MiMeDB: Showing metabocard for (1S,2R)-3-oxo-2-(2Z-pentenyl)cyclopentane-1-butyric acid methyl ester (MMDBc0009922)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 02:17:23 UTC

Update Date

2025-10-07 16:05:40 UTC

Metabolite ID

MMDBc0009922

Metabolite Identification

Common Name

(1S,2R)-3-oxo-2-(2Z-pentenyl)cyclopentane-1-butyric acid methyl ester

Description

(1S,2R)-3-oxo-2-(2Z-pentenyl)cyclopentane-1-butyric acid methyl ester is a cyclopentane derivative and belongs to the class of fatty acid esters. There is limited literature available on this metabolite, indicating that further research may be necessary to fully understand its biological significance and potential applications.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152104172D          

 22 22  0  0  1  0            999 V2000
   -1.8655   -0.7791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9049    1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6502   -1.0341    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2633   -0.4820    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0917    0.3250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470    1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674    1.3099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3071    0.5799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7615    1.3099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4681    2.5429    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2751    2.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3819    1.7224    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1356    1.3869    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6876    2.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4760    1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5081    1.9137    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4760    2.5474    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1904    1.3099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0479   -0.7370    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7048    0.8770    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4251    0.8986    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9325    1.1733    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  2  0  0  0  0
  7  6  1  0  0  0  0
  8  5  1  0  0  0  0
  9  6  1  0  0  0  0
 11 10  1  0  0  0  0
 12  7  1  6  0  0  0
 12 10  1  0  0  0  0
 13  8  1  1  0  0  0
 13 12  1  0  0  0  0
 14 11  1  0  0  0  0
 14 13  1  0  0  0  0
 15  9  1  0  0  0  0
 16 14  2  0  0  0  0
 17 15  2  0  0  0  0
 18  2  1  0  0  0  0
 18 15  1  0  0  0  0
 19  4  1  0  0  0  0
 20  5  1  0  0  0  0
 12 21  1  1  0  0  0
 13 22  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0009922

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C(CC)=C(/[H])C[C@@]1([H])C(=O)CC[C@]1([H])CCCC(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C15H24O3/c1-3-4-5-8-13-12(10-11-14(13)16)7-6-9-15(17)18-2/h4-5,12-13H,3,6-11H2,1-2H3/b5-4-/t12-,13+/m0/s1

> <INCHI_KEY>
NFKJKGVJZFWDKI-OEFFGFFESA-N

> <FORMULA>
C15H24O3

> <MOLECULAR_WEIGHT>
252.354

> <EXACT_MASS>
252.172544633

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
29.222185687639314

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl 4-[(1S,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl]butanoate

> <ALOGPS_LOGP>
3.58

> <JCHEM_LOGP>
3.449342263666666

> <ALOGPS_LOGS>
-3.90

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.877910125248225

> <JCHEM_POLAR_SURFACE_AREA>
43.370000000000005

> <JCHEM_REFRACTIVITY>
72.52759999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.17e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl 4-[(1S,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl]butanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0      -3.482  -1.454   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.423   3.215   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.947  -1.930   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -6.091  -0.900   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.771   0.607   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.088   3.215   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.246   2.445   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.307   1.082   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.421   2.445   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.741   4.747   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -4.247   5.067   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.580   3.215   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -3.986   2.589   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -5.017   3.733   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.755   3.215   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -6.548   3.572   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       2.755   4.755   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       4.089   2.445   0.000  0.00  0.00           O+0
HETATM   19  H   UNK     0      -7.556  -1.376   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0      -6.916   1.637   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0      -2.660   1.677   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0      -5.474   2.190   0.000  0.00  0.00           H+0
CONECT    1    3                                                            
CONECT    2   18                                                            
CONECT    3    1    4                                                       
CONECT    4    3    5   19                                                  
CONECT    5    4    8   20                                                  
CONECT    6    7    9                                                       
CONECT    7    6   12                                                       
CONECT    8    5   13                                                       
CONECT    9    6   15                                                       
CONECT   10   11   12                                                       
CONECT   11   10   14                                                       
CONECT   12    7   10   13   21                                             
CONECT   13    8   12   14   22                                             
CONECT   14   11   13   16                                                  
CONECT   15    9   17   18                                                  
CONECT   16   14                                                            
CONECT   17   15                                                            
CONECT   18    2   15                                                       
CONECT   19    4                                                            
CONECT   20    5                                                            
CONECT   21   12                                                            
CONECT   22   13                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

