MiMeDB: Showing metabocard for (+)-epoxyserinone B (MMDBc0001003)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-14 18:40:51 UTC

Update Date

2025-10-07 16:04:24 UTC

Metabolite ID

MMDBc0001003

Metabolite Identification

Common Name

(+)-epoxyserinone B

Description

(+)-epoxyserinone B is a member of the chemical class of pentaketides, which are secondary metabolites produced by fungi. This compound was identified alongside other metabolites in a marine-derived saltwater fungal culture isolated from deep water environments. The structural features of (+)-epoxyserinone B include a unique epoxy group, which is characteristic of certain fungal metabolites, contributing to its potential biological activities. In terms of biosynthetic pathways, (+)-epoxyserinone B is part of the polyketide synthesis pathway, which involves the assembly of acetyl-CoA units through a series of condensation reactions. This pathway is crucial for the production of various bioactive compounds, including antibiotics and antifungal agents. The discovery of (+)-epoxyserinone B, along with other related compounds, highlights the rich chemical diversity present in marine fungi and their potential roles in ecological interactions and biotechnological applications (PMID:15043411 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305142120402D          

 17 19  0  0  1  0            999 V2000
   -0.1712    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0503    3.0624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.5396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    2.3479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8371    0.2900    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -0.1271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    2.7604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2793    0.7879    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  0  0  0  0
  6  5  1  0  0  0  0
  7  4  1  0  0  0  0
  8  4  2  0  0  0  0
  9  2  1  6  0  0  0
  9  7  1  0  0  0  0
 10  5  1  0  0  0  0
 10  9  1  0  0  0  0
 11  8  1  0  0  0  0
 11 10  1  0  0  0  0
 12  7  2  0  0  0  0
 13 11  1  0  0  0  0
 14  3  1  0  0  0  0
 14  8  1  0  0  0  0
 15  6  1  0  0  0  0
 15 11  1  0  0  0  0
 16  9  1  0  0  0  0
 10 16  1  1  0  0  0
 17  6  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0001003

> <DATABASE_NAME>
MIME

> <SMILES>
[H]C1(C)C[C@]23O[C@@]2(C)C(=O)C=C(OC)C3(O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C11H14O5/c1-6-5-10-9(2,16-10)7(12)4-8(14-3)11(10,13)15-6/h4,6,13H,5H2,1-3H3/t6?,9-,10-,11?/m0/s1

> <INCHI_KEY>
GGPRMSQKBVQHAH-NBHGFOHDSA-N

> <FORMULA>
C11H14O5

> <MOLECULAR_WEIGHT>
226.228

> <EXACT_MASS>
226.084123551

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
22.067185233087486

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,3R)-7-hydroxy-6-methoxy-3,9-dimethyl-2,8-dioxatricyclo[5.3.0.0^{1,3}]dec-5-en-4-one

> <ALOGPS_LOGP>
0.17

> <JCHEM_LOGP>
0.3397230243333338

> <ALOGPS_LOGS>
-0.99

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.66295379303469

> <JCHEM_PKA_STRONGEST_BASIC>
-4.015869749942289

> <JCHEM_POLAR_SURFACE_AREA>
68.29

> <JCHEM_REFRACTIVITY>
54.67190000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.31e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,3R)-7-hydroxy-6-methoxy-3,9-dimethyl-2,8-dioxatricyclo[5.3.0.0^{1,3}]dec-5-en-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 14-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-21         0                                  
HETATM    1  C   UNK     0      -0.320   2.843   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.694   5.717   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.258  -1.007   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.126   4.089   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       7.591   4.383   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       3.429   0.541   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       4.924  -0.237   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       2.126   1.597   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       3.590   5.153   0.000  0.00  0.00           O+0
HETATM   17  H   UNK     0       0.521   1.471   0.000  0.00  0.00           H+0
CONECT    1    6                                                            
CONECT    2    9                                                            
CONECT    3   14                                                            
CONECT    4    7    8                                                       
CONECT    5    6   10                                                       
CONECT    6    1    5   15   17                                             
CONECT    7    4    9   12                                                  
CONECT    8    4   11   14                                                  
CONECT    9    2    7   10   16                                             
CONECT   10    5    9   11   16                                             
CONECT   11    8   10   13   15                                             
CONECT   12    7                                                            
CONECT   13   11                                                            
CONECT   14    3    8                                                       
CONECT   15    6   11                                                       
CONECT   16    9   10                                                       
CONECT   17    6                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   38    0
END

