NP-MRD: Showing NP-Card for [(1s,5r)-4-oxo-5-pentylcyclopent-2-en-1-yl]acetic acid (NP0330679)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

1.0

Created at

2022-09-12 16:15:32 UTC

Updated at

2022-09-12 16:15:32 UTC

NP-MRD ID

NP0330679

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(1s,5r)-4-oxo-5-pentylcyclopent-2-en-1-yl]acetic acid

Description

4,5-Didehydro-9,10-dihydrojasmonic acid belongs to the class of organic compounds known as cyclic ketones. These are organic compounds containing a ketone that is conjugated to a cyclic moiety. It was first documented in 2022 (PMID: 36130802). Based on a literature review a significant number of articles have been published on 4,5-Didehydro-9,10-dihydrojasmonic acid (PMID: 36130727) (PMID: 36130648) (PMID: 36130642) (PMID: 36130465) (PMID: 36130296) (PMID: 36130216).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 33  0  0  0  0  0  0  0  0999 V2000
   -4.1859   -0.0556    0.7473 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8095    0.3274   -0.6683 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3072    0.3387   -0.8582 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6830   -0.9762   -0.5864 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2034   -0.9248   -0.7825 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5141    0.0783    0.0991 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5087   -0.4085    1.4997 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2714   -0.0864    2.4230 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6193   -1.3556    1.5865 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4728   -1.1018    0.6093 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0052    0.0273   -0.2072 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7062    1.3206    0.1599 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1418    1.2125   -0.1529 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7954    0.2012    0.2377 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8487    2.1690   -0.8733 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0265   -1.1494    0.9226 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2736    0.1137    0.8506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6791    0.5797    1.5042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2058    1.3382   -0.8618 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2980   -0.3724   -1.3651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8688    1.0835   -0.1653 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0764    0.6538   -1.8889 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9669   -1.4083    0.4017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0935   -1.7084   -1.3431 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1225   -0.7549   -1.8183 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2605   -1.9295   -0.5065 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1360    1.1010    0.0088 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7100   -2.1362    2.3369 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4087   -1.6288    0.3903 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1081   -0.1838   -1.2930 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5284    1.5496    1.2305 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2857    2.1270   -0.4349 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7769    2.0341   -1.2023 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6 11  1  0
 11 12  1  0
 12 13  1  0
 13 15  1  0
 13 14  2  0
 11 10  1  0
 10  9  2  0
  9  7  1  0
  7  8  2  0
  7  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
  3 22  1  0
  4 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
  6 27  1  1
 11 30  1  6
 12 31  1  0
 12 32  1  0
 15 33  1  0
 10 29  1  0
  9 28  1  0
M  END


  Mrv1652309122218152D          

 15 15  0  0  1  0            999 V2000
   -0.6865   -2.4373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0280   -2.0248    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7425   -2.4373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4569   -2.0248    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1714   -2.4373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8859   -2.0248    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9721   -1.2043    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3590   -0.6523    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7791   -1.0328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1916   -1.7472    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6396   -2.3603    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8111   -3.1673    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5957   -3.4222    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2088   -2.8702    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7672   -4.2292    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
  4  5  1  0  0  0  0
  6  5  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  2  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>
NP0330679

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCC[C@@H]1[C@@H](CC(O)=O)C=CC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C12H18O3/c1-2-3-4-5-10-9(8-12(14)15)6-7-11(10)13/h6-7,9-10H,2-5,8H2,1H3,(H,14,15)/t9-,10-/m1/s1

> <INCHI_KEY>
MIIKBIRJDZKJEO-NXEZZACHSA-N

> <FORMULA>
C12H18O3

> <MOLECULAR_WEIGHT>
210.273

> <EXACT_MASS>
210.12559444

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
23.271120056310735

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[(1S,5R)-4-oxo-5-pentylcyclopent-2-en-1-yl]acetic acid

> <JCHEM_LOGP>
2.7740560240000005

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
18.051399689469015

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.709772283246733

> <JCHEM_PKA_STRONGEST_BASIC>
-4.997254822587072

> <JCHEM_POLAR_SURFACE_AREA>
54.370000000000005

> <JCHEM_REFRACTIVITY>
58.5332

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[(1S,5R)-4-oxo-5-pentylcyclopent-2-en-1-yl]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0      -1.281  -4.550   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.052  -3.780   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.386  -4.550   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.720  -3.780   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.053  -4.550   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.387  -3.780   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.548  -2.248   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.404  -1.218   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       7.054  -1.928   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.824  -3.262   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.794  -4.406   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.114  -5.912   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.579  -6.388   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       9.723  -5.358   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       8.899  -7.895   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
4,5-Didehydro-9,10-dihydrojasmonate	Generator

Chemical Formula

C₁₂H₁₈O₃

Average Mass

210.2730 Da

Monoisotopic Mass

210.12559 Da

IUPAC Name

2-[(1S,5R)-4-oxo-5-pentylcyclopent-2-en-1-yl]acetic acid

Traditional Name

[(1S,5R)-4-oxo-5-pentylcyclopent-2-en-1-yl]acetic acid

CAS Registry Number

Not Available

SMILES

CCCCC[C@@H]1[C@@H](CC(O)=O)C=CC1=O

InChI Identifier

InChI=1S/C12H18O3/c1-2-3-4-5-10-9(8-12(14)15)6-7-11(10)13/h6-7,9-10H,2-5,8H2,1H3,(H,14,15)/t9-,10-/m1/s1

InChI Key

MIIKBIRJDZKJEO-NXEZZACHSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclic ketones. These are organic compounds containing a ketone that is conjugated to a cyclic moiety.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Cyclic ketones

