MiMeDB: Showing metabocard for Pentalenolactone F (MMDBc0020969)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 11:06:38 UTC

Update Date

2025-10-07 16:07:08 UTC

Metabolite ID

MMDBc0020969

Metabolite Identification

Common Name

Pentalenolactone F

Description

Pentalenolactone F is a sesquiterpenoid, a class of terpenes consisting of three isoprene units. It is an advanced intermediate in the biosynthetic pathway leading to the antibiotic pentalenolactone. The conversion of pentalenolactone F to pentalenolactone involves a cytochrome P450-catalyzed oxidative rearrangement, which is characterized by the stereospecific removal of hydrogen and the migration of a methyl group, as well as the formation and rearrangement of a neopentyl cation (PMID:29999312 ). This transformation highlights the complexity of the chemical reactions involved in sesquiterpenoid biosynthesis. Additionally, studies have shown that the enzyme PntM interacts specifically with pentalenolactone F, demonstrating unique binding characteristics compared to other P450 enzymes (PMID:27588339 ). The accumulation of pentalenolactone F has been observed in mutants lacking certain biosynthetic genes, indicating its role as a precursor in the production of pentalenolactone (PMID:21284395 ). Furthermore, pentalenolactone F can be generated through the Fe(2+)-α-ketoglutarate-dependent oxidation of pentalenolactone D, showcasing its place within a broader metabolic framework (PMID:21250661 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152113062D          

 22 25  0  0  1  0            999 V2000
    2.5123   -1.1775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0062   -0.1901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0752   -0.0874    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4786   -0.7895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8801    1.9049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0758    0.4044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8538    0.5392    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8910   -0.2104    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0599    0.7265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6724    1.1064    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7977    1.0956    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2630    1.5453    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2109   -0.4095    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2601    0.5274    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0554    0.7468    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4863    0.6412    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8470    1.9191    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0583    1.7647    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6753    2.1243    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2748   -0.0485    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5219   -0.9483    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4677    1.3258    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  3  1  0  0  0  0
  8  4  1  0  0  0  0
  9  3  2  0  0  0  0
 10  5  1  0  0  0  0
 10  9  1  0  0  0  0
 11  9  1  0  0  0  0
 13  1  1  0  0  0  0
 13  2  1  0  0  0  0
 13  4  1  0  0  0  0
 13  6  1  0  0  0  0
 14  6  1  6  0  0  0
 14  8  1  0  0  0  0
 14 10  1  0  0  0  0
 15  7  1  0  0  0  0
 15 12  1  0  0  0  0
 15 14  1  0  0  0  0
 16 11  2  0  0  0  0
 17 11  1  0  0  0  0
 18 12  2  0  0  0  0
 19  5  1  0  0  0  0
 19 12  1  0  0  0  0
 20  7  1  0  0  0  0
 15 20  1  1  0  0  0
  8 21  1  1  0  0  0
 10 22  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0020969

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]12CC(C)(C)C[C@@]11[C@@]([H])(COC(=O)[C@]11CO1)C(=C2)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H18O5/c1-13(2)4-8-3-9(11(16)17)10-5-19-12(18)15(7-20-15)14(8,10)6-13/h3,8,10H,4-7H2,1-2H3,(H,16,17)/t8-,10-,14-,15+/m0/s1

> <INCHI_KEY>
UUDKOVSZNMZKND-VUBPOPHZSA-N

> <FORMULA>
C15H18O5

> <MOLECULAR_WEIGHT>
278.304

> <EXACT_MASS>
278.11542368

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
27.71232481712775

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1'S,2R,5'R,8'R)-3',3'-dimethyl-11'-oxo-10'-oxaspiro[oxirane-2,12'-tricyclo[6.4.0.0^{1,5}]dodecan]-6'-ene-7'-carboxylic acid

> <ALOGPS_LOGP>
1.63

> <JCHEM_LOGP>
1.2874630956666662

> <ALOGPS_LOGS>
-2.20

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.271231946873091

> <JCHEM_PKA_STRONGEST_BASIC>
-4.281608883396899

> <JCHEM_POLAR_SURFACE_AREA>
76.13

> <JCHEM_REFRACTIVITY>
68.7752

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.74e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1'S,2R,5'R,8'R)-3',3'-dimethyl-11'-oxo-10'-oxaspiro[oxirane-2,12'-tricyclo[6.4.0.0^{1,5}]dodecan]-6'-ene-7'-carboxylic acid