Synonyms

Not Available

Molecular Formula

C₁₁H₁₄O₅

Average Mass

226.228

Monoisotopic Mass

226.084123551

IUPAC Name

(1S,3R)-7-hydroxy-6-methoxy-3,9-dimethyl-2,8-dioxatricyclo[5.3.0.0^{1,3}]dec-5-en-4-one

Traditional Name

(1S,3R)-7-hydroxy-6-methoxy-3,9-dimethyl-2,8-dioxatricyclo[5.3.0.0^{1,3}]dec-5-en-4-one

CAS Registry Number

Not Available

SMILES

[H]C1(C)C[C@]23O[C@@]2(C)C(=O)C=C(OC)C3(O)O1

InChI Identifier

InChI=1S/C11H14O5/c1-6-5-10-9(2,16-10)7(12)4-8(14-3)11(10,13)15-6/h4,6,13H,5H2,1-3H3/t6?,9-,10-,11?/m0/s1

InChI Key

GGPRMSQKBVQHAH-NBHGFOHDSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclohexenones. Cyclohexenones are compounds containing a cylohexenone moiety, which is a six-membered aliphatic ring that carries a ketone and has one endocyclic double bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Cyclohexenones

Alternative Parents

Substituents

Cyclohexenone
Vinylogous ester
Oxolane
Hemiacetal
Oxacycle
Organoheterocyclic compound
Ether
Oxirane
Dialkyl ether
Organic oxide
Hydrocarbon derivative
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	23.1 g/L	ALOGPS
logP	0.17	ALOGPS
logP	0.34	ChemAxon
logS	-0.99	ALOGPS
pKa (Strongest Acidic)	9.66	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	68.29 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	54.67 m³·mol⁻¹	ChemAxon
Polarizability	22.07 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

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (void)	2025-10-23	46.3
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (void)	2025-10-23	23.7
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	307.8
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	578.1
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	494.7
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	306.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	1871.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	68.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	603.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	379.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	299.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	169.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	124.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (void)	2025-10-23	66.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	379.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	51.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	279.7
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	1305.3
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	899.8

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	(+)-epoxyserinone B_TMS_1	COC1=CC(=O)[C@]2(C)O[C@@]23CC(C)OC13O[Si](C)(C)C	standard non polar	2025-10-23	2382.51
Gas Chromatography	(+)-epoxyserinone B_TMS_1	COC1=CC(=O)[C@]2(C)O[C@@]23CC(C)OC13O[Si](C)(C)C	standard polar	2025-10-23	2110.17

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
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

10185957

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21576221

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 (+)-epoxyserinone B (MMDBc0001003)

MOL for #<Metabolite:0x00007f9af045a3e8>

3D MOL for #<Metabolite:0x00007f9af045a3e8>

3D SDF for #<Metabolite:0x00007f9af045a3e8>

3D-SDF for #<Metabolite:0x00007f9af045a3e8>

PDB for #<Metabolite:0x00007f9af045a3e8>

3D PDB for #<Metabolite:0x00007f9af045a3e8>

SMILES for #<Metabolite:0x00007f9af045a3e8>

INCHI for #<Metabolite:0x00007f9af045a3e8>

Structure for #<Metabolite:0x00007f9af045a3e8>

3D Structure for #<Metabolite:0x00007f9af045a3e8>