MiMeDB: Showing metabocard for Decarestrictine D (MMDBc0006947)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 00:17:40 UTC

Update Date

2025-10-07 16:05:16 UTC

Metabolite ID

MMDBc0006947

Metabolite Identification

Common Name

Decarestrictine D

Description

Decarestrictine D is a 10-membered lactone belonging to the class of natural products known as macrolides. It has garnered attention due to its unique structural features and potential biological activities. The synthesis of decarestrictine D has been explored through various methods, including asymmetric synthesis and nickel-catalyzed coupling reactions that facilitate the construction of its complex carbon skeleton. Notably, the stereoselective synthesis of decarestrictine D was achieved from a (2Z,4E)-alkadienyl alcohol precursor, showcasing innovative synthetic strategies (PMID:15816745 ). Additionally, the synthesis of decarestrictine D has been reported through the borylation of lithiated carbamates and the conversion of triol derivatives, highlighting its versatility in synthetic organic chemistry (PMID:20446329 , PMID:17253757 ). In natural settings, decarestrictine D is produced during fermentation processes, where it is derived from other decarestrictines under acidic conditions (PMID:8226316 ). The exploration of decarestrictine D not only emphasizes its chemical significance but also opens avenues for studying its biological implications, particularly in the context of its derivatives and metabolic pathways.

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004171523462D          

 15 15  0  0  0  0            999 V2000
    0.8889    2.1275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.5039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2391    1.6598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7792    1.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5893    1.1921    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5091    0.2566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6990    0.1007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.6789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9690   -1.3025    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6188   -0.8348    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3488   -1.6143    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0787   -0.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3488    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1913    1.1921    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1589    0.7243    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
  6  4  1  4  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 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
  2 15  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0006947

> <DATABASE_NAME>
MIME

> <SMILES>
CC1CC(O)C=CC(O)C(O)CC(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C10H16O5/c1-6-4-7(11)2-3-8(12)9(13)5-10(14)15-6/h2-3,6-9,11-13H,4-5H2,1H3

> <INCHI_KEY>
HWMMWMJBUOCCFZ-UHFFFAOYSA-N

> <FORMULA>
C10H16O5

> <MOLECULAR_WEIGHT>
216.233

> <EXACT_MASS>
216.099773615

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
21.5291034233828

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4,5,8-trihydroxy-10-methyl-3,4,5,8,9,10-hexahydro-2H-oxecin-2-one

> <ALOGPS_LOGP>
-0.97

> <JCHEM_LOGP>
-1.0263642883333333

> <ALOGPS_LOGS>
-0.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.613388708682042

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.521447327290709

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8844112587560664

> <JCHEM_POLAR_SURFACE_AREA>
86.99

> <JCHEM_REFRACTIVITY>
53.043400000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.03e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4,5,8-trihydroxy-10-methyl-3,4,5,8,9,10-hexahydrooxecin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0       1.659   3.971   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   2.807   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.180   3.098   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.188   1.934   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       6.700   2.225   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       4.684   0.479   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.171   0.188   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667  -1.267   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       3.676  -2.431   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       1.155  -1.558   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.651  -3.013   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.147  -0.394   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.651   1.061   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -0.357   2.225   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       2.163   1.352   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   15                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    2                                                       
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

Synonyms

Value	Source
Tuckolide	MeSH

Molecular Formula

C₁₀H₁₆O₅

Average Mass

216.233

Monoisotopic Mass

216.099773615

IUPAC Name

4,5,8-trihydroxy-10-methyl-3,4,5,8,9,10-hexahydro-2H-oxecin-2-one

Traditional Name

4,5,8-trihydroxy-10-methyl-3,4,5,8,9,10-hexahydrooxecin-2-one

CAS Registry Number

Not Available

SMILES

CC1CC(O)C=CC(O)C(O)CC(=O)O1

InChI Identifier

InChI=1S/C10H16O5/c1-6-4-7(11)2-3-8(12)9(13)5-10(14)15-6/h2-3,6-9,11-13H,4-5H2,1H3

InChI Key

HWMMWMJBUOCCFZ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oxocins. Oxocins are compounds containing an oxocin ring, which is a eight-member unsaturated aromatic ring containing one oxygen atom and seven carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Oxocins

Sub Class

Not Available

Direct Parent

Oxocins

Alternative Parents

Substituents

Oxocin
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
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	103 g/L	ALOGPS
logP	-0.97	ALOGPS
logP	-1	ChemAxon
logS	-0.32	ALOGPS
pKa (Strongest Acidic)	13.52	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	86.99 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	53.04 m³·mol⁻¹	ChemAxon
Polarizability	21.53 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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
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

78174212

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

References

Synthesis Reference

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 Decarestrictine D (MMDBc0006947)

MOL for #<Metabolite:0x00007f2ab9eca0a0>

3D MOL for #<Metabolite:0x00007f2ab9eca0a0>

3D SDF for #<Metabolite:0x00007f2ab9eca0a0>

3D-SDF for #<Metabolite:0x00007f2ab9eca0a0>

PDB for #<Metabolite:0x00007f2ab9eca0a0>

3D PDB for #<Metabolite:0x00007f2ab9eca0a0>

SMILES for #<Metabolite:0x00007f2ab9eca0a0>

INCHI for #<Metabolite:0x00007f2ab9eca0a0>

Structure for #<Metabolite:0x00007f2ab9eca0a0>

3D Structure for #<Metabolite:0x00007f2ab9eca0a0>