  1.00  0.00           O  
HETATM    9  C8  UNL     1      -2.000  -2.512  -1.864  1.00  0.00           C  
HETATM   10  C9  UNL     1      -1.037  -1.701  -2.273  1.00  0.00           C  
HETATM   11  C10 UNL     1      -1.412  -0.294  -1.843  1.00  0.00           C  
HETATM   12  C11 UNL     1      -0.692  -0.154  -0.523  1.00  0.00           C  
HETATM   13  C12 UNL     1       0.821  -0.078  -0.831  1.00  0.00           C  
HETATM   14  C13 UNL     1       1.621   0.063   0.421  1.00  0.00           C  
HETATM   15  C14 UNL     1       3.081   0.129   0.029  1.00  0.00           C  
HETATM   16  C15 UNL     1       3.989   0.271   1.215  1.00  0.00           C  
HETATM   17  C16 UNL     1       5.411   0.331   0.759  1.00  0.00           C  
HETATM   18  C17 UNL     1       6.383   0.475   1.911  1.00  0.00           C  
HETATM   19  C18 UNL     1       7.767   0.527   1.383  1.00  0.00           C  
HETATM   20  O2  UNL     1       8.025   0.456   0.151  1.00  0.00           O  
HETATM   21  O3  UNL     1       8.830   0.658   2.264  1.00  0.00           O  
HETATM   22  H1  UNL     1      -5.665  -1.155   1.444  1.00  0.00           H  
HETATM   23  H2  UNL     1      -7.110  -0.323   2.042  1.00  0.00           H  
HETATM   24  H3  UNL     1      -7.213  -1.461   0.596  1.00  0.00           H  
HETATM   25  H4  UNL     1      -7.090   1.219   0.398  1.00  0.00           H  
HETATM   26  H5  UNL     1      -6.346   0.072  -0.808  1.00  0.00           H  
HETATM   27  H6  UNL     1      -4.948   1.372   1.687  1.00  0.00           H  
HETATM   28  H7  UNL     1      -2.981   1.538   0.470  1.00  0.00           H  
HETATM   29  H8  UNL     1      -4.772   0.465  -1.886  1.00  0.00           H  
HETATM   30  H9  UNL     1      -3.445   1.587  -2.005  1.00  0.00           H  
HETATM   31  H10 UNL     1      -3.152  -0.650  -2.918  1.00  0.00           H  
HETATM   32  H11 UNL     1      -1.967  -3.596  -2.045  1.00  0.00           H  
HETATM   33  H12 UNL     1      -0.137  -1.955  -2.814  1.00  0.00           H  
HETATM   34  H13 UNL     1      -1.012   0.429  -2.599  1.00  0.00           H  
HETATM   35  H14 UNL     1      -0.913  -1.011   0.111  1.00  0.00           H  
HETATM   36  H15 UNL     1      -0.889   0.769   0.020  1.00  0.00           H  
HETATM   37  H16 UNL     1       1.143  -0.972  -1.379  1.00  0.00           H  
HETATM   38  H17 UNL     1       1.030   0.801  -1.474  1.00  0.00           H  
HETATM   39  H18 UNL     1       1.366   0.970   1.000  1.00  0.00           H  
HETATM   40  H19 UNL     1       1.517  -0.791   1.114  1.00  0.00           H  
HETATM   41  H20 UNL     1       3.279   1.012  -0.634  1.00  0.00           H  
HETATM   42  H21 UNL     1       3.396  -0.761  -0.551  1.00  0.00           H  
HETATM   43  H22 UNL     1       3.776   1.208   1.774  1.00  0.00           H  
HETATM   44  H23 UNL     1       3.899  -0.587   1.919  1.00  0.00           H  
HETATM   45  H24 UNL     1       5.580   1.213   0.092  1.00  0.00           H  
HETATM   46  H25 UNL     1       5.728  -0.552   0.177  1.00  0.00           H  
HETATM   47  H26 UNL     1       6.338  -0.409   2.589  1.00  0.00           H  
HETATM   48  H27 UNL     1       6.218   1.380   2.501  1.00  0.00           H  
HETATM   49  H28 UNL     1       8.760   1.112   3.159  1.00  0.00           H  
CONECT    1    2   22   23   24
CONECT    2    3   25   26
CONECT    3    4    4   27
CONECT    4    5   28
CONECT    5    6   29   30
CONECT    6    7   11   31
CONECT    7    8    8    9
CONECT    9   10   10   32
CONECT   10   11   33
CONECT   11   12   34
CONECT   12   13   35   36
CONECT   13   14   37   38
CONECT   14   15   39   40
CONECT   15   16   41   42
CONECT   16   17   43   44
CONECT   17   18   45   46
CONECT   18   19   47   48
CONECT   19   20   20   21
CONECT   21   49
END

