NP-MRD: Showing NP-Card for 6-Epi-7-isocucurbic acid (NP0047581)

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Record Information

Version

1.0

Created at

2022-03-17 20:42:31 UTC

Updated at

2022-03-17 20:42:31 UTC

NP-MRD ID

NP0047581

Secondary Accession Numbers

None

Natural Product Identification

Common Name

6-Epi-7-isocucurbic acid

Description

Cucurbic acid, also known as cucurbate, belongs to the class of organic compounds known as jasmonic acids. These are lipids containing or derived from a jasmonic acid, with a structure characterized by the presence of an alkene chain linked to a 2-(3-oxocyclopentyl)acetic acid moiety. Cucurbic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Cucurbic acid has been detected, but not quantified in, a few different foods, such as nuts, pulses, and ryes. 6-Epi-7-isocucurbic acid is found in Cucurbita pepo , Juglans regia , Lasiodiplodia theobromae and Vicia faba . It was first documented in 2000 (PMID: 11413487). This could make cucurbic acid a potential biomarker for the consumption of these foods (PMID: 16902246) (PMID: 17374880) (PMID: 20044567).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241211082D          

 15 15  0  0  0  0            999 V2000
    0.2062    1.8962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7007    1.2366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2062    0.5770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4534   -0.1647    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2781   -0.4119    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5253   -1.1545    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0301   -2.1442    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7726   -1.8140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8555   -0.9893    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1951   -0.4949    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2781    0.3298    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6177    0.8243    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6177    1.6490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2781    2.1442    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8555    0.2468    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1 13  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3 12  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5 15  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  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  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0047581

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC\C=C\CC1C(O)CCC1CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C12H20O3/c1-2-3-4-5-10-9(8-12(14)15)6-7-11(10)13/h3-4,9-11,13H,2,5-8H2,1H3,(H,14,15)/b4-3+

> <INCHI_KEY>
LYSGIJUGUGJIPS-ONEGZZNKSA-N

> <FORMULA>
C12H20O3

> <MOLECULAR_WEIGHT>
212.2854

> <EXACT_MASS>
212.141244506

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
23.748740551566755

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-{3-hydroxy-2-[(2E)-pent-2-en-1-yl]cyclopentyl}acetic acid

> <ALOGPS_LOGP>
2.86

> <JCHEM_LOGP>
2.028796624

> <ALOGPS_LOGS>
-1.97

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
18.999427344551062

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.849855366098545

> <JCHEM_PKA_STRONGEST_BASIC>
-1.049451099996372

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
59.4817

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.29e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{3-hydroxy-2-[(2E)-pent-2-en-1-yl]cyclopentyl}acetic 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  C   UNK     0       0.385   3.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.308   2.308   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.385   1.077   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.846  -0.307   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.386  -0.769   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.847  -2.155   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.923  -4.003   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.309  -3.386   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.464  -1.847   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.231  -0.924   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.386   0.616   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.153   1.539   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.153   3.078   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -2.386   4.003   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       3.464   0.461   0.000  0.00  0.00           O+0
CONECT    1    2   13                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   12                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   15                                                  
CONECT    6    5                                                            
CONECT    7    8                                                            
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12    3   11   13                                                  
CONECT   13    1   12   14                                                  
CONECT   14   13                                                            
CONECT   15    5                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

View in JSmol

Synonyms

Value	Source
Cucurbate	Generator
(+)-Cucurbic acid	HMDB
(3R,6S,7S)-Cucurbic acid	HMDB
3-Hydroxy-2-(2-pentenyl)cyclopentaneacetic acid	HMDB
2-{3-hydroxy-2-[(2E)-pent-2-en-1-yl]cyclopentyl}acetate	Generator
6-Epi-7-isocucurbate	Generator

Chemical Formula

C₁₂H₂₀O₃

Average Mass

212.2854 Da

Monoisotopic Mass

212.14124 Da

IUPAC Name

2-{3-hydroxy-2-[(2E)-pent-2-en-1-yl]cyclopentyl}acetic acid

Traditional Name

{3-hydroxy-2-[(2E)-pent-2-en-1-yl]cyclopentyl}acetic acid

CAS Registry Number

58240-50-9

SMILES

CC\C=C\CC1C(O)CCC1CC(O)=O

InChI Identifier

InChI=1S/C12H20O3/c1-2-3-4-5-10-9(8-12(14)15)6-7-11(10)13/h3-4,9-11,13H,2,5-8H2,1H3,(H,14,15)/b4-3+

InChI Key

LYSGIJUGUGJIPS-ONEGZZNKSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Cucurbita pepo	Plant	KNApSAcK
Juglans regia	Plant	KNApSAcK
Lasiodiplodia theobromae	LOTUS Database	35616633
Secale cereale	FooDB	KNAPSACK
Vicia faba	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as jasmonic acids. These are lipids containing or derived from a jasmonic acid, with a structure characterized by the presence of an alkene chain linked to a 2-(3-oxocyclopentyl)acetic acid moiety.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Lineolic acids and derivatives

Direct Parent

Jasmonic acids

Alternative Parents

Substituents

Jasmonic acid
Cyclopentanol
Cyclic alcohol
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
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	2.86	ALOGPS
logP	2.03	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	4.85	ChemAxon
pKa (Strongest Basic)	-1	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.53 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	59.48 m³·mol⁻¹	ChemAxon
Polarizability	23.75 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

External Links

HMDB ID

HMDB0029388

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB011264

KNApSAcK ID

C00000234

Chemspider ID

19015737

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6123064

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]

Showing NP-Card for 6-Epi-7-isocucurbic acid (NP0047581)

MOL for NP0047581 (6-Epi-7-isocucurbic acid)

3D MOL for NP0047581 (6-Epi-7-isocucurbic acid)

3D SDF for NP0047581 (6-Epi-7-isocucurbic acid)

3D-SDF for NP0047581 (6-Epi-7-isocucurbic acid)

PDB for NP0047581 (6-Epi-7-isocucurbic acid)

3D PDB for NP0047581 (6-Epi-7-isocucurbic acid)

SMILES for NP0047581 (6-Epi-7-isocucurbic acid)

INCHI for NP0047581 (6-Epi-7-isocucurbic acid)

Structure for NP0047581 (6-Epi-7-isocucurbic acid)

3D Structure for NP0047581 (6-Epi-7-isocucurbic acid)