Synonyms

Value	Source
(1S,2R)-3-oxo-2-(2Z-Pentenyl)cyclopentane-1-butyrate methyl ester	Generator

Molecular Formula

C₁₅H₂₄O₃

Average Mass

252.354

Monoisotopic Mass

252.172544633

IUPAC Name

methyl 4-[(1S,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl]butanoate

Traditional Name

methyl 4-[(1S,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl]butanoate

CAS Registry Number

Not Available

SMILES

[H]\C(CC)=C(/[H])C[C@@]1([H])C(=O)CC[C@]1([H])CCCC(=O)OC

InChI Identifier

InChI=1S/C15H24O3/c1-3-4-5-8-13-12(10-11-14(13)16)7-6-9-15(17)18-2/h4-5,12-13H,3,6-11H2,1-2H3/b5-4-/t12-,13+/m0/s1

InChI Key

NFKJKGVJZFWDKI-OEFFGFFESA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as fatty acid methyl esters. Fatty acid methyl esters are compounds containing a fatty acid that is esterified with a methyl group. They have the general structure RC(=O)OR', where R=fatty aliphatic tail or organyl group and R'=methyl group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acid esters

Direct Parent

Fatty acid methyl esters

Alternative Parents

Substituents

Fatty acid methyl ester
Methyl ester
Cyclic ketone
Ketone
Carboxylic acid ester
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.032 g/L	ALOGPS
logP	3.58	ALOGPS
logP	3.45	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Basic)	-6.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	43.37 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	72.53 m³·mol⁻¹	ChemAxon
Polarizability	29.22 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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-10	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum

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)	2025-10-23	200.7
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (void)	2025-10-23	26.6
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	506.7
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	637.3
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	693.2
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-23	469.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	2669.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	80.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	423.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	645.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	397.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	260.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	202.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (void)	2025-10-23	8.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	357.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	371.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	407.5
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	1462.6
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	1525.6

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	(1S,2R)-3-oxo-2-(2Z-pentenyl)cyclopentane-1-butyric acid methyl ester_TMS_1	CC/C=C\CC1=C(O[Si](C)(C)C)CC[C@@H]1CCCC(=O)OC	standard non polar	2025-10-23	1721.0
Gas Chromatography	(1S,2R)-3-oxo-2-(2Z-pentenyl)cyclopentane-1-butyric acid methyl ester_TMS_2	CC/C=C\C[C@H]1C(O[Si](C)(C)C)=CC[C@@H]1CCCC(=O)OC	standard non polar	2025-10-23	2381.09
Gas Chromatography	(1S,2R)-3-oxo-2-(2Z-pentenyl)cyclopentane-1-butyric acid methyl ester_TMS_1	CC/C=C\CC1=C(O[Si](C)(C)C)CC[C@@H]1CCCC(=O)OC	standard polar	2025-10-23	2234.93
Gas Chromatography	(1S,2R)-3-oxo-2-(2Z-pentenyl)cyclopentane-1-butyric acid methyl ester_TMS_2	CC/C=C\C[C@H]1C(O[Si](C)(C)C)=CC[C@@H]1CCCC(=O)OC	standard polar	2025-10-23	1888.47

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	Microbial Links
Eukaryota/Fungi	Ascomycota	1	Human feces	Metabolic reconstruction

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

8928647

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10753324

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for (1S,2R)-3-oxo-2-(2Z-pentenyl)cyclopentane-1-butyric acid methyl ester (MMDBc0009922)

MOL for #<Metabolite:0x00007f2dc8364b90>

3D MOL for #<Metabolite:0x00007f2dc8364b90>

3D SDF for #<Metabolite:0x00007f2dc8364b90>

3D-SDF for #<Metabolite:0x00007f2dc8364b90>

PDB for #<Metabolite:0x00007f2dc8364b90>

3D PDB for #<Metabolite:0x00007f2dc8364b90>

SMILES for #<Metabolite:0x00007f2dc8364b90>

INCHI for #<Metabolite:0x00007f2dc8364b90>

Structure for #<Metabolite:0x00007f2dc8364b90>

3D Structure for #<Metabolite:0x00007f2dc8364b90>