MiMeDB: Showing metabocard for Conidiogenone C (MMDBc0009817)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 02:13:28 UTC

Update Date

2025-10-07 16:05:40 UTC

Metabolite ID

MMDBc0009817

Metabolite Identification

Common Name

Conidiogenone C

Description

Conidiogenone C is a cyclopiane diterpene, a class of chemical compounds known for their complex structures and diverse biological activities. This metabolite has garnered attention in biomedical research due to its interaction with Immunity-related GTPase family M protein 1 (IRGM1), which is identified as a key cellular target responsible for the compound's anti-inflammatory effects (PMID:39738095 ). The asymmetric total synthesis of conidiogenone C, alongside other related compounds, has been achieved through innovative synthetic and chemical proteomics studies (PMID:39738095 ). Furthermore, conidiogenone C is shown to activate IRGM1-mediated autophagy of dysfunctional mitochondria, thereby playing a critical role in maintaining mitochondrial quality control in inflammatory macrophages (PMID:39738095 ). This suggests that conidiogenone C may have potential therapeutic applications in conditions characterized by inflammation and mitochondrial dysfunction. The ongoing exploration of its chemical properties and biological mechanisms highlights the significance of conidiogenone C in the context of drug discovery and development.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152104132D          

 25 28  0  0  1  0            999 V2000
    3.0239    0.3239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2911    0.0837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3134    2.5786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9536    2.4841    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5951    0.3412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8857    0.7624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6179    2.8722    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7964    2.7959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1818    0.4674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8015    1.0119    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6509    0.8123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2628    2.0150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3145    0.7450    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9443    2.1145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8957    1.5873    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6537    1.6934    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4724    0.8885    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4752    1.7696    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6151    1.9911    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3245    1.5700    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.4441    2.8199    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1863    2.0085    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3045   -0.0799    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5640    2.6591    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1982    1.0736    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  2  0  0  0  0
  8  7  1  0  0  0  0
 10  9  1  0  0  0  0
 13  1  1  6  0  0  0
 13  5  1  0  0  0  0
 14  7  1  0  0  0  0
 15  6  1  0  0  0  0
 16 14  1  0  0  0  0
 17  2  1  6  0  0  0
 17  9  1  0  0  0  0
 17 11  1  0  0  0  0
 17 16  1  0  0  0  0
 18  3  1  1  0  0  0
 18 10  1  0  0  0  0
 18 12  1  6  0  0  0
 18 16  1  0  0  0  0
 19  4  1  6  0  0  0
 19  8  1  0  0  0  0
 19 15  1  0  0  0  0
 20 11  1  6  0  0  0
 20 13  1  0  0  0  0
 20 14  1  0  0  0  0
 20 19  1  0  0  0  0
 21 12  1  0  0  0  0
 22 15  2  0  0  0  0
 13 23  1  1  0  0  0
 14 24  1  1  0  0  0
 16 25  1  6  0  0  0
M  END


  Mrv1652305152104132D          

 25 28  0  0  1  0            999 V2000
    3.0239    0.3239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2911    0.0837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3134    2.5786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9536    2.4841    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5951    0.3412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8857    0.7624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6179    2.8722    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7964    2.7959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1818    0.4674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8015    1.0119    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6509    0.8123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2628    2.0150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3145    0.7450    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9443    2.1145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8957    1.5873    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6537    1.6934    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4724    0.8885    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4752    1.7696    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6151    1.9911    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3245    1.5700    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.4441    2.8199    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1863    2.0085    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3045   -0.0799    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5640    2.6591    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1982    1.0736    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  2  0  0  0  0
  8  7  1  0  0  0  0
 10  9  1  0  0  0  0
 13  1  1  6  0  0  0
 13  5  1  0  0  0  0
 14  7  1  0  0  0  0
 15  6  1  0  0  0  0
 16 14  1  0  0  0  0
 17  2  1  6  0  0  0
 17  9  1  0  0  0  0
 17 11  1  0  0  0  0
 17 16  1  0  0  0  0
 18  3  1  1  0  0  0
 18 10  1  0  0  0  0
 18 12  1  6  0  0  0
 18 16  1  0  0  0  0
 19  4  1  6  0  0  0
 19  8  1  0  0  0  0
 19 15  1  0  0  0  0
 20 11  1  6  0  0  0
 20 13  1  0  0  0  0
 20 14  1  0  0  0  0
 20 19  1  0  0  0  0
 21 12  1  0  0  0  0
 22 15  2  0  0  0  0
 13 23  1  1  0  0  0
 14 24  1  1  0  0  0
 16 25  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0009817

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]12CC[C@]3(C)C(=O)C=C[C@@]([H])(C)[C@]13C[C@]1(C)CC[C@@](C)(CO)[C@]21[H]

> <INCHI_IDENTIFIER>
InChI=1S/C20H30O2/c1-13-5-6-15(22)19(4)8-7-14-16-17(2,11-20(13,14)19)9-10-18(16,3)12-21/h5-6,13-14,16,21H,7-12H2,1-4H3/t13-,14-,16-,17+,18+,19-,20-/m1/s1

