MiMeDB: Showing metabocard for Methylenolactocin (MMDBc0014667)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 05:38:59 UTC

Update Date

2025-10-07 16:06:18 UTC

Metabolite ID

MMDBc0014667

Metabolite Identification

Common Name

Methylenolactocin

Description

Methylenolactocin is a γ-butyrolactone class compound and a metabolite described in biomedical literature. Its synthesis has been explored through various methodologies, showcasing its potential utility in organic chemistry. For instance, the formal synthesis of (+)-methylenolactocin was demonstrated, highlighting its accessibility for research applications (PMID:36861961 ). Additionally, a protecting-group-free synthesis method has been reported, which includes methylenolactocin among other compounds (PMID:27995236 ). The compound's synthetic utility is further emphasized by enantioselective synthesis techniques, achieving high enantiomeric excesses through kinetic enzymatic resolutions (PMID:25581906 ). Furthermore, innovative approaches such as polar radical crossover cycloaddition reactions have enabled the diastereoselective synthesis of methylenolactocin (PMID:25190259 ). Its relevance is underscored by its association with biologically significant paraconic acids, which possess antibiotic and antitumor properties, indicating potential therapeutic applications (PMID:12506382 ). Overall, methylenolactocin represents a significant target for synthetic chemists and biologists alike, given its intricate synthesis pathways and biological implications.

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004231521502D          

 15 15  0  0  0  0            999 V2000
    0.6725   -1.9957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3870   -2.4082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1015   -1.9957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8159   -2.4082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5304   -1.9957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2449   -2.4082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9986   -2.0727    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5506   -2.6857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3711   -2.5995    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1381   -3.4002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4736   -4.1539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3311   -3.2287    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7180   -3.7807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9334   -3.5258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8896   -4.5877    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
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  6 12  1  0  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>
MMDBc0014667

> <DATABASE_NAME>
MIME

> <SMILES>
CCCCCC1OC(=O)C(=C)C1C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H16O4/c1-3-4-5-6-8-9(10(12)13)7(2)11(14)15-8/h8-9H,2-6H2,1H3,(H,12,13)

> <INCHI_KEY>
YZCRACGZKLIGLZ-UHFFFAOYSA-N

> <FORMULA>
C11H16O4

> <MOLECULAR_WEIGHT>
212.245

> <EXACT_MASS>
212.104858995

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
22.564535078897215

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-methylidene-5-oxo-2-pentyloxolane-3-carboxylic acid

> <ALOGPS_LOGP>
2.55

> <JCHEM_LOGP>
2.485647676333333

> <ALOGPS_LOGS>
-2.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
18.008225671198478

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.314610833269499

> <JCHEM_PKA_STRONGEST_BASIC>
-6.890480411760126

> <JCHEM_POLAR_SURFACE_AREA>
63.60000000000001

> <JCHEM_REFRACTIVITY>
53.517700000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.89e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-methylidene-5-oxo-2-pentyloxolane-3-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-APR-15         0                                  
HETATM    1  C   UNK     0       1.255  -3.725   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.589  -4.495   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.923  -3.725   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.256  -4.495   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.590  -3.725   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.924  -4.495   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       9.331  -3.869   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      10.361  -5.013   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      11.893  -4.852   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       9.591  -6.347   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.217  -7.754   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.085  -6.027   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.940  -7.057   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       5.476  -6.581   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       7.260  -8.564   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   12                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    6   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

Synonyms

Value	Source
4-Methylidene-5-oxo-2-pentyloxolane-3-carboxylate	Generator
3-Carboxy-2-methylene-4-nonanolide	MeSH

Molecular Formula

C₁₁H₁₆O₄

Average Mass

212.245

Monoisotopic Mass

212.104858995

IUPAC Name

4-methylidene-5-oxo-2-pentyloxolane-3-carboxylic acid

Traditional Name

4-methylidene-5-oxo-2-pentyloxolane-3-carboxylic acid

CAS Registry Number

Not Available

SMILES

CCCCCC1OC(=O)C(=C)C1C(O)=O

InChI Identifier

InChI=1S/C11H16O4/c1-3-4-5-6-8-9(10(12)13)7(2)11(14)15-8/h8-9H,2-6H2,1H3,(H,12,13)

InChI Key

YZCRACGZKLIGLZ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Lactones

Sub Class

Gamma butyrolactones

Direct Parent

Gamma butyrolactones

Alternative Parents

Substituents

Gamma butyrolactone
Dicarboxylic acid or derivatives
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Tetrahydrofuran
Carboxylic acid ester
Oxacycle
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	1.89 g/L	ALOGPS
logP	2.55	ALOGPS
logP	2.49	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	4.31	ChemAxon
pKa (Strongest Basic)	-6.9	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	63.6 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	53.52 m³·mol⁻¹	ChemAxon
Polarizability	22.56 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

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 (void)	2025-10-23	125.8
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (void)	2025-10-23	29.1
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	452.4
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	647.6
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	516.9
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	383.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	2100.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	91.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	488.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	450.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	327.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	219.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	149.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	76.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	459.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	226.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	404.4
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	1402.2
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	1132.8

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	Methylenolactocin_TMS_1	C=C1C(=O)OC(CCCCC)C1C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	1424.38
Gas Chromatography	Methylenolactocin_TMS_1	C=C1C(=O)OC(CCCCC)C1C(=O)O[Si](C)(C)C	standard polar	2025-10-23	1980.45

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

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

363541

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 Methylenolactocin (MMDBc0014667)

MOL for #<Metabolite:0x00007f9aad662b10>

3D MOL for #<Metabolite:0x00007f9aad662b10>

3D SDF for #<Metabolite:0x00007f9aad662b10>

3D-SDF for #<Metabolite:0x00007f9aad662b10>

PDB for #<Metabolite:0x00007f9aad662b10>

3D PDB for #<Metabolite:0x00007f9aad662b10>

SMILES for #<Metabolite:0x00007f9aad662b10>

INCHI for #<Metabolite:0x00007f9aad662b10>

Structure for #<Metabolite:0x00007f9aad662b10>

3D Structure for #<Metabolite:0x00007f9aad662b10>