HMDB0301804
     RDKit          3D
12-oxo-PDA
 49 49  0  0  0  0  0  0  0  0999 V2000
   -6.6219   -0.7043    1.1099 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2618    0.4786    0.1881 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9870    1.0037    0.6436 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8477    1.1021   -0.0316 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7666    0.6554   -1.4069 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8688   -0.4023   -1.8142 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0311   -1.7381   -1.1720 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7942   -2.1627   -0.2953 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9998   -2.5119   -1.8638 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0370   -1.7005   -2.2730 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4122   -0.2937   -1.8434 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6915   -0.1535   -0.5229 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8212   -0.0779   -0.8314 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6211    0.0625    0.4214 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0814    0.1287    0.0287 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9886    0.2713    1.2151 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4108    0.3306    0.7591 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3832    0.4750    1.9110 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7669    0.5267    1.3825 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0253    0.4560    0.1508 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.8301    0.6578    2.2639 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6653   -1.1552    1.4438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1099   -0.3232    2.0415 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2132   -1.4605    0.5959 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0896    1.2194    0.3981 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3456    0.0723   -0.8076 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9482    1.3723    1.6867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9809    1.5385    0.4699 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7724    0.4650   -1.8862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4448    1.5866   -2.0046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1523   -0.6503   -2.9181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9668   -3.5959   -2.0445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1372   -1.9546   -2.8141 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0116    0.4290   -2.5994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9129   -1.0114    0.1109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8893    0.7693    0.0200 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1434   -0.9721   -1.3791 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0299    0.8007   -1.4739 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3664    0.9702    1.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5169   -0.7914    1.1138 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2794    1.0123   -0.6342 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3956   -0.7613   -0.5506 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7762    1.2084    1.7744 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8991   -0.5874    1.9189 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5800    1.2133    0.0918 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7281   -0.5520    0.1775 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3383   -0.4093    2.5888 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2181    1.3799    2.5011 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7595    1.1117    3.1592 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  2  0
 19 21  1  0
 11  6  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  2 26  1  0
  3 27  1  0
  4 28  1  0
  5 29  1  0
  5 30  1  0
  6 31  1  6
  9 32  1  0
 10 33  1  0
 11 34  1  6
 12 35  1  0
 12 36  1  0
 13 37  1  0
 13 38  1  0
 14 39  1  0
 14 40  1  0
 15 41  1  0
 15 42  1  0
 16 43  1  0
 16 44  1  0
 17 45  1  0
 17 46  1  0
 18 47  1  0
 18 48  1  0
 21 49  1  0
M  END

View in JSmol View Stereo Labels

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
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
12-oxo-PDA	MeSH
OPDA acid	MeSH
12-oxo-cis-10, cis-15-Phytodienoic acid	MeSH
(15Z)-12-oxophyto-10,15-Dienoic acid	Generator, KEGG

Chemical Formula

C₁₈H₂₈O₃

Average Molecular Weight

292.4131

Monoisotopic Molecular Weight

292.203844762

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

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 )

Ontology

Not Available

Exogenous (HMDB: HMDB0301804)

Food

Cereal and cereal product

Cereal

Corn (FooDB: FOOD00205)

Process

Not Available

Role

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	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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
AllCCS	[M+H]+	176.196	32859911
AllCCS	[M+H-H2O]+	173.072	32859911
AllCCS	[M+Na]+	179.921	32859911
AllCCS	[M+NH4]+	179.09	32859911
AllCCS	[M-H]-	179.05	32859911
AllCCS	[M+Na-2H]-	179.972	32859911
AllCCS	[M+HCOO]-	181.13	32859911
DeepCCS	[M+H]+	181.238	30932474
DeepCCS	[M-H]-	178.88	30932474
DeepCCS	[M-2H]-	211.767	30932474
DeepCCS	[M+Na]+	187.331	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	18.1294 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	0.61 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2734.4 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	423.8 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	201.0 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	227.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	496.6 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	787.4 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	623.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	87.6 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1693.6 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	536.8 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1567.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	550.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	442.2 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	401.2 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	422.4 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	7.9 seconds	40023050

