MiMeDB: Showing metabocard for 13(S)-HPODE (MMDBc0055172)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:45:25 UTC

Update Date

2025-10-07 16:08:59 UTC

Metabolite ID

MMDBc0055172

Metabolite Identification

Common Name

13(S)-HPODE

Description

13(S)-HPODE is a hydroperoxide derivative of linoleic acid, belonging to the class of oxylipins. Its chemical structure features a hydroperoxy group at the 13th carbon position of the fatty acid chain, which plays a crucial role in various biochemical pathways. 13(S)-HPODE is involved in linoleic acid metabolism, where it participates in the production of other bioactive lipids, such as 13-HODE and 9-HODE, through enzymatic reactions catalyzed by lipoxygenases (LOXs) (PMID:37734909 ). It is also implicated in the regulation of lipid biosynthesis, with genes such as LOX2S-2, LOX2S-3, and LOX2S-4 being associated with its metabolic pathways (PMID:39949634 ). Additionally, 13(S)-HPODE has been shown to influence inflammatory responses, as its injection into mice led to significant changes in plasma lipid profiles and a reduction in the anti-inflammatory properties of high-density lipoprotein (HDL) (PMID:20642447 ). Furthermore, it has been identified as a key oxylipin distinguishing diabetic kidney disease (DKD) groups, highlighting its relevance in metabolic disorders (PMID:41043691 ). Overall, 13(S)-HPODE serves as a significant metabolite in lipid metabolism and inflammatory processes.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221452D          

 27 26  0  0  1  0            999 V2000
   -2.2285    0.4027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4183    0.2467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8783    0.8704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2526    1.3381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9825   -0.0651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9825    2.1177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7927   -0.2210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1724    2.2736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3328    0.4027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0681    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6323    1.6499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1429    0.2467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4720    1.3381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8222    1.8058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6830    0.8704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2821    1.1822    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.4931    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0332    1.3381    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7632   -0.0651    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.0121   -0.2210    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5521    0.4027    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5226    2.7413    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9024    3.0531    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9024    0.8704    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5521    2.5854    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0121    1.9618    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  5  4  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  6  1  0  0  0  0
  9  7  2  0  0  0  0
 10  8  1  0  0  0  0
 11  3  1  0  0  0  0
 12  9  1  0  0  0  0
 13 10  1  0  0  0  0
 14 11  1  0  0  0  0
 15 12  2  0  0  0  0
 16 13  1  0  0  0  0
 17 14  1  0  0  0  0
 17 15  1  0  0  0  0
 18 16  1  0  0  0  0
 19 18  2  0  0  0  0
 20 18  1  0  0  0  0
 17 22  1  6  0  0  0
 22 21  1  0  0  0  0
 23  7  1  0  0  0  0
 24  9  1  0  0  0  0
 25 12  1  0  0  0  0
 26 15  1  0  0  0  0
 17 27  1  6  0  0  0
M  CHG  1  20  -1
M  END


  Mrv1652306172221452D          

 27 26  0  0  1  0            999 V2000
   -2.2285    0.4027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4183    0.2467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8783    0.8704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2526    1.3381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9825   -0.0651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9825    2.1177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7927   -0.2210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1724    2.2736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3328    0.4027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0681    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6323    1.6499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1429    0.2467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4720    1.3381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8222    1.8058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6830    0.8704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2821    1.1822    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.4931    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0332    1.3381    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7632   -0.0651    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.0121   -0.2210    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5521    0.4027    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5226    2.7413    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9024    3.0531    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9024    0.8704    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5521    2.5854    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0121    1.9618    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  5  4  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  6  1  0  0  0  0
  9  7  2  0  0  0  0
 10  8  1  0  0  0  0
 11  3  1  0  0  0  0
 12  9  1  0  0  0  0
 13 10  1  0  0  0  0
 14 11  1  0  0  0  0
 15 12  2  0  0  0  0
 16 13  1  0  0  0  0
 17 14  1  0  0  0  0
 17 15  1  0  0  0  0
 18 16  1  0  0  0  0
 19 18  2  0  0  0  0
 20 18  1  0  0  0  0
 17 22  1  6  0  0  0
 22 21  1  0  0  0  0
 23  7  1  0  0  0  0
 24  9  1  0  0  0  0
 25 12  1  0  0  0  0
 26 15  1  0  0  0  0
 17 27  1  6  0  0  0
M  CHG  1  20  -1
M  END
> <DATABASE_ID>
MMDBc0055172

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C(CCCCCCCC([O-])=O)=C(/[H])\C(\[H])=C(/[H])[C@]([H])(CCCCC)OO

> <INCHI_IDENTIFIER>
InChI=1S/C18H32O4/c1-2-3-11-14-17(22-21)15-12-9-7-5-4-6-8-10-13-16-18(19)20/h7,9,12,15,17,21H,2-6,8,10-11,13-14,16H2,1H3,(H,19,20)/p-1/b9-7-,15-12+/t17-/m0/s1

> <INCHI_KEY>
JDSRHVWSAMTSSN-IRQZEAMPSA-M

> <FORMULA>
C18H31O4

> <MOLECULAR_WEIGHT>
311.443

> <EXACT_MASS>
311.222783058

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
53

> <JCHEM_AVERAGE_POLARIZABILITY>
36.72286581053814

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(9Z,11E,13S)-13-hydroperoxyoctadeca-9,11-dienoate

> <JCHEM_LOGP>
5.640401104666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.712374089551586

