MiMeDB: Showing metabocard for Edaxadiene (MMDBc0003019)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-14 21:10:48 UTC

Update Date

2025-10-07 16:04:40 UTC

Metabolite ID

MMDBc0003019

Metabolite Identification

Common Name

Edaxadiene

Description

Edaxadiene is a diterpene metabolite described in biomedical literature. It is produced in vitro from geranylgeranyl diphosphate by the enzymes Rv3377c and Rv3378c in Mycobacterium tuberculosis (Mtb), where it is the most abundant diterpene, exhibiting a specific mass fragmentation pattern (PMID:20670276 ). A related compound, olefin edaxadiene B, is consistently found in the same proportions relative to edaxadiene, suggesting it is a side product of the Rv3378c reaction in vivo (PMID:20670276 ). Additionally, tuberculosinol, a dephosphorylated side-product of the edaxadiene pathway, is the least abundant diterpene in Mtb extracts (PMID:20670276 ). The biosynthetic pathway of edaxadiene and edaxadiene B has been defined through these studies (PMID:20670276 ). Synthesis efforts have led to a structural revision of edaxadiene, with a stereodivergent synthesis of its bicyclic core achieved through a key intramolecular oxidative ketone allylation (PMID:22114734 ). However, discrepancies between spectroscopic data of synthetic constructs and natural isolates have raised questions regarding the structural assignment of edaxadiene (PMID:22114734 ). Further synthesis work has also focused on related compounds, including isotuberculosinol (PMID:20462237 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305142123102D          

 23 25  0  0  1  0            999 V2000
   -0.8609   -1.4870    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5229    0.5713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5682   -1.5264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6249   -1.4365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5006   -0.5250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8454    1.6388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0389   -1.4170    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6499    0.4419    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9031    0.7923    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7199   -0.3801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2416    0.1519    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7734    0.7826    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7643   -1.1320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0120   -0.0931    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2261    0.3207    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9423   -1.2020    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2961   -0.5013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0430   -0.8517    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3115   -0.6702    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5954    0.8525    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7982   -0.3430    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9730   -0.0297    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6923   -1.9882    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  1  2  0  0  0  0
  9  8  1  0  0  0  0
 10  8  1  0  0  0  0
 12 11  1  0  0  0  0
 14  2  1  0  0  0  0
 15  9  1  0  0  0  0
 16 13  1  0  0  0  0
 16 14  1  0  0  0  0
 17 13  2  0  0  0  0
 17 15  1  0  0  0  0
 18  3  1  0  0  0  0
 18  4  1  0  0  0  0
 18 10  1  0  0  0  0
 18 17  1  0  0  0  0
 19  5  1  0  0  0  0
 19  7  1  0  0  0  0
 19 11  1  0  0  0  0
 19 16  1  0  0  0  0
 20  6  1  6  0  0  0
 20 12  1  0  0  0  0
 20 14  1  0  0  0  0
 20 15  1  0  0  0  0
 14 21  1  1  0  0  0
 15 22  1  1  0  0  0
 16 23  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0003019

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(C)[C@@]2([H])C=C3[C@@]([H])(CCCC3(C)C)[C@]1(C)CCC2(C)C=C

> <INCHI_IDENTIFIER>
InChI=1S/C20H32/c1-7-19(5)11-12-20(6)14(2)16(19)13-17-15(20)9-8-10-18(17,3)4/h7,13-16H,1,8-12H2,2-6H3/t14-,15+,16+,19?,20+/m0/s1

> <INCHI_KEY>
LVOPFKOBFNNZTP-HQCSLPMPSA-N

> <FORMULA>
C20H32

> <MOLECULAR_WEIGHT>
272.476

> <EXACT_MASS>
272.25040103

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
52

> <JCHEM_AVERAGE_POLARIZABILITY>
34.174299417444

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2S,9R,13S)-10-ethenyl-1,6,6,10,13-pentamethyltricyclo[7.3.1.0^{2,7}]tridec-7-ene

> <ALOGPS_LOGP>
5.83

> <JCHEM_LOGP>
5.717942411333334

> <ALOGPS_LOGS>
-6.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
88.56519999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.84e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S,9R,13S)-10-ethenyl-1,6,6,10,13-pentamethyltricyclo[7.3.1.0^{2,7}]tridec-7-ene

