MiMeDB: Showing metabocard for Penicitrinone A (MMDBc0008896)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 01:35:12 UTC

Update Date

2025-10-07 16:05:31 UTC

Metabolite ID

MMDBc0008896

Metabolite Identification

Common Name

Penicitrinone A

Description

Penicitrinone A is a secondary metabolite belonging to the chemical class of isocoumarins. Isolated from marine-derived Penicillium citrinum, it has been characterized alongside other compounds such as epiremisporine derivatives and citrinin. Research indicates that penicitrinone A exhibits weak antitumor activities against the 22Rv1 cell line (PMID:39140462 ). In a study focusing on the structural elucidation of secondary metabolites, penicitrinone A was identified among eight compounds, highlighting its significance in the metabolic profile of the organism (PMID:28074 ...). Additionally, a mutant strain of Penicillium produced penicitrinone A along with other bioactive metabolites, suggesting its potential role in biological activity and interaction with various cellular processes (PMID:25913704 ). The exploration of penicitrinone A's properties and its biological implications continues to be an area of interest in natural product chemistry and pharmacology.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152103352D          

 32 36  0  0  1  0            999 V2000
   -1.3049   -2.5748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9984   -1.5793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6116   -1.1791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8364   -2.9081    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1924   -3.7933    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7986    0.2044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2496   -0.0386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4991   -2.3977    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2811   -1.1717    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8058   -1.0021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2802   -2.2988    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0571   -3.0070    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1893   -0.3519    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5562   -0.2157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8058   -0.6479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2496   -1.6114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5298   -1.5124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5562   -1.4343    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9182   -1.8665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4744   -2.4758    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1124   -2.0436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9736   -0.9031    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1678   -1.0802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1124    0.3936    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2249   -3.2622    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8629   -2.8299    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3811   -0.1859    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6116   -0.4709    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7487   -3.1841    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9699   -0.7177    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6133   -3.6163    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9703    0.4436    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  1  1  1  0  0  0
  9  2  1  1  0  0  0
 10  3  1  0  0  0  0
 11  4  1  0  0  0  0
 12  5  1  6  0  0  0
 12  8  1  0  0  0  0
 13  6  1  6  0  0  0
 13  9  1  0  0  0  0
 14  7  1  0  0  0  0
 14 10  1  0  0  0  0
 15  7  2  0  0  0  0
 16  8  1  0  0  0  0
 16 10  2  0  0  0  0
 17  9  1  0  0  0  0
 17 11  2  0  0  0  0
 18 15  1  0  0  0  0
 18 16  1  0  0  0  0
 20 11  1  0  0  0  0
 20 19  2  0  0  0  0
 21 18  2  0  0  0  0
 21 19  1  0  0  0  0
 22 17  1  0  0  0  0
 23 19  1  0  0  0  0
 23 22  2  0  0  0  0
 24 14  2  0  0  0  0
 25 20  1  0  0  0  0
 26 12  1  0  0  0  0
 26 21  1  0  0  0  0
 27 13  1  0  0  0  0
 27 22  1  0  0  0  0
 28 15  1  0  0  0  0
 28 23  1  0  0  0  0
  8 29  1  6  0  0  0
  9 30  1  6  0  0  0
 12 31  1  1  0  0  0
 13 32  1  1  0  0  0
M  END


