MiMeDB: Showing metabocard for Pentalenolactone D (MMDBc0016964)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 07:27:44 UTC

Update Date

2025-10-07 16:06:36 UTC

Metabolite ID

MMDBc0016964

Metabolite Identification

Common Name

Pentalenolactone D

Description

Pentalenolactone D is a member of the chemical class of lactones, specifically a cyclic ester derived from pentalenic acid. Its biosynthesis involves the flavin-dependent Baeyer-Villiger oxidation of 1-deoxy-11-oxopentalenic acid, catalyzed by enzymes from various Streptomyces species, including Streptomyces arenae and Streptomyces avermitilis (PMID:27933799 ). This reaction results in the migration of a methylene carbon to form pentalenolactone D. Additionally, pentalenolactone D serves as a substrate for further enzymatic transformations, being oxidized to pentalenolactone E and F by recombinant enzymes such as PenD, PntD, and PtlD (PMID:21250661 ). The compound is also involved in the production pathways of neopentalenolactone D, which represents a new branch of the pentalenolactone biosynthetic pathway (PMID:19485417 ). The structural characterization of neopentalenolactone D has been achieved through techniques like GC-MS, NMR, and X-ray crystallography (PMID:19485417 ). Thus, pentalenolactone D plays a crucial role in the complex biosynthetic network of pentalenolactones, contributing to the diversity of metabolites produced by these actinobacteria.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152109272D          

 22 24  0  0  1  0            999 V2000
    1.6629   -1.3325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3327   -1.0932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2768   -1.6655    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6167    1.2475    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8032   -0.0944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5372    0.2839    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9447   -0.7864    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2877   -0.7937    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4280    0.4444    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4389    1.3162    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7582    0.5555    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8666    2.0217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0667   -1.0654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1226   -0.8551    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1335    0.0167    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4694    2.7448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6914    2.0040    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2209   -1.8759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6915   -0.5266    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9125   -0.2549    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7225    0.8721    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3233    1.1567    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  1  1  6  0  0  0
  9  4  1  0  0  0  0
  9  5  1  0  0  0  0
 10  4  2  0  0  0  0
 11  6  1  0  0  0  0
 11 10  1  0  0  0  0
 12 10  1  0  0  0  0
 13  8  1  0  0  0  0
 14  2  1  0  0  0  0
 14  3  1  0  0  0  0
 14  5  1  0  0  0  0
 14  7  1  0  0  0  0
 15  7  1  1  0  0  0
 15  8  1  0  0  0  0
 15  9  1  0  0  0  0
 15 11  1  0  0  0  0
 16 12  2  0  0  0  0
 17 12  1  0  0  0  0
 18 13  2  0  0  0  0
 19  6  1  0  0  0  0
 19 13  1  0  0  0  0
  8 20  1  6  0  0  0
  9 21  1  6  0  0  0
 11 22  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0016964

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]12CC(C)(C)C[C@]11[C@@]([H])(COC(=O)[C@@]1([H])C)C(=C2)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H20O4/c1-8-13(18)19-6-11-10(12(16)17)4-9-5-14(2,3)7-15(8,9)11/h4,8-9,11H,5-7H2,1-3H3,(H,16,17)/t8-,9-,11+,15-/m1/s1

> <INCHI_KEY>
MRLXXQBBRNRWDA-LIEMUPCESA-N

> <FORMULA>
C15H20O4

> <MOLECULAR_WEIGHT>
264.321

> <EXACT_MASS>
264.136159124

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
27.68763375262794

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,5S,8R,12S)-3,3,12-trimethyl-11-oxo-10-oxatricyclo[6.4.0.0^{1,5}]dodec-6-ene-7-carboxylic acid