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 14-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-21         0                                  
HETATM    1  C   UNK     0      -1.607  -2.776   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.976   1.066   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.794  -2.849   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.767  -2.681   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.934  -0.980   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.445   3.059   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.073  -2.645   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.813   0.825   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.419   1.479   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.944  -0.710   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.451   0.283   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.444   1.461   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.293  -2.113   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.889  -0.174   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.155   0.599   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.759  -2.244   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.286  -0.936   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.680  -1.590   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.582  -1.251   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.978   1.591   0.000  0.00  0.00           C+0
HETATM   21  H   UNK     0       3.357  -0.640   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       5.550  -0.055   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       1.292  -3.711   0.000  0.00  0.00           H+0
CONECT    1    7                                                            
CONECT    2   14                                                            
CONECT    3   18                                                            
CONECT    4   18                                                            
CONECT    5   19                                                            
CONECT    6   20                                                            
CONECT    7    1   19                                                       
CONECT    8    9   10                                                       
CONECT    9    8   15                                                       
CONECT   10    8   18                                                       
CONECT   11   12   19                                                       
CONECT   12   11   20                                                       
CONECT   13   16   17                                                       
CONECT   14    2   16   20   21                                             
CONECT   15    9   17   20   22                                             
CONECT   16   13   14   19   23                                             
CONECT   17   13   15   18                                                  
CONECT   18    3    4   10   17                                             
CONECT   19    5    7   11   16                                             
CONECT   20    6   12   14   15                                             
CONECT   21   14                                                            
CONECT   22   15                                                            
CONECT   23   16                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   50    0
END

Synonyms

Value	Source
Edaxadiene	ChEBI

Molecular Formula

C₂₀H₃₂

Average Mass

272.476

Monoisotopic Mass

272.25040103

IUPAC Name

(1R,2S,9R,13S)-10-ethenyl-1,6,6,10,13-pentamethyltricyclo[7.3.1.0^{2,7}]tridec-7-ene

Traditional Name

(1R,2S,9R,13S)-10-ethenyl-1,6,6,10,13-pentamethyltricyclo[7.3.1.0^{2,7}]tridec-7-ene

CAS Registry Number

Not Available

SMILES

[H][C@]1(C)[C@@]2([H])C=C3[C@@]([H])(CCCC3(C)C)[C@]1(C)CCC2(C)C=C

InChI Identifier

InChI=1S/C20H32/c1-7-19(5)11-12-20(6)14(2)16(19)13-17-15(20)9-8-10-18(17,3)4/h7,13-16H,1,8-12H2,2-6H3/t14-,15+,16+,19?,20+/m0/s1

InChI Key

LVOPFKOBFNNZTP-HQCSLPMPSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as polycyclic hydrocarbons. These are polycyclic organic compounds made up only of carbon and hydrogen atoms.

Kingdom

Organic compounds

Super Class

Hydrocarbons

Class

Polycyclic hydrocarbons

Sub Class

Not Available

Direct Parent

Polycyclic hydrocarbons

Alternative Parents

Substituents

Polycyclic hydrocarbon
Cyclic olefin
Unsaturated aliphatic hydrocarbon
Unsaturated hydrocarbon
Olefin
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

halimane diterpenoid (CHEBI:59694 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.00018 g/L	ALOGPS
logP	5.83	ALOGPS
logP	5.72	ChemAxon
logS	-6.2	ALOGPS
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	0 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	88.57 m³·mol⁻¹	ChemAxon
Polarizability	34.17 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

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 (void)	2025-10-23	483.7
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (void)	2025-10-23	32.7
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	688.3
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	1126.9
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	1030.4
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-23	869.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	3090.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	104.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	558.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	996.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	811.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	473.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	309.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (void)	2025-10-23	8.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	566.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	571.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	575.4
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	1998.1
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	2056.8

Retention Indices

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

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
Bacteria/Eubacteria	Actinobacteria	1	Human	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

26331711

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44607095

PDB ID

Not Available

ChEBI ID

59694

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 Edaxadiene (MMDBc0003019)

MOL for #<Metabolite:0x00007f2e25aff528>

3D MOL for #<Metabolite:0x00007f2e25aff528>

3D SDF for #<Metabolite:0x00007f2e25aff528>

3D-SDF for #<Metabolite:0x00007f2e25aff528>

PDB for #<Metabolite:0x00007f2e25aff528>

3D PDB for #<Metabolite:0x00007f2e25aff528>

SMILES for #<Metabolite:0x00007f2e25aff528>

INCHI for #<Metabolite:0x00007f2e25aff528>

Structure for #<Metabolite:0x00007f2e25aff528>

3D Structure for #<Metabolite:0x00007f2e25aff528>