MiMeDB: Showing metabocard for neopentalenolactone D (MMDBc0056213)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:19:42 UTC

Update Date

2025-10-07 16:09:39 UTC

Metabolite ID

MMDBc0056213

Metabolite Identification

Common Name

neopentalenolactone D

Description

Neopentalenolactone D is a member of the chemical class of lactones, specifically a metabolite involved in the biosynthetic pathways of pentalenolactones. Its structure is characterized by a unique arrangement of carbon atoms resulting from the oxidation of 4, as catalyzed by avermitilis, which leads to a migration of more substituted methane groups (PMID:27933799 ). This compound has been shown to be produced through the Baeyer-Villiger oxidation of 1-deoxy-11-oxopentalenic acid when incubated with the recombinant PtlE protein from Streptomyces avermitilis in the presence of NADPH and catalytic FAD, indicating its role in a new branch of the pentalenolactone biosynthetic pathway (PMID:19485417 ). Furthermore, structural analysis of neopentalenolactone D methyl ester has been conducted using GC-MS, NMR, and X-ray crystallography, confirming its stereochemistry (PMID:19485417 ). Additionally, incubation of neopentalenolactone D with various enzymes has yielded other compounds, such as PL308 and neopentalenolactone E, highlighting its involvement in complex metabolic processes (PMID:21250661 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222192D          

 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
    3.5372    0.2839    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
    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  1  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
    3.6915   -0.5266    0.0000 C   0  0  0  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
    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
    4.4704   -0.7983    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
    2.4694    2.7448    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.0667   -1.0654    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  6  1  0  0  0  0
 10  4  2  0  0  0  0
 11  5  1  0  0  0  0
 11 10  1  0  0  0  0
 12  5  1  0  0  0  0
 13 10  1  0  0  0  0
 14  2  1  0  0  0  0
 14  3  1  0  0  0  0
 14  6  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 13  2  0  0  0  0
 18 13  1  0  0  0  0
 19  8  1  0  0  0  0
 19 12  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  CHG  1  18  -1
M  END
> <DATABASE_ID>
MMDBc0056213

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C15H20O4/c1-8-15-7-14(2,3)6-9(15)4-10(13(17)18)11(15)5-12(16)19-8/h4,8-9,11H,5-7H2,1-3H3,(H,17,18)/p-1/t8-,9+,11-,15+/m0/s1

> <INCHI_KEY>
ZMLAXRVFMBEJIF-GCTGHDABSA-M

> <FORMULA>
C15H19O4

> <MOLECULAR_WEIGHT>
263.314

> <EXACT_MASS>
263.128882672

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
27.187870985874653

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
1

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

> <JCHEM_LOGP>
1.9495908193333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.515499456469595

> <JCHEM_PKA_STRONGEST_BASIC>
-7.049216781510163

> <JCHEM_POLAR_SURFACE_AREA>
66.43

> <JCHEM_REFRACTIVITY>
79.86900000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         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       6.603   0.530   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.499  -0.176   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       6.891  -0.983   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.351   3.774   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       8.345  -1.490   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       4.610   5.124   0.000  0.00  0.00           O-1
HETATM   19  O   UNK     0       5.725  -1.989   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   11   12                                                       
CONECT    6    9   14                                                       
CONECT    7   14   15                                                       
CONECT    8    1   15   19   20                                             
CONECT    9    4    6   15   21                                             
CONECT   10    4   11   13                                                  
CONECT   11    5   10   15   22                                             
CONECT   12    5   16   19                                                  
CONECT   13   10   17   18                                                  
CONECT   14    2    3    6    7                                             
CONECT   15    7    8    9   11                                             
CONECT   16   12                                                            
CONECT   17   13                                                            
CONECT   18   13                                                            
CONECT   19    8   12                                                       
CONECT   20    8                                                            
CONECT   21    9                                                            
CONECT   22   11                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

Synonyms

Value	Source
Neopentalenolactone D	ChEBI

Molecular Formula

C₁₅H₁₉O₄

Average Mass

263.314

Monoisotopic Mass

263.128882672

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C15H20O4/c1-8-15-7-14(2,3)6-9(15)4-10(13(17)18)11(15)5-12(16)19-8/h4,8-9,11H,5-7H2,1-3H3,(H,17,18)/p-1/t8-,9+,11-,15+/m0/s1

InChI Key

ZMLAXRVFMBEJIF-GCTGHDABSA-M

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
Oxane
Dicarboxylic acid or derivatives
Lactone
Carboxylic acid ester
Carboxylic acid
Carboxylic acid derivative
Organoheterocyclic compound
Oxacycle
Hydrocarbon derivative
Organooxygen compound
Organic oxide
Carbonyl group
Organic oxygen compound
Organic anion
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

monocarboxylic acid anion (CHEBI:70859 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	1.95	ChemAxon
pKa (Strongest Acidic)	4.52	ChemAxon
pKa (Strongest Basic)	-7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	66.43 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	79.87 m³·mol⁻¹	ChemAxon
Polarizability	27.19 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

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

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

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/Eubacteria	Actinobacteria	1

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

28533335

KEGG Compound ID

Not Available

BioCyc ID

CPD-13623

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

70679217

PDB ID

Not Available

ChEBI ID

70859

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 neopentalenolactone D (MMDBc0056213)

MOL for #<Metabolite:0x0000561537e6e130>

3D MOL for #<Metabolite:0x0000561537e6e130>

3D SDF for #<Metabolite:0x0000561537e6e130>

3D-SDF for #<Metabolite:0x0000561537e6e130>

PDB for #<Metabolite:0x0000561537e6e130>

3D PDB for #<Metabolite:0x0000561537e6e130>

SMILES for #<Metabolite:0x0000561537e6e130>

INCHI for #<Metabolite:0x0000561537e6e130>

Structure for #<Metabolite:0x0000561537e6e130>

3D Structure for #<Metabolite:0x0000561537e6e130>