  Mrv1652305152103352D          

 32 36  0  0  1  0            999 V2000
   -1.3049   -2.5748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9984   -1.5793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6116   -1.1791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8364   -2.9081    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1924   -3.7933    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7986    0.2044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2496   -0.0386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4991   -2.3977    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2811   -1.1717    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8058   -1.0021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2802   -2.2988    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0571   -3.0070    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1893   -0.3519    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5562   -0.2157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8058   -0.6479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2496   -1.6114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5298   -1.5124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5562   -1.4343    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9182   -1.8665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4744   -2.4758    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1124   -2.0436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9736   -0.9031    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1678   -1.0802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1124    0.3936    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2249   -3.2622    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8629   -2.8299    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3811   -0.1859    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6116   -0.4709    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7487   -3.1841    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9699   -0.7177    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6133   -3.6163    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9703    0.4436    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  1  1  1  0  0  0
  9  2  1  1  0  0  0
 10  3  1  0  0  0  0
 11  4  1  0  0  0  0
 12  5  1  6  0  0  0
 12  8  1  0  0  0  0
 13  6  1  6  0  0  0
 13  9  1  0  0  0  0
 14  7  1  0  0  0  0
 14 10  1  0  0  0  0
 15  7  2  0  0  0  0
 16  8  1  0  0  0  0
 16 10  2  0  0  0  0
 17  9  1  0  0  0  0
 17 11  2  0  0  0  0
 18 15  1  0  0  0  0
 18 16  1  0  0  0  0
 20 11  1  0  0  0  0
 20 19  2  0  0  0  0
 21 18  2  0  0  0  0
 21 19  1  0  0  0  0
 22 17  1  0  0  0  0
 23 19  1  0  0  0  0
 23 22  2  0  0  0  0
 24 14  2  0  0  0  0
 25 20  1  0  0  0  0
 26 12  1  0  0  0  0
 26 21  1  0  0  0  0
 27 13  1  0  0  0  0
 27 22  1  0  0  0  0
 28 15  1  0  0  0  0
 28 23  1  0  0  0  0
  8 29  1  6  0  0  0
  9 30  1  6  0  0  0
 12 31  1  1  0  0  0
 13 32  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0008896

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(C)OC2=C3OC4=CC(=O)C(C)=C5C4=C(O[C@]([H])(C)[C@@]5([H])C)C3=C(O)C(C)=C2[C@]1([H])C

> <INCHI_IDENTIFIER>
InChI=1S/C23H24O5/c1-8-12(5)26-21-18-15(7-14(24)10(3)16(8)18)28-23-19(21)20(25)11(4)17-9(2)13(6)27-22(17)23/h7-9,12-13,25H,1-6H3/t8-,9-,12-,13-/m1/s1

> <INCHI_KEY>
WZDGQCYEIYZRBL-NRMKKVEVSA-N

> <FORMULA>
C23H24O5

> <MOLECULAR_WEIGHT>
380.44

> <EXACT_MASS>
380.162373873

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
52

> <JCHEM_AVERAGE_POLARIZABILITY>
42.41050445020458

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(6S,7R,17S,18R)-3-hydroxy-4,6,7,15,17,18-hexamethyl-8,11,19-trioxapentacyclo[10.7.1.0^{2,10}.0^{5,9}.0^{16,20}]icosa-1(20),2,4,9,12,15-hexaen-14-one

> <ALOGPS_LOGP>
4.18

> <JCHEM_LOGP>
3.4056083316666674

> <ALOGPS_LOGS>
-3.98

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.683238182287198

> <JCHEM_PKA_STRONGEST_BASIC>
2.0744631262457705

> <JCHEM_POLAR_SURFACE_AREA>
64.99000000000001

> <JCHEM_REFRACTIVITY>
108.74949999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.95e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(6S,7R,17S,18R)-3-hydroxy-4,6,7,15,17,18-hexamethyl-8,11,19-trioxapentacyclo[10.7.1.0^{2,10}.0^{5,9}.0^{16,20}]icosa-1(20),2,4,9,12,15-hexaen-14-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      -2.436  -4.806   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.330  -2.948   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.008  -2.201   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.161  -5.428   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.359  -7.081   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.957   0.381   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.466  -0.072   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.932  -4.476   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.991  -2.187   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.504  -1.870   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.123  -4.291   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.107  -5.613   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.820  -0.657   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.038  -0.403   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.504  -1.210   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.466  -3.008   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.589  -2.823   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.038  -2.677   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.581  -3.484   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.619  -4.622   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.077  -3.815   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.551  -1.686   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.047  -2.016   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -2.077   0.735   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       4.153  -6.089   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       1.611  -5.283   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       6.311  -0.347   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       3.008  -0.879   0.000  0.00  0.00           O+0
HETATM   29  H   UNK     0      -1.398  -5.944   0.000  0.00  0.00           H+0
HETATM   30  H   UNK     0       9.277  -1.340   0.000  0.00  0.00           H+0
HETATM   31  H   UNK     0       1.145  -6.750   0.000  0.00  0.00           H+0
HETATM   32  H   UNK     0       7.411   0.828   0.000  0.00  0.00           H+0
CONECT    1    8                                                            
CONECT    2    9                                                            
CONECT    3   10                                                            
CONECT    4   11                                                            
CONECT    5   12                                                            
CONECT    6   13                                                            
CONECT    7   14   15                                                       
CONECT    8    1   12   16   29                                             
CONECT    9    2   13   17   30                                             
CONECT   10    3   14   16                                                  
CONECT   11    4   17   20                                                  
CONECT   12    5    8   26   31                                             
CONECT   13    6    9   27   32                                             
CONECT   14    7   10   24                                                  
CONECT   15    7   18   28                                                  
CONECT   16    8   10   18                                                  
CONECT   17    9   11   22                                                  
CONECT   18   15   16   21                                                  
CONECT   19   20   21   23                                                  
CONECT   20   11   19   25                                                  
CONECT   21   18   19   26                                                  
CONECT   22   17   23   27                                                  
CONECT   23   19   22   28                                                  
CONECT   24   14                                                            
CONECT   25   20                                                            
CONECT   26   12   21                                                       
CONECT   27   13   22                                                       
CONECT   28   15   23                                                       
CONECT   29    8                                                            
CONECT   30    9                                                            
CONECT   31   12                                                            
CONECT   32   13                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   72    0
END

