NP-MRD: Showing NP-Card for [(1r,2s,3s)-3-hydroxy-2-(pent-2-en-1-yl)cyclopentyl]acetic acid (NP0196373)

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Record Information

Version

1.0

Created at

2022-09-04 14:27:21 UTC

Updated at

2022-09-04 14:27:21 UTC

NP-MRD ID

NP0196373

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(1r,2s,3s)-3-hydroxy-2-(pent-2-en-1-yl)cyclopentyl]acetic 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. [(1r,2s,3s)-3-hydroxy-2-(pent-2-en-1-yl)cyclopentyl]acetic acid is found in Cucurbita pepo. It was first documented in 2004 (PMID: 15636363). Based on a literature review a small amount of articles have been published on Cucurbic acid (PMID: 34556726) (PMID: 27502354) (PMID: 25879500) (PMID: 16180811).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 35 35  0  0  0  0  0  0  0  0999 V2000
    5.0009    0.9868   -0.5323 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1075    0.3152    0.4887 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6873    0.7247    0.2012 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7936   -0.1735   -0.0824 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4385    0.2844   -0.3508 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5699   -0.2583    0.5625 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5648   -1.7816    0.4422 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3156   -2.3501    1.6812 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8925   -2.1776   -0.1182 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4561   -0.8728   -0.6897 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9717    0.1274    0.3029 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1696    1.5525   -0.1243 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5729    1.8976   -0.3724 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8347    3.0737   -0.7354 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6400    1.0271   -0.2385 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4347    1.6240   -1.2201 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5063    0.2124   -1.1566 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7860    1.5791   -0.0125 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3375    0.6740    1.5183 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2013   -0.7832    0.4484 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4911    1.7847    0.2506 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0348   -1.2155   -0.1200 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2151    0.3051   -1.0830 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2146    0.7906   -1.2466 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2311    0.0185    1.5774 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2159   -2.1256   -0.2733 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1483   -3.2155    1.5187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5627   -2.4902    0.7230 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8372   -2.9363   -0.9181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5725   -1.0109   -0.6580 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0822   -0.7306   -1.7080 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5427   -0.0350    1.2520 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7903    2.2223    0.6759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5742    1.7844   -1.0305 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4327    1.1721    0.3537 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  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 15  1  0
 13 14  2  0
 11  6  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  2 19  1  0
  2 20  1  0
  3 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  1
  7 26  1  6
  8 27  1  0
  9 28  1  0
  9 29  1  0
 10 30  1  0
 10 31  1  0
 11 32  1  1
 12 33  1  0
 12 34  1  0
 15 35  1  0
M  END


  Mrv1652309042216272D          

 15 15  0  0  1  0            999 V2000
    3.4256    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7112    2.3518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9967    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8405    1.9462    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4427    2.2433    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  4  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  6  5  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  6 11  1  0  0  0  0
 11 12  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0196373

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC=CC[C@@H]1[C@@H](O)CC[C@@H]1CC(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)/t9-,10+,11+/m1/s1

> <INCHI_KEY>
LYSGIJUGUGJIPS-VWYCJHECSA-N

> <FORMULA>
C12H20O3

> <MOLECULAR_WEIGHT>
212.289

> <EXACT_MASS>
212.141244504

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
24.28976724781461

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[(1R,2S,3S)-3-hydroxy-2-(pent-2-en-1-yl)cyclopentyl]acetic acid

> <JCHEM_LOGP>
2.028796624

> <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>
59.481700000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[(1R,2S,3S)-3-hydroxy-2-(pent-2-en-1-yl)cyclopentyl]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0       6.395   3.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.061   4.390   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.727   3.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.393   4.390   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       3.770   1.651   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.651   1.651   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.971   3.157   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -3.436   3.633   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -0.826   4.188   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    6   12                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

View in JSmol

Synonyms

Value	Source
Cucurbate	Generator

Chemical Formula

C₁₂H₂₀O₃

Average Mass

212.2890 Da

Monoisotopic Mass

212.14124 Da

IUPAC Name

2-[(1R,2S,3S)-3-hydroxy-2-(pent-2-en-1-yl)cyclopentyl]acetic acid

Traditional Name

[(1R,2S,3S)-3-hydroxy-2-(pent-2-en-1-yl)cyclopentyl]acetic acid

CAS Registry Number

Not Available

SMILES

CCC=CC[C@@H]1[C@@H](O)CC[C@@H]1CC(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)/t9-,10+,11+/m1/s1

