MiMeDB: Showing metabocard for Penienone (MMDBc0005067)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-14 22:47:59 UTC

Update Date

2025-10-07 16:04:58 UTC

Metabolite ID

MMDBc0005067

Metabolite Identification

Common Name

Penienone

Description

Penienone is a bicyclic lactam belonging to the class of natural products. It has garnered attention in biomedical literature due to its notable phytotoxic and antifungal properties. Isolated from Penicillium palitans, a fungus found in deep-sea sediments of the Southern Ocean, (-)-penienone exhibits significant biological activity. At a concentration of 1 mg/mL, it completely inhibits seed germination, while its analog (-)-palitantin shows only moderate effects (PMID:39626084 ). Additionally, (-)-penienone demonstrates a 50% growth inhibition of Lemna paucicostata at 57 μM (IC50) and an impressive antifungal efficacy against Colletotrichum fragariae, with an IC50 value of 0.3 μM (PMID:39626084 ). The compound has been synthesized through various methods, including a four-step total synthesis that achieved a 24% overall yield, significantly reducing the steps compared to previous syntheses (PMID:35838547 ). The enantioselective organocatalytic conjugate addition has also been applied in its synthesis (PMID:35838547 ). Overall, penienone's unique structural features and biological activities make it a compound of interest for further research in both chemistry and biology.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152100482D          

 22 22  0  0  1  0            999 V2000
   -1.4289    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    2.4750    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    2.0625    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
   -0.7145    1.2375    0.0000 C   0  0  0  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
    0.0000    0.8250    0.0000 C   0  0  1  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    0.8250    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
   -1.4289    3.3000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    3.7125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    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
    0.0000    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  2  0  0  0  0
  6  5  1  0  0  0  0
  8  6  2  0  0  0  0
  9  7  1  0  0  0  0
 10  7  2  0  0  0  0
 12  8  1  6  0  0  0
 12  9  1  0  0  0  0
 13 11  1  1  0  0  0
 13 12  1  0  0  0  0
 14 10  1  0  0  0  0
 14 13  1  0  0  0  0
 15 11  1  0  0  0  0
 16 14  2  0  0  0  0
 17  4  1  0  0  0  0
 18  5  1  0  0  0  0
 19  6  1  0  0  0  0
 20  8  1  0  0  0  0
 12 21  1  1  0  0  0
 13 22  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0005067

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C(CCC)=C(\[H])/C(/[H])=C(\[H])[C@]1([H])CC=CC(=O)[C@@]1([H])CO

> <INCHI_IDENTIFIER>
InChI=1S/C14H20O2/c1-2-3-4-5-6-8-12-9-7-10-14(16)13(12)11-15/h4-8,10,12-13,15H,2-3,9,11H2,1H3/b5-4+,8-6+/t12-,13+/m1/s1

> <INCHI_KEY>
UBYAOVYCJUQGIG-FILRKKLKSA-N

> <FORMULA>
C14H20O2

> <MOLECULAR_WEIGHT>
220.312

> <EXACT_MASS>
220.146329884

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
26.138151120756845

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(5S,6R)-5-[(1E,3E)-hepta-1,3-dien-1-yl]-6-(hydroxymethyl)cyclohex-2-en-1-one

> <ALOGPS_LOGP>
2.54

> <JCHEM_LOGP>
2.978820649

> <ALOGPS_LOGS>
-3.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.710835711393294

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.283811864658887

> <JCHEM_PKA_STRONGEST_BASIC>
-2.6743891802227315

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
70.0777

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.21e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(5S,6R)-5-[(1E,3E)-hepta-1,3-dien-1-yl]-6-(hydroxymethyl)cyclohex-2-en-1-one

> <JCHEM_VEBER_RULE>
1

$$$$

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      -2.667  10.780   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.667   9.240   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334   8.470   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.334   6.930   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.000   6.160   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.000   4.620   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       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667   1.540   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      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   17  H   UNK     0      -2.667   6.160   0.000  0.00  0.00           H+0
HETATM   18  H   UNK     0       1.334   6.930   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0      -1.334   3.850   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       2.667   4.620   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       2.667   3.080   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       0.000   3.080   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   17                                                  
CONECT    5    4    6   18                                                  
CONECT    6    5    8   19                                                  
CONECT    7    9   10                                                       
CONECT    8    6   12   20                                                  
CONECT    9    7   12                                                       
CONECT   10    7   14                                                       
CONECT   11   13   15                                                       
CONECT   12    8    9   13   21                                             
CONECT   13   11   12   14   22                                             
CONECT   14   10   13   16                                                  
CONECT   15   11                                                            
CONECT   16   14                                                            
CONECT   17    4                                                            
CONECT   18    5                                                            
CONECT   19    6                                                            
CONECT   20    8                                                            
CONECT   21   12                                                            
CONECT   22   13                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

Synonyms

Not Available

Molecular Formula

C₁₄H₂₀O₂

Average Mass

220.312

Monoisotopic Mass

220.146329884

IUPAC Name

(5S,6R)-5-[(1E,3E)-hepta-1,3-dien-1-yl]-6-(hydroxymethyl)cyclohex-2-en-1-one

Traditional Name

(5S,6R)-5-[(1E,3E)-hepta-1,3-dien-1-yl]-6-(hydroxymethyl)cyclohex-2-en-1-one

CAS Registry Number

Not Available

SMILES

[H]\C(CCC)=C(\[H])/C(/[H])=C(\[H])[C@]1([H])CC=CC(=O)[C@@]1([H])CO

InChI Identifier

InChI=1S/C14H20O2/c1-2-3-4-5-6-8-12-9-7-10-14(16)13(12)11-15/h4-8,10,12-13,15H,2-3,9,11H2,1H3/b5-4+,8-6+/t12-,13+/m1/s1

InChI Key

UBYAOVYCJUQGIG-FILRKKLKSA-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
Organic oxide
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.12 g/L	ALOGPS
logP	2.54	ALOGPS
logP	2.98	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Acidic)	15.28	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	37.3 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	70.08 m³·mol⁻¹	ChemAxon
Polarizability	26.14 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	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

8974275

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10798969

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 Penienone (MMDBc0005067)

MOL for #<Metabolite:0x00007f2adc5acf68>

3D MOL for #<Metabolite:0x00007f2adc5acf68>

3D SDF for #<Metabolite:0x00007f2adc5acf68>

3D-SDF for #<Metabolite:0x00007f2adc5acf68>

PDB for #<Metabolite:0x00007f2adc5acf68>

3D PDB for #<Metabolite:0x00007f2adc5acf68>

SMILES for #<Metabolite:0x00007f2adc5acf68>

INCHI for #<Metabolite:0x00007f2adc5acf68>

Structure for #<Metabolite:0x00007f2adc5acf68>

3D Structure for #<Metabolite:0x00007f2adc5acf68>