Synonyms

Not Available

Molecular Formula

C₂₃H₂₄O₅

Average Mass

380.44

Monoisotopic Mass

380.162373873

IUPAC Name

(6S,7R,17S,18R)-3-hydroxy-4,6,7,15,17,18-hexamethyl-8,11,19-trioxapentacyclo[10.7.1.0^{2,10}.0^{5,9}.0^{16,20}]icosa-1(20),2,4,9,12,15-hexaen-14-one

Traditional Name

(6S,7R,17S,18R)-3-hydroxy-4,6,7,15,17,18-hexamethyl-8,11,19-trioxapentacyclo[10.7.1.0^{2,10}.0^{5,9}.0^{16,20}]icosa-1(20),2,4,9,12,15-hexaen-14-one

CAS Registry Number

Not Available

SMILES

[H][C@]1(C)OC2=C3OC4=CC(=O)C(C)=C5C4=C(O[C@]([H])(C)[C@@]5([H])C)C3=C(O)C(C)=C2[C@]1([H])C

InChI Identifier

InChI=1S/C23H24O5/c1-8-12(5)26-21-18-15(7-14(24)10(3)16(8)18)28-23-19(21)20(25)11(4)17-9(2)13(6)27-22(17)23/h7-9,12-13,25H,1-6H3/t8-,9-,12-,13-/m1/s1

InChI Key

WZDGQCYEIYZRBL-NRMKKVEVSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as xanthenes. These are polycyclic aromatic compounds containing a xanthene moiety, which consists of two benzene rings joined to each other by a pyran ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

Xanthenes

Alternative Parents

Substituents

Xanthene
2-benzopyran
Coumaran
Phenol
Alkyl aryl ether
Benzenoid
Heteroaromatic compound
Cyclic ketone
Oxacycle
Ether
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	0.04 g/L	ALOGPS
logP	4.18	ALOGPS
logP	3.41	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Acidic)	6.68	ChemAxon
pKa (Strongest Basic)	2.07	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	64.99 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	108.75 m³·mol⁻¹	ChemAxon
Polarizability	42.41 Å³	ChemAxon
Number of Rings	5	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	2	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

9857099

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11682371

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 Penicitrinone A (MMDBc0008896)

MOL for #<Metabolite:0x00007f2a7f152d80>

3D MOL for #<Metabolite:0x00007f2a7f152d80>

3D SDF for #<Metabolite:0x00007f2a7f152d80>

3D-SDF for #<Metabolite:0x00007f2a7f152d80>

PDB for #<Metabolite:0x00007f2a7f152d80>

3D PDB for #<Metabolite:0x00007f2a7f152d80>

SMILES for #<Metabolite:0x00007f2a7f152d80>

INCHI for #<Metabolite:0x00007f2a7f152d80>

Structure for #<Metabolite:0x00007f2a7f152d80>

3D Structure for #<Metabolite:0x00007f2a7f152d80>