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
12-oxo-PDA,2TMS,isomer #1	CC/C=C\CC1=C(O[Si](C)(C)C)C=C[C@@H]1CCCCCCCC(=O)O[Si](C)(C)C	2556.8	Semi standard non polar	33892256
12-oxo-PDA,2TMS,isomer #1	CC/C=C\CC1=C(O[Si](C)(C)C)C=C[C@@H]1CCCCCCCC(=O)O[Si](C)(C)C	2455.3	Standard non polar	33892256
12-oxo-PDA,2TMS,isomer #1	CC/C=C\CC1=C(O[Si](C)(C)C)C=C[C@@H]1CCCCCCCC(=O)O[Si](C)(C)C	2671.0	Standard polar	33892256
12-oxo-PDA,2TBDMS,isomer #1	CC/C=C\CC1=C(O[Si](C)(C)C(C)(C)C)C=C[C@@H]1CCCCCCCC(=O)O[Si](C)(C)C(C)(C)C	3007.3	Semi standard non polar	33892256
12-oxo-PDA,2TBDMS,isomer #1	CC/C=C\CC1=C(O[Si](C)(C)C(C)(C)C)C=C[C@@H]1CCCCCCCC(=O)O[Si](C)(C)C(C)(C)C	2807.3	Standard non polar	33892256
12-oxo-PDA,2TBDMS,isomer #1	CC/C=C\CC1=C(O[Si](C)(C)C(C)(C)C)C=C[C@@H]1CCCCCCCC(=O)O[Si](C)(C)C(C)(C)C	2843.9	Standard polar	33892256

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 12-oxo-PDA 10V, Positive-QTOF	splash10-002f-0090000000-9e001b387642892b2e29	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 12-oxo-PDA 20V, Positive-QTOF	splash10-003r-9670000000-2542263ca019f7436aa5	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 12-oxo-PDA 40V, Positive-QTOF	splash10-0f9x-9110000000-fd1ef2bcb07783aa0e38	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 12-oxo-PDA 10V, Negative-QTOF	splash10-0006-0090000000-abdf8cebd8c34aacba6d	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 12-oxo-PDA 20V, Negative-QTOF	splash10-0007-1090000000-87a6bfb759bfc815f3d6	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 12-oxo-PDA 40V, Negative-QTOF	splash10-0a4i-9330000000-b99bb0a622dfcba347b7	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 12-oxo-PDA 10V, Positive-QTOF	splash10-056u-0190000000-da1bad165a31b446f505	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 12-oxo-PDA 20V, Positive-QTOF	splash10-0a59-9720000000-580231e8f4b969fef8c0	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 12-oxo-PDA 40V, Positive-QTOF	splash10-0a7l-9400000000-8826088cd520b5bc978b	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 12-oxo-PDA 10V, Negative-QTOF	splash10-0006-0090000000-6beab8184e0b594e850e	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 12-oxo-PDA 20V, Negative-QTOF	splash10-006x-0190000000-2d9bc33999bf3ae546a6	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 12-oxo-PDA 40V, Negative-QTOF	splash10-00ds-3930000000-cafd59fefd47e0c5d5cd	2021-10-21	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

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

FDB001432

KNApSAcK ID

Not Available

Chemspider ID

4444088

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

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1663101

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for 12-oxo-PDA (HMDB0301804)

MOL for HMDB0301804 (12-oxo-PDA)

3D MOL for HMDB0301804 (12-oxo-PDA)

3D SDF for HMDB0301804 (12-oxo-PDA)

3D-SDF for HMDB0301804 (12-oxo-PDA)

PDB for HMDB0301804 (12-oxo-PDA)

3D PDB for HMDB0301804 (12-oxo-PDA)

SMILES for HMDB0301804 (12-oxo-PDA)

INCHI for HMDB0301804 (12-oxo-PDA)

Structure for HMDB0301804 (12-oxo-PDA)

3D Structure for HMDB0301804 (12-oxo-PDA)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Derivatized

MS/MS Spectra