> <ALOGPS_LOGP>
2.55

> <JCHEM_LOGP>
1.9980483429999998

> <ALOGPS_LOGS>
-2.65

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.511338521755116

> <JCHEM_PKA_STRONGEST_BASIC>
-7.076596611239839

> <JCHEM_POLAR_SURFACE_AREA>
63.599999999999994

> <JCHEM_REFRACTIVITY>
69.2646

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.98e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,5S,8R,12S)-3,3,12-trimethyl-11-oxo-10-oxatricyclo[6.4.0.0^{1,5}]dodec-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       3.104  -2.487   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.621  -2.041   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.383  -3.109   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.018   2.329   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.499  -0.176   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.603   0.530   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.630  -1.468   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.270  -1.482   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.666   0.830   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.553   2.457   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.149   1.037   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.351   3.774   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.725  -1.989   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.096  -1.596   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.982   0.031   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       4.610   5.124   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       6.891   3.741   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       6.012  -3.502   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       6.891  -0.983   0.000  0.00  0.00           O+0
HETATM   20  H   UNK     0       5.437  -0.476   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       1.349   1.628   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       6.203   2.159   0.000  0.00  0.00           H+0
CONECT    1    8                                                            
CONECT    2   14                                                            
CONECT    3   14                                                            
CONECT    4    9   10                                                       
CONECT    5    9   14                                                       
CONECT    6   11   19                                                       
CONECT    7   14   15                                                       
CONECT    8    1   13   15   20                                             
CONECT    9    4    5   15   21                                             
CONECT   10    4   11   12                                                  
CONECT   11    6   10   15   22                                             
CONECT   12   10   16   17                                                  
CONECT   13    8   18   19                                                  
CONECT   14    2    3    5    7                                             
CONECT   15    7    8    9   11                                             
CONECT   16   12                                                            
CONECT   17   12                                                            
CONECT   18   13                                                            
CONECT   19    6   13                                                       
CONECT   20    8                                                            
CONECT   21    9                                                            
CONECT   22   11                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

Synonyms

Not Available

Molecular Formula

C₁₅H₂₀O₄

Average Mass

264.321

Monoisotopic Mass

264.136159124

IUPAC Name

(1R,5S,8R,12S)-3,3,12-trimethyl-11-oxo-10-oxatricyclo[6.4.0.0^{1,5}]dodec-6-ene-7-carboxylic acid

Traditional Name

(1R,5S,8R,12S)-3,3,12-trimethyl-11-oxo-10-oxatricyclo[6.4.0.0^{1,5}]dodec-6-ene-7-carboxylic acid

CAS Registry Number

Not Available

SMILES

[H][C@@]12CC(C)(C)C[C@]11[C@@]([H])(COC(=O)[C@@]1([H])C)C(=C2)C(O)=O

InChI Identifier

InChI=1S/C15H20O4/c1-8-13(18)19-6-11-10(12(16)17)4-9-5-14(2,3)7-15(8,9)11/h4,8-9,11H,5-7H2,1-3H3,(H,16,17)/t8-,9-,11+,15-/m1/s1

InChI Key

MRLXXQBBRNRWDA-LIEMUPCESA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Terpene lactones

Alternative Parents

Substituents

Terpene lactone
Iridoid-skeleton
Monoterpenoid
Delta valerolactone
Delta_valerolactone
Dicarboxylic acid or derivatives
Oxane
Carboxylic acid ester
Lactone
Oxacycle
Carboxylic acid
Carboxylic acid derivative
Organoheterocyclic compound
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organooxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

organic heterotricyclic compound (CHEBI:70805 )
alpha,beta-unsaturated monocarboxylic acid (CHEBI:70805 )
sesquiterpene lactone (CHEBI:70805 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.6 g/L	ALOGPS
logP	2.55	ALOGPS
logP	2	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	4.51	ChemAxon
pKa (Strongest Basic)	-7.1	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	1	ChemAxon
Refractivity	69.26 m³·mol⁻¹	ChemAxon
Polarizability	27.69 Å³	ChemAxon
Number of Rings	3	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

This table shows at most 5 pathways. For the full list of associated pathways:

See All Associated Bacterial Pathways

Name	SMPDB/PathBank	Species

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
Bacteria	Actinobacteria	3	Human	Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	1	Human	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

28533315

KEGG Compound ID

C20399

BioCyc ID

CPD-13621

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

15127669

PDB ID

Not Available

ChEBI ID

70805

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

References

Synthesis Reference

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 D (MMDBc0016964)

MOL for #<Metabolite:0x00007fb4d35b7dd8>

3D MOL for #<Metabolite:0x00007fb4d35b7dd8>

3D SDF for #<Metabolite:0x00007fb4d35b7dd8>

3D-SDF for #<Metabolite:0x00007fb4d35b7dd8>

PDB for #<Metabolite:0x00007fb4d35b7dd8>

3D PDB for #<Metabolite:0x00007fb4d35b7dd8>

SMILES for #<Metabolite:0x00007fb4d35b7dd8>

INCHI for #<Metabolite:0x00007fb4d35b7dd8>

Structure for #<Metabolite:0x00007fb4d35b7dd8>

3D Structure for #<Metabolite:0x00007fb4d35b7dd8>