> <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       4.690  -2.198   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.612  -0.355   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.140  -0.163   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.760  -1.474   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.643   3.556   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.875   0.755   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.327   1.006   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.663  -0.393   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.112   1.356   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.255   2.065   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.489   2.045   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.224   2.884   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.127  -0.764   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.352   0.984   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.837   1.394   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -2.774   1.197   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -1.581   3.582   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       5.709   3.294   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       3.127   3.965   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       4.246  -0.090   0.000  0.00  0.00           O+0
HETATM   21  H   UNK     0       0.974  -1.770   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       2.740   2.475   0.000  0.00  0.00           H+0
CONECT    1   13                                                            
CONECT    2   13                                                            
CONECT    3    8    9                                                       
CONECT    4    8   13                                                       
CONECT    5   10   19                                                       
CONECT    6   13   14                                                       
CONECT    7   15   20                                                       
CONECT    8    3    4   14   21                                             
CONECT    9    3   10   11                                                  
CONECT   10    5    9   14   22                                             
CONECT   11    9   16   17                                                  
CONECT   12   15   18   19                                                  
CONECT   13    1    2    4    6                                             
CONECT   14    6    8   10   15                                             
CONECT   15    7   12   14   20                                             
CONECT   16   11                                                            
CONECT   17   11                                                            
CONECT   18   12                                                            
CONECT   19    5   12                                                       
CONECT   20    7   15                                                       
CONECT   21    8                                                            
CONECT   22   10                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   50    0
END

Synonyms

Value	Source
(1's,2R,5'r,8'r)-3',3'-Dimethyl-11'-oxo-10'-oxaspiro[oxirane-2,12'-tricyclo[6.4.0.0,]dodecan]-6'-ene-7'-carboxylate	Generator

Molecular Formula

C₁₅H₁₈O₅

Average Mass

278.304

Monoisotopic Mass

278.11542368

IUPAC Name

(1'S,2R,5'R,8'R)-3',3'-dimethyl-11'-oxo-10'-oxaspiro[oxirane-2,12'-tricyclo[6.4.0.0^{1,5}]dodecan]-6'-ene-7'-carboxylic acid

Traditional Name

(1'S,2R,5'R,8'R)-3',3'-dimethyl-11'-oxo-10'-oxaspiro[oxirane-2,12'-tricyclo[6.4.0.0^{1,5}]dodecan]-6'-ene-7'-carboxylic acid

CAS Registry Number

Not Available

SMILES

[H][C@]12CC(C)(C)C[C@@]11[C@@]([H])(COC(=O)[C@]11CO1)C(=C2)C(O)=O

InChI Identifier

InChI=1S/C15H18O5/c1-13(2)4-8-3-9(11(16)17)10-5-19-12(18)15(7-20-15)14(8,10)6-13/h3,8,10H,4-7H2,1-2H3,(H,16,17)/t8-,10-,14-,15+/m0/s1

InChI Key

UUDKOVSZNMZKND-VUBPOPHZSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as delta valerolactones. These are cyclic organic compounds containing an oxan-2- one moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Lactones

Sub Class

Delta valerolactones

Direct Parent

Delta valerolactones

Alternative Parents

Substituents

Delta_valerolactone
Delta valerolactone
Oxane
Dicarboxylic acid or derivatives
Carboxylic acid ester
Oxacycle
Ether
Oxirane
Dialkyl ether
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	1.74 g/L	ALOGPS
logP	1.63	ALOGPS
logP	1.29	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	4.27	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	76.13 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	68.78 m³·mol⁻¹	ChemAxon
Polarizability	27.71 Å³	ChemAxon
Number of Rings	4	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

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
MMDBr0024930	di-mu-Sulfido-diiron(1+)	di-mu-Sulfido-diiron(2+)	Pentalenolactone synthase	Synthesis	RHEA	34755880

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
Bacteria	Actinobacteria	3		Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	1		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

78443060

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139589061

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for Pentalenolactone F (MMDBc0020969)

MOL for #<Metabolite:0x00007f8de9186c98>

3D MOL for #<Metabolite:0x00007f8de9186c98>

3D SDF for #<Metabolite:0x00007f8de9186c98>

3D-SDF for #<Metabolite:0x00007f8de9186c98>

PDB for #<Metabolite:0x00007f8de9186c98>

3D PDB for #<Metabolite:0x00007f8de9186c98>

SMILES for #<Metabolite:0x00007f8de9186c98>

INCHI for #<Metabolite:0x00007f8de9186c98>

Structure for #<Metabolite:0x00007f8de9186c98>

3D Structure for #<Metabolite:0x00007f8de9186c98>