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.988167201984285

> <JCHEM_PKA_STRONGEST_BASIC>
-4.2368076090774425

> <JCHEM_POLAR_SURFACE_AREA>
69.59

> <JCHEM_REFRACTIVITY>
102.2216

> <JCHEM_ROTATABLE_BOND_COUNT>
15

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
13(S)-hpode anion

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      -4.160   0.752   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.648   0.461   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.639   1.625   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.930   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.938   2.498   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.434  -0.121   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.434   3.953   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.946  -0.413   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.922   4.244   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.954   0.752   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.127   1.334   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.914   3.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      11.467   0.461   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.881   2.498   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.401   3.371   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      12.475   1.625   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.393   2.207   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      13.987   1.334   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      14.995   2.498   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      14.491  -0.121   0.000  0.00  0.00           O-1
HETATM   21  O   UNK     0       1.889  -0.413   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       2.897   0.752   0.000  0.00  0.00           O+0
HETATM   23  H   UNK     0       8.442   5.117   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       5.418   5.699   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0       5.418   1.625   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0       2.897   4.826   0.000  0.00  0.00           H+0
HETATM   27  H   UNK     0       1.889   3.662   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2   11                                                       
CONECT    4    5    6                                                       
CONECT    5    4    7                                                       
CONECT    6    4    8                                                       
CONECT    7    5    9   23                                                  
CONECT    8    6   10                                                       
CONECT    9    7   12   24                                                  
CONECT   10    8   13                                                       
CONECT   11    3   14                                                       
CONECT   12    9   15   25                                                  
CONECT   13   10   16                                                       
CONECT   14   11   17                                                       
CONECT   15   12   17   26                                                  
CONECT   16   13   18                                                       
CONECT   17   14   15   22   27                                             
CONECT   18   16   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   22                                                            
CONECT   22   17   21                                                       
CONECT   23    7                                                            
CONECT   24    9                                                            
CONECT   25   12                                                            
CONECT   26   15                                                            
CONECT   27   17                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   52    0
END

Synonyms

Value	Source
(13S)-Hydroperoxy-(9Z,11E)-octadecadienoate	ChEBI
13(S)-HPODE anion	ChEBI
(13S)-Hydroperoxy-(9Z,11E)-octadecadienoic acid	Generator

Molecular Formula

C₁₈H₃₁O₄

Average Mass

311.443

Monoisotopic Mass

311.222783058

IUPAC Name

(9Z,11E,13S)-13-hydroperoxyoctadeca-9,11-dienoate

Traditional Name

13(S)-hpode anion

CAS Registry Number

Not Available

SMILES

[H]\C(CCCCCCCC([O-])=O)=C(/[H])\C(\[H])=C(/[H])[C@]([H])(CCCCC)OO

InChI Identifier

InChI=1S/C18H32O4/c1-2-3-11-14-17(22-21)15-12-9-7-5-4-6-8-10-13-16-18(19)20/h7,9,12,15,17,21H,2-6,8,10-11,13-14,16H2,1H3,(H,19,20)/p-1/b9-7-,15-12+/t17-/m0/s1

InChI Key

JDSRHVWSAMTSSN-IRQZEAMPSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as lineolic acids and derivatives. These are derivatives of lineolic acid. Lineolic acid is a polyunsaturated omega-6 18 carbon long fatty acid, with two CC double bonds at the 9- and 12-positions.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Lineolic acids and derivatives

Direct Parent

Lineolic acids and derivatives

Alternative Parents

Substituents

Octadecanoid
Long-chain fatty acid
Hydroperoxy fatty acid
Unsaturated fatty acid
Fatty acid
Allylic hydroperoxide
Hydroperoxide
Peroxol
Monocarboxylic acid or derivatives
Alkyl hydroperoxide
Carboxylic acid
Carboxylic acid derivative
Carbonyl group
Organooxygen compound
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

monocarboxylic acid anion (CHEBI:57466 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	5.64	ChemAxon
pKa (Strongest Acidic)	4.99	ChemAxon
pKa (Strongest Basic)	-4.2	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	69.59 Å²	ChemAxon
Rotatable Bond Count	15	ChemAxon
Refractivity	102.22 m³·mol⁻¹	ChemAxon
Polarizability	36.72 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	235.9
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	34.8
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-24	662.8
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	763.6
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	1016.9
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-24	602.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	3248.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	96.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	473.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	809.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	605.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	353.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	244.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	8.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	558.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	612.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	508.4
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	1804.0
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	2233.5

Retention Indices

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites
Bacteria/Eubacteria	Proteobacteria	2	Human ; Human sputum; Human subgingival plaque; Human feces
Eukaryota/Fungi	Ascomycota	1
Eukaryota/Fungi	Basidiomycota	1

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

20118012

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21158461

PDB ID

Not Available

ChEBI ID

57466

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 13(S)-HPODE (MMDBc0055172)

MOL for #<Metabolite:0x00007fadc4350fd8>

3D MOL for #<Metabolite:0x00007fadc4350fd8>

3D SDF for #<Metabolite:0x00007fadc4350fd8>

3D-SDF for #<Metabolite:0x00007fadc4350fd8>

PDB for #<Metabolite:0x00007fadc4350fd8>

3D PDB for #<Metabolite:0x00007fadc4350fd8>

SMILES for #<Metabolite:0x00007fadc4350fd8>

INCHI for #<Metabolite:0x00007fadc4350fd8>

Structure for #<Metabolite:0x00007fadc4350fd8>

3D Structure for #<Metabolite:0x00007fadc4350fd8>