> <INCHI_KEY>
WXDDMOJVZBYBSW-QAJMTZOZSA-N

> <FORMULA>
C20H30O2

> <MOLECULAR_WEIGHT>
302.458

> <EXACT_MASS>
302.224580206

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
52

> <JCHEM_AVERAGE_POLARIZABILITY>
35.07914096769093

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2R,6S,9R,10R,11R,14S)-11-(hydroxymethyl)-2,6,11,14-tetramethyltetracyclo[7.6.0.0^{1,6}.0^{10,14}]pentadec-3-en-5-one

> <ALOGPS_LOGP>
3.32

> <JCHEM_LOGP>
3.869031403000001

> <ALOGPS_LOGS>
-4.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.323782677709083

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.53213766649497

> <JCHEM_PKA_STRONGEST_BASIC>
-1.253755599574347

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
89.30419999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.06e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,6S,9R,10R,11R,14S)-11-(hydroxymethyl)-2,6,11,14-tetramethyltetracyclo[7.6.0.0^{1,6}.0^{10,14}]pentadec-3-en-5-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       5.645   0.605   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.143   0.156   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.052   4.813   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.780   4.637   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.977   0.637   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.653   1.423   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.887   5.361   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.353   5.219   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.806   0.872   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.963   1.889   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.948   1.516   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.824   3.761   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.320   1.391   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.496   3.947   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.672   2.963   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.820   3.161   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.482   1.659   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.354   3.303   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.015   3.717   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.339   2.931   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      10.162   5.264   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       0.348   3.749   0.000  0.00  0.00           O+0
HETATM   23  H   UNK     0       4.302  -0.149   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       6.653   4.964   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0       7.837   2.004   0.000  0.00  0.00           H+0
CONECT    1   13                                                            
CONECT    2   17                                                            
CONECT    3   18                                                            
CONECT    4   19                                                            
CONECT    5    6   13                                                       
CONECT    6    5   15                                                       
CONECT    7    8   14                                                       
CONECT    8    7   19                                                       
CONECT    9   10   17                                                       
CONECT   10    9   18                                                       
CONECT   11   17   20                                                       
CONECT   12   18   21                                                       
CONECT   13    1    5   20   23                                             
CONECT   14    7   16   20   24                                             
CONECT   15    6   19   22                                                  
CONECT   16   14   17   18   25                                             
CONECT   17    2    9   11   16                                             
CONECT   18    3   10   12   16                                             
CONECT   19    4    8   15   20                                             
CONECT   20   11   13   14   19                                             
CONECT   21   12                                                            
CONECT   22   15                                                            
CONECT   23   13                                                            
CONECT   24   14                                                            
CONECT   25   16                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   56    0
END

Synonyms

Not Available

Molecular Formula

C₂₀H₃₀O₂

Average Mass

302.458

Monoisotopic Mass

302.224580206

IUPAC Name

(1R,2R,6S,9R,10R,11R,14S)-11-(hydroxymethyl)-2,6,11,14-tetramethyltetracyclo[7.6.0.0^{1,6}.0^{10,14}]pentadec-3-en-5-one

Traditional Name

(1R,2R,6S,9R,10R,11R,14S)-11-(hydroxymethyl)-2,6,11,14-tetramethyltetracyclo[7.6.0.0^{1,6}.0^{10,14}]pentadec-3-en-5-one

CAS Registry Number

Not Available

SMILES

[H][C@]12CC[C@]3(C)C(=O)C=C[C@@]([H])(C)[C@]13C[C@]1(C)CC[C@@](C)(CO)[C@]21[H]

InChI Identifier

InChI=1S/C20H30O2/c1-13-5-6-15(22)19(4)8-7-14-16-17(2,11-20(13,14)19)9-10-18(16,3)12-21/h5-6,13-14,16,21H,7-12H2,1-4H3/t13-,14-,16-,17+,18+,19-,20-/m1/s1

InChI Key

WXDDMOJVZBYBSW-QAJMTZOZSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Sesquiterpenoids

Alternative Parents

Substituents

Spirovetivane-type sesquiterpenoid
Sesquiterpenoid
Cyclohexenone
Ketone
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.0071 g/L	ALOGPS
logP	3.32	ALOGPS
logP	3.87	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	18.53	ChemAxon
pKa (Strongest Basic)	-1.3	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	1	ChemAxon
Refractivity	89.3 m³·mol⁻¹	ChemAxon
Polarizability	35.08 Å³	ChemAxon
Number of Rings	4	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

78437359

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25194901

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 Conidiogenone C (MMDBc0009817)

MOL for #<Metabolite:0x0000564fa02a6660>

3D MOL for #<Metabolite:0x0000564fa02a6660>

3D SDF for #<Metabolite:0x0000564fa02a6660>

3D-SDF for #<Metabolite:0x0000564fa02a6660>

PDB for #<Metabolite:0x0000564fa02a6660>

3D PDB for #<Metabolite:0x0000564fa02a6660>

SMILES for #<Metabolite:0x0000564fa02a6660>

INCHI for #<Metabolite:0x0000564fa02a6660>

Structure for #<Metabolite:0x0000564fa02a6660>

3D Structure for #<Metabolite:0x0000564fa02a6660>