MiMeDB: Showing metabocard for Prelactone B (MMDBc0017852)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 08:08:36 UTC

Update Date

2025-10-07 16:06:45 UTC

Metabolite ID

MMDBc0017852

Metabolite Identification

Common Name

Prelactone B

Description

Prelactone B is a member of the lactone chemical class, characterized by its cyclic ester structure. This compound is produced by the endophytic bacterium Streptomyces cavourensis strain YBQ59, which also synthesizes other notable antibiotics such as bafilomycin D and nonactic acid (PMID:30533639 ). The isolation of prelactone B was achieved through the ethyl acetate extraction of the culture broth, where it was identified among several secondary metabolites (PMID:29869093 ). The chemical synthesis of prelactone B has been explored, including total syntheses and transformations leading to methyl-protected derivatives (PMID:28282511 , PMID:21707114 ). Additionally, its synthesis has been facilitated by silenes in organic chemistry (PMID:17036108 ). In terms of biological pathways, prelactone B is implicated in the biosynthesis of various secondary metabolites, which may contribute to the ecological interactions of its producing organism, although specific pathways involving prelactone B have not been extensively detailed in the literature. Overall, prelactone B represents a notable compound within the rich chemical diversity of microbial metabolites.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152110082D          

 15 15  0  0  1  0            999 V2000
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  1  0  0  0
  7  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  4  1  0  0  0  0
  9  5  1  6  0  0  0
  9  6  1  0  0  0  0
  7 10  1  6  0  0  0
 11  8  2  0  0  0  0
 12  8  1  0  0  0  0
 12  9  1  0  0  0  0
  6 13  1  6  0  0  0
  7 14  1  1  0  0  0
  9 15  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0017852

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(O)CC(=O)O[C@]([H])(C(C)C)[C@@]1([H])C

> <INCHI_IDENTIFIER>
InChI=1S/C9H16O3/c1-5(2)9-6(3)7(10)4-8(11)12-9/h5-7,9-10H,4H2,1-3H3/t6-,7+,9+/m0/s1

> <INCHI_KEY>
GZGROEXVPWSNDV-LKEWCRSYSA-N

> <FORMULA>
C9H16O3

> <MOLECULAR_WEIGHT>
172.224

> <EXACT_MASS>
172.109944375

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
18.514800683539708

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(4R,5S,6R)-4-hydroxy-5-methyl-6-(propan-2-yl)oxan-2-one

> <ALOGPS_LOGP>
0.80

> <JCHEM_LOGP>
1.0739087030000005

> <ALOGPS_LOGS>
-0.70

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.610493181364767

> <JCHEM_PKA_STRONGEST_BASIC>
-2.96917028247105

> <JCHEM_POLAR_SURFACE_AREA>
46.53

> <JCHEM_REFRACTIVITY>
44.211800000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.43e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4R,5S,6R)-4-hydroxy-6-isopropyl-5-methyloxan-2-one

> <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      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   13  H   UNK     0       0.000   3.080   0.000  0.00  0.00           H+0
HETATM   14  H   UNK     0       2.667   3.080   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0      -1.334   0.770   0.000  0.00  0.00           H+0
CONECT    1    5                                                            
CONECT    2    5                                                            
CONECT    3    6                                                            
CONECT    4    7    8                                                       
CONECT    5    1    2    9                                                  
CONECT    6    3    7    9   13                                             
CONECT    7    4    6   10   14                                             
CONECT    8    4   11   12                                                  
CONECT    9    5    6   12   15                                             
CONECT   10    7                                                            
CONECT   11    8                                                            
CONECT   12    8    9                                                       
CONECT   13    6                                                            
CONECT   14    7                                                            
CONECT   15    9                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

Synonyms

Not Available

Molecular Formula

C₉H₁₆O₃

Average Mass

172.224

Monoisotopic Mass

172.109944375

IUPAC Name

(4R,5S,6R)-4-hydroxy-5-methyl-6-(propan-2-yl)oxan-2-one

Traditional Name

(4R,5S,6R)-4-hydroxy-6-isopropyl-5-methyloxan-2-one

CAS Registry Number

Not Available

SMILES

[H][C@@]1(O)CC(=O)O[C@]([H])(C(C)C)[C@@]1([H])C

InChI Identifier

InChI=1S/C9H16O3/c1-5(2)9-6(3)7(10)4-8(11)12-9/h5-7,9-10H,4H2,1-3H3/t6-,7+,9+/m0/s1

InChI Key

GZGROEXVPWSNDV-LKEWCRSYSA-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
Secondary alcohol
Carboxylic acid ester
Oxacycle
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	34.3 g/L	ALOGPS
logP	0.8	ALOGPS
logP	1.07	ChemAxon
logS	-0.7	ALOGPS
pKa (Strongest Acidic)	14.61	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	46.53 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	44.21 m³·mol⁻¹	ChemAxon
Polarizability	18.51 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

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		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

9280957

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11105821

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 Prelactone B (MMDBc0017852)

MOL for #<Metabolite:0x00007f8dc4a2e618>

3D MOL for #<Metabolite:0x00007f8dc4a2e618>

3D SDF for #<Metabolite:0x00007f8dc4a2e618>

3D-SDF for #<Metabolite:0x00007f8dc4a2e618>

PDB for #<Metabolite:0x00007f8dc4a2e618>

3D PDB for #<Metabolite:0x00007f8dc4a2e618>

SMILES for #<Metabolite:0x00007f8dc4a2e618>

INCHI for #<Metabolite:0x00007f8dc4a2e618>

Structure for #<Metabolite:0x00007f8dc4a2e618>

3D Structure for #<Metabolite:0x00007f8dc4a2e618>