InChI Key

LYSGIJUGUGJIPS-VWYCJHECSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Cucurbita pepo	LOTUS Database	35616633

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	2.03	ChemAxon
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	24.29 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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00000234

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

441565

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Ren Z, Fang M, Muhae-Ud-Din G, Gao H, Yang Y, Liu T, Chen W, Gao L: Metabolomics analysis of grains of wheat infected and noninfected with Tilletia controversa Kuhn. Sci Rep. 2021 Sep 23;11(1):18876. doi: 10.1038/s41598-021-98283-3. [PubMed:34556726 ]
Rontani JF, Galeron MA, Aubert C: Electron ionization mass spectrometric fragmentation and multiple reaction monitoring quantification of trimethylsilyl derivatives of cucurbic acid and its 6,7-stereoisomers. Rapid Commun Mass Spectrom. 2016 Oct 30;30(20):2253-64. doi: 10.1002/rcm.7711. [PubMed:27502354 ]
Zhang J, Kurita M, Ebina K, Ukiya M, Tokuda H, Yasukawa K, Masters ET, Shimizu N, Akihisa M, Feng F, Akihisa T: Melanogenesis-inhibitory activity and cancer chemopreventive effect of glucosylcucurbic acid from shea (Vitellaria paradoxa) kernels. Chem Biodivers. 2015 Apr;12(4):547-58. doi: 10.1002/cbdv.201400424. [PubMed:25879500 ]
Kramell R, Schmidt J, Herrmann G, Schliemann W: N-(jasmonoyl)tyrosine-derived compounds from flowers of broad beans (Vicia faba). J Nat Prod. 2005 Sep;68(9):1345-9. doi: 10.1021/np0501482. [PubMed:16180811 ]
Gan LJ, Xia K, Wang CL, Zhou X: [Preparation of a monoclonal antibody against methyl jasmonate and quantification of jasmonic acid in florets of wheat and Italian ryegrass]. Shi Yan Sheng Wu Xue Bao. 2004 Oct;37(5):359-66. [PubMed:15636363 ]
LOTUS database [Link]

Showing NP-Card for [(1r,2s,3s)-3-hydroxy-2-(pent-2-en-1-yl)cyclopentyl]acetic acid (NP0196373)

MOL for NP0196373 ([(1r,2s,3s)-3-hydroxy-2-(pent-2-en-1-yl)cyclopentyl]acetic acid)

3D MOL for NP0196373 ([(1r,2s,3s)-3-hydroxy-2-(pent-2-en-1-yl)cyclopentyl]acetic acid)

3D SDF for NP0196373 ([(1r,2s,3s)-3-hydroxy-2-(pent-2-en-1-yl)cyclopentyl]acetic acid)

3D-SDF for NP0196373 ([(1r,2s,3s)-3-hydroxy-2-(pent-2-en-1-yl)cyclopentyl]acetic acid)

PDB for NP0196373 ([(1r,2s,3s)-3-hydroxy-2-(pent-2-en-1-yl)cyclopentyl]acetic acid)

3D PDB for NP0196373 ([(1r,2s,3s)-3-hydroxy-2-(pent-2-en-1-yl)cyclopentyl]acetic acid)

SMILES for NP0196373 ([(1r,2s,3s)-3-hydroxy-2-(pent-2-en-1-yl)cyclopentyl]acetic acid)

INCHI for NP0196373 ([(1r,2s,3s)-3-hydroxy-2-(pent-2-en-1-yl)cyclopentyl]acetic acid)

Structure for NP0196373 ([(1r,2s,3s)-3-hydroxy-2-(pent-2-en-1-yl)cyclopentyl]acetic acid)

3D Structure for NP0196373 ([(1r,2s,3s)-3-hydroxy-2-(pent-2-en-1-yl)cyclopentyl]acetic acid)