MiMeDB: Showing metabocard for Penialidin A (MMDBc0006748)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 00:10:34 UTC

Update Date

2025-10-07 16:05:13 UTC

Metabolite ID

MMDBc0006748

Metabolite Identification

Common Name

Penialidin A

Description

Penialidin A is a secondary metabolite belonging to the chemical class of xanthones. It was first isolated from the endophytic fungus of Ageratina adenophora, highlighting its potential as a novel compound in natural product chemistry (PMID:31638432 ). The extraction and fractionation processes of the crude extract yielded penialidin A along with other compounds, indicating its significance in the chemical profile of the source organism (PMID:27917206 ). Although primarily characterized through its chemical structure and isolation, the biological implications of penialidin A remain an area of interest, particularly in understanding its ecological role and potential applications in pharmacology. The study of such metabolites can provide insights into their biosynthetic pathways and their interactions within their ecological niches, suggesting that penialidin A may possess unique biological activities worthy of further investigation.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152102102D          

 22 24  0  0  1  0            999 V2000
    3.6704    0.6817    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
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    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
   -1.4289    0.0000    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    1.2375    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
   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  1  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   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1401    1.6002    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  5  2  2  0  0  0  0
  6  4  1  0  0  0  0
  7  2  1  0  0  0  0
  8  3  1  0  0  0  0
  8  6  2  0  0  0  0
 10  5  1  0  0  0  0
 10  6  1  0  0  0  0
 11  7  2  0  0  0  0
 11  9  1  0  0  0  0
 12  5  1  0  0  0  0
 12  9  2  0  0  0  0
 13  9  1  0  0  0  0
 14  1  1  1  0  0  0
 14  3  1  0  0  0  0
 15  7  1  0  0  0  0
 16 10  2  0  0  0  0
 17 11  1  0  0  0  0
 18 13  2  0  0  0  0
 19 13  1  0  0  0  0
 14 20  1  6  0  0  0
 21  4  1  0  0  0  0
 21 14  1  0  0  0  0
 22  8  1  0  0  0  0
 22 12  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0006748

> <DATABASE_NAME>
MIME

> <SMILES>
C[C@]1(O)CC2=C(CO1)C(=O)C1=CC(O)=C(O)C(C(O)=O)=C1O2

> <INCHI_IDENTIFIER>
InChI=1S/C14H12O8/c1-14(20)3-8-6(4-21-14)10(16)5-2-7(15)11(17)9(13(18)19)12(5)22-8/h2,15,17,20H,3-4H2,1H3,(H,18,19)/t14-/m1/s1

> <INCHI_KEY>
WHDZYZDPVJODPJ-CQSZACIVSA-N

> <FORMULA>
C14H12O8

> <MOLECULAR_WEIGHT>
308.242

> <EXACT_MASS>
308.053217346

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
28.538915723340097

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3R)-3,7,8-trihydroxy-3-methyl-10-oxo-1H,3H,4H,10H-pyrano[4,3-b]chromene-6-carboxylic acid

> <ALOGPS_LOGP>
0.84

> <JCHEM_LOGP>
0.9557203773333334

> <ALOGPS_LOGS>
-2.31

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
7.591541318509188

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.896717028976186

> <JCHEM_PKA_STRONGEST_BASIC>
-4.036418376776877

> <JCHEM_POLAR_SURFACE_AREA>
133.52

> <JCHEM_REFRACTIVITY>
72.99410000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.52e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R)-3,7,8-trihydroxy-3-methyl-10-oxo-1H,4H-pyrano[4,3-b]chromene-6-carboxylic acid

> <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       6.851   1.273   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -4.001   2.310   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -2.667   4.620   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       5.861   2.987   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1   14                                                            
CONECT    2    5    7                                                       
CONECT    3    8   14                                                       
CONECT    4    6   21                                                       
CONECT    5    2   10   12                                                  
CONECT    6    4    8   10                                                  
CONECT    7    2   11   15                                                  
CONECT    8    3    6   22                                                  
CONECT    9   11   12   13                                                  
CONECT   10    5    6   16                                                  
CONECT   11    7    9   17                                                  
CONECT   12    5    9   22                                                  
CONECT   13    9   18   19                                                  
CONECT   14    1    3   20   21                                             
CONECT   15    7                                                            
CONECT   16   10                                                            
CONECT   17   11                                                            
CONECT   18   13                                                            
CONECT   19   13                                                            
CONECT   20   14                                                            
CONECT   21    4   14                                                       
CONECT   22    8   12                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

Synonyms

Not Available

Molecular Formula

C₁₄H₁₂O₈

Average Mass

308.242

Monoisotopic Mass

308.053217346

IUPAC Name

(3R)-3,7,8-trihydroxy-3-methyl-10-oxo-1H,3H,4H,10H-pyrano[4,3-b]chromene-6-carboxylic acid

Traditional Name

(3R)-3,7,8-trihydroxy-3-methyl-10-oxo-1H,4H-pyrano[4,3-b]chromene-6-carboxylic acid

CAS Registry Number

Not Available

SMILES

C[C@]1(O)CC2=C(CO1)C(=O)C1=CC(O)=C(O)C(C(O)=O)=C1O2

InChI Identifier

InChI=1S/C14H12O8/c1-14(20)3-8-6(4-21-14)10(16)5-2-7(15)11(17)9(13(18)19)12(5)22-8/h2,15,17,20H,3-4H2,1H3,(H,18,19)/t14-/m1/s1

InChI Key

WHDZYZDPVJODPJ-CQSZACIVSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as chromones. Chromones are compounds containing a benzopyran-4-one moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

Chromones

Alternative Parents

Substituents

Chromone
Salicylic acid or derivatives
Hydroxybenzoic acid
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Benzenoid
Pyran
Heteroaromatic compound
Vinylogous acid
Hemiacetal
Oxacycle
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	0.84	ALOGPS
logP	0.96	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	1.9	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	133.52 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	72.99 m³·mol⁻¹	ChemAxon
Polarizability	28.54 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

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

78443361

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139584805

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 Penialidin A (MMDBc0006748)

MOL for #<Metabolite:0x00007fb4c57338c8>

3D MOL for #<Metabolite:0x00007fb4c57338c8>

3D SDF for #<Metabolite:0x00007fb4c57338c8>

3D-SDF for #<Metabolite:0x00007fb4c57338c8>

PDB for #<Metabolite:0x00007fb4c57338c8>

3D PDB for #<Metabolite:0x00007fb4c57338c8>

SMILES for #<Metabolite:0x00007fb4c57338c8>

INCHI for #<Metabolite:0x00007fb4c57338c8>

Structure for #<Metabolite:0x00007fb4c57338c8>

3D Structure for #<Metabolite:0x00007fb4c57338c8>