MiMeDB: Showing metabocard for Phomapyrone B (MMDBc0018683)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 08:50:35 UTC

Update Date

2025-10-07 16:06:52 UTC

Metabolite ID

MMDBc0018683

Metabolite Identification

Common Name

Phomapyrone B

Description

Phomapyrone B is a pyranone derivative, a chemical class known for its diverse biological activities and structural complexity. This compound is characterized by a fused pyran ring and a carbonyl group, contributing to its potential reactivity and interactions in various biological pathways. It was isolated from the endophytic fungus Phoma sp., alongside other metabolites, highlighting the rich chemical diversity produced by this organism (PMID:35873041 ). Pyranones, including phomapyrone B, are often involved in secondary metabolite pathways, which can play roles in plant-fungal interactions and may possess antimicrobial properties. The structural features of phomapyrone B suggest it could participate in biochemical processes such as enzyme inhibition or modulation of signaling pathways, although specific pathways involving phomapyrone B remain to be fully elucidated. Its unique structure and origin from a fungal source position phomapyrone B as a compound of interest for further exploration in both chemistry and potential applications in biotechnology or pharmacology.

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004251512452D          

 16 16  0  0  0  0            999 V2000
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -2.4750    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
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
  8 15  1  0  0  0  0
 10 16  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0018683

> <DATABASE_NAME>
MIME

> <SMILES>
CCC(C)C(=O)CC1=CC(O)=C(C)C(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C12H16O4/c1-4-7(2)10(13)5-9-6-11(14)8(3)12(15)16-9/h6-7,14H,4-5H2,1-3H3

> <INCHI_KEY>
CRWYBXBKGMHTRM-UHFFFAOYSA-N

> <FORMULA>
C12H16O4

> <MOLECULAR_WEIGHT>
224.256

> <EXACT_MASS>
224.104858995

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
23.139451067656445

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-hydroxy-3-methyl-6-(3-methyl-2-oxopentyl)-2H-pyran-2-one

> <ALOGPS_LOGP>
1.54

> <JCHEM_LOGP>
2.3205365420000006

> <ALOGPS_LOGS>
-2.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.338058462715722

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.65075274554941

> <JCHEM_PKA_STRONGEST_BASIC>
-6.013360071378654

> <JCHEM_POLAR_SURFACE_AREA>
63.60000000000001

> <JCHEM_REFRACTIVITY>
61.55290000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.52e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-hydroxy-3-methyl-6-(3-methyl-2-oxopentyl)pyran-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.669  -7.700   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       8.002  -9.240   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      10.669  -4.620   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   15                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   16                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    8                                                       
CONECT   16   10                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

Synonyms

Not Available

Molecular Formula

C₁₂H₁₆O₄

Average Mass

224.256

Monoisotopic Mass

224.104858995

IUPAC Name

4-hydroxy-3-methyl-6-(3-methyl-2-oxopentyl)-2H-pyran-2-one

Traditional Name

4-hydroxy-3-methyl-6-(3-methyl-2-oxopentyl)pyran-2-one

CAS Registry Number

Not Available

SMILES

CCC(C)C(=O)CC1=CC(O)=C(C)C(=O)O1

InChI Identifier

InChI=1S/C12H16O4/c1-4-7(2)10(13)5-9-6-11(14)8(3)12(15)16-9/h6-7,14H,4-5H2,1-3H3

InChI Key

CRWYBXBKGMHTRM-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyranones and derivatives. Pyranones and derivatives are compounds containing a pyran ring which bears a ketone.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyrans

Sub Class

Pyranones and derivatives

Direct Parent

Pyranones and derivatives

Alternative Parents

Substituents

Pyranone
Heteroaromatic compound
Vinylogous acid
Lactone
Ketone
Oxacycle
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	1.52 g/L	ALOGPS
logP	1.54	ALOGPS
logP	2.32	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	7.65	ChemAxon
pKa (Strongest Basic)	-6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	63.6 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	61.55 m³·mol⁻¹	ChemAxon
Polarizability	23.14 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-09	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum

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 (eluted)	2025-10-23	134.4
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	25.3
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	354.2
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	384.6
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	402.1
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	271.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	1159.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	99.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	279.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	301.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	313.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	158.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	138.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	60.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	300.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	67.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	245.8
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	1110.0
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	799.1

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	Phomapyrone B_TMS_1	CCC(C)C(=O)CC1=CC(O[Si](C)(C)C)=C(C)C(=O)O1	standard non polar	2025-10-23	1944.76
Gas Chromatography	Phomapyrone B_TMS_2	CCC(C)=C(CC1=CC(O)=C(C)C(=O)O1)O[Si](C)(C)C	standard non polar	2025-10-23	1920.33
Gas Chromatography	Phomapyrone B_TMS_3	CCC(C)C(=CC1=CC(O)=C(C)C(=O)O1)O[Si](C)(C)C	standard non polar	2025-10-23	2024.71
Gas Chromatography	Phomapyrone B_TMS_4	CCC(C)=C(CC1=CC(O[Si](C)(C)C)=C(C)C(=O)O1)O[Si](C)(C)C	standard non polar	2025-10-23	1836.38
Gas Chromatography	Phomapyrone B_TMS_5	CCC(C)C(=CC1=CC(O[Si](C)(C)C)=C(C)C(=O)O1)O[Si](C)(C)C	standard non polar	2025-10-23	2207.54
Gas Chromatography	Phomapyrone B_TMS_1	CCC(C)C(=O)CC1=CC(O[Si](C)(C)C)=C(C)C(=O)O1	standard polar	2025-10-23	2411.28
Gas Chromatography	Phomapyrone B_TMS_2	CCC(C)=C(CC1=CC(O)=C(C)C(=O)O1)O[Si](C)(C)C	standard polar	2025-10-23	1964.15
Gas Chromatography	Phomapyrone B_TMS_3	CCC(C)C(=CC1=CC(O)=C(C)C(=O)O1)O[Si](C)(C)C	standard polar	2025-10-23	2005.76
Gas Chromatography	Phomapyrone B_TMS_4	CCC(C)=C(CC1=CC(O[Si](C)(C)C)=C(C)C(=O)O1)O[Si](C)(C)C	standard polar	2025-10-23	2077.46
Gas Chromatography	Phomapyrone B_TMS_5	CCC(C)C(=CC1=CC(O[Si](C)(C)C)=C(C)C(=O)O1)O[Si](C)(C)C	standard polar	2025-10-23	2189.08

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

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

54676992

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 Phomapyrone B (MMDBc0018683)

MOL for #<Metabolite:0x000056431f92d250>

3D MOL for #<Metabolite:0x000056431f92d250>

3D SDF for #<Metabolite:0x000056431f92d250>

3D-SDF for #<Metabolite:0x000056431f92d250>

PDB for #<Metabolite:0x000056431f92d250>

3D PDB for #<Metabolite:0x000056431f92d250>

SMILES for #<Metabolite:0x000056431f92d250>

INCHI for #<Metabolite:0x000056431f92d250>

Structure for #<Metabolite:0x000056431f92d250>

3D Structure for #<Metabolite:0x000056431f92d250>