Alternative Parents

Substituents

Cyclic ketone
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxide
Hydrocarbon derivative
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	2.77	ChemAxon
pKa (Strongest Acidic)	4.71	ChemAxon
pKa (Strongest Basic)	-5	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	6	ChemAxon
Refractivity	58.53 m³·mol⁻¹	ChemAxon
Polarizability	23.27 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

Not Available

Chemspider ID

110564201

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101634567

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Ahmad A, Ghufran R: Microbial granules on reactors performance during organic butyrate digestion: clean production. Crit Rev Biotechnol. 2022 Sep 21:1-21. doi: 10.1080/07388551.2022.2103641. [PubMed:36130802 ]
Trimble JS, Crawshaw R, Hardy FJ, Levy CW, Brown MJB, Fuerst DE, Heyes DJ, Obexer R, Green AP: A Designed Photoenzyme for Enantioselective [2+2]-Cycloadditions. Nature. 2022 Sep 21. pii: 10.1038/s41586-022-05335-3. doi: 10.1038/s41586-022-05335-3. [PubMed:36130727 ]
Contursi A, Tacconelli S, Hofling U, Bruno A, Dovizio M, Ballerini P, Patrignani P: Biology and pharmacology of platelet-type 12-lipoxygenase in platelets, cancer cells, and their crosstalk. Biochem Pharmacol. 2022 Sep 18;205:115252. doi: 10.1016/j.bcp.2022.115252. [PubMed:36130648 ]
Brindisi M, Curcio M, Frattaruolo L, Cirillo G, Leggio A, Rago V, Nicoletta FP, Cappello AR, Iemma F: CD44-targeted nanoparticles with GSH-responsive activity as powerful therapeutic agents against breast cancer. Int J Biol Macromol. 2022 Sep 18;221:1491-1503. doi: 10.1016/j.ijbiomac.2022.09.157. [PubMed:36130642 ]
Grassi A, Cristani C, Palla M, Di Giorgi R, Giovannetti M, Agnolucci M: Storage time and temperature affect microbial dynamics of yeasts and acetic acid bacteria in a kombucha beverage. Int J Food Microbiol. 2022 Sep 16;382:109934. doi: 10.1016/j.ijfoodmicro.2022.109934. [PubMed:36130465 ]
Kerr BJ, Trachsel JM, Bearson BL, Loving CL, Bearson SMD, Byrne KA, Pearce SC, Ramirez SM, Gabler NK, Schweer WP, Helm ET, de Mille CM: Evaluation of digestively resistant or soluble fibers, short- and medium-chain fatty acids, trace minerals, and antibiotics in non-challenged nursery pigs on performance, digestibility, and intestinal integrity. J Anim Sci. 2022 Sep 21. pii: 6709322. doi: 10.1093/jas/skac282. [PubMed:36130296 ]
Seo B, Yang K, Kahe K, Qureshi AA, Chan AT, De Vivo I, Cho E, Giovannucci EL, Nan H: Association of omega-3 and omega-6 fatty acid intake with leukocyte telomere length in US males. Am J Clin Nutr. 2022 Sep 20. pii: 6708365. doi: 10.1093/ajcn/nqac263. [PubMed:36130216 ]
Smith LJ, Bolsinger MM, Chau KY, Gegg ME, Schapira AHV: The GBA variant E326K is associated with alpha-synuclein aggregation and lipid droplet accumulation in human cell lines. Hum Mol Genet. 2022 Sep 20. pii: 6708353. doi: 10.1093/hmg/ddac233. [PubMed:36130205 ]
Liu X, Zhang X, Khakhulin D, Su P, Wulff M, Baudelet F, Weng TC, Kong Q, Sun Y: Deciphering Photochemical Reaction Pathways of Aqueous Tetrachloroauric Acid by X-ray Transient Absorption Spectroscopy. J Phys Chem Lett. 2022 Sep 29;13(38):8921-8927. doi: 10.1021/acs.jpclett.2c02335. Epub 2022 Sep 21. [PubMed:36130195 ]
Zibako P, Tsikai N, Manyame S, Ginindza TG: Cervical cancer management in Zimbabwe (2019-2020). PLoS One. 2022 Sep 21;17(9):e0274884. doi: 10.1371/journal.pone.0274884. eCollection 2022. [PubMed:36129898 ]
LOTUS database [Link]

Showing NP-Card for [(1s,5r)-4-oxo-5-pentylcyclopent-2-en-1-yl]acetic acid (NP0330679)

MOL for NP0330679 ([(1s,5r)-4-oxo-5-pentylcyclopent-2-en-1-yl]acetic acid)

3D MOL for NP0330679 ([(1s,5r)-4-oxo-5-pentylcyclopent-2-en-1-yl]acetic acid)

3D SDF for NP0330679 ([(1s,5r)-4-oxo-5-pentylcyclopent-2-en-1-yl]acetic acid)

3D-SDF for NP0330679 ([(1s,5r)-4-oxo-5-pentylcyclopent-2-en-1-yl]acetic acid)

PDB for NP0330679 ([(1s,5r)-4-oxo-5-pentylcyclopent-2-en-1-yl]acetic acid)

3D PDB for NP0330679 ([(1s,5r)-4-oxo-5-pentylcyclopent-2-en-1-yl]acetic acid)

SMILES for NP0330679 ([(1s,5r)-4-oxo-5-pentylcyclopent-2-en-1-yl]acetic acid)

INCHI for NP0330679 ([(1s,5r)-4-oxo-5-pentylcyclopent-2-en-1-yl]acetic acid)

Structure for NP0330679 ([(1s,5r)-4-oxo-5-pentylcyclopent-2-en-1-yl]acetic acid)

3D Structure for NP0330679 ([(1s,5r)-4-oxo-5-pentylcyclopent-2-en-1-yl]acetic acid)