MiMeDB: Showing metabocard for (13R)-Edaxadiene (MMDBc0057114)

Microbial

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-10-17 17:53:55 UTC

Update Date

2025-10-07 16:09:50 UTC

Metabolite ID

MMDBc0057114

Metabolite Identification

Common Name

(13R)-Edaxadiene

Description

(13R)-Edaxadiene is a sesquiterpene, a class of terpenes composed of three isoprene units. There is limited literature available on this metabolite, indicating that further research may be necessary to fully understand its biological significance and potential applications.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652310172219532D          

 22 23  0  0  1  0            999 V2000
    1.4289   -0.8250    0.0000 H   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   -1.6500    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
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5303    0.6320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5303    0.6320    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   -0.0000    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
    2.1434   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8163   -2.3784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0416   -2.3784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4788   -3.0781    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0915   -3.8065    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3631   -3.4192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8199   -4.1938    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7042   -4.5349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1414   -5.2346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  1  0  0  0  0
  2  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  6  0  0  0
 12 14  1  0  0  0  0
  2 14  1  0  0  0  0
 14 15  1  6  0  0  0
 14 16  1  1  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  6  0  0  0
 18 20  1  6  0  0  0
 18 21  1  0  0  0  0
 21 22  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0057114

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]12CCCC(C)(C)C1=CC[C@H](C)[C@@]2(C)CC[C@@](C)(O)C=C

> <INCHI_IDENTIFIER>
InChI=1S/C20H34O/c1-7-19(5,21)13-14-20(6)15(2)10-11-16-17(20)9-8-12-18(16,3)4/h7,11,15,17,21H,1,8-10,12-14H2,2-6H3/t15-,17+,19-,20+/m0/s1

> <INCHI_KEY>
TXBORCBWDUAHAC-MFHCWRBVSA-N

> <FORMULA>
C20H34O

> <MOLECULAR_WEIGHT>
290.491

> <EXACT_MASS>
290.260965715

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
55

> <JCHEM_AVERAGE_POLARIZABILITY>
36.055740863729746

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3R)-5-[(1R,2S,8aS)-1,2,5,5-tetramethyl-1,2,3,5,6,7,8,8a-octahydronaphthalen-1-yl]-3-methylpent-1-en-3-ol

> <ALOGPS_LOGP>
6.28

> <JCHEM_LOGP>
5.246485932666667

> <ALOGPS_LOGS>
-5.54

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.200526862364963

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3988895504015648

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
92.1508

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.42e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(13R)-edaxadiene

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 17-OCT-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-OCT-22         0                                  
HETATM    1  H   UNK     0       2.667  -1.540   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.990   1.180   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.990   1.180   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.390  -4.440   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.944  -4.440   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.760  -5.746   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.037  -7.105   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.678  -6.382   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       3.397  -7.828   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       1.314  -8.465   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.131  -9.771   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    9   14                                             
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8    9                                             
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    6    2   10                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12    2   15   16                                             
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20   21                                             
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   18   22                                                       
CONECT   22   21                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   46    0
END

Synonyms

Value	Source
(13R)-Isotuberculosinol	ChEBI
(13R)-Nosyberkol	ChEBI

Molecular Formula

C₂₀H₃₄O

Average Mass

290.491

Monoisotopic Mass

290.260965715

IUPAC Name

(3R)-5-[(1R,2S,8aS)-1,2,5,5-tetramethyl-1,2,3,5,6,7,8,8a-octahydronaphthalen-1-yl]-3-methylpent-1-en-3-ol

Traditional Name

(13R)-edaxadiene

CAS Registry Number

Not Available

SMILES

[H][C@@]12CCCC(C)(C)C1=CC[C@H](C)[C@@]2(C)CC[C@@](C)(O)C=C

InChI Identifier

InChI=1S/C20H34O/c1-7-19(5,21)13-14-20(6)15(2)10-11-16-17(20)9-8-12-18(16,3)4/h7,11,15,17,21H,1,8-10,12-14H2,2-6H3/t15-,17+,19-,20+/m0/s1

InChI Key

TXBORCBWDUAHAC-MFHCWRBVSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tertiary alcohols. Tertiary alcohols are compounds in which a hydroxy group, -OH, is attached to a saturated carbon atom R3COH (R not H ).

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Alcohols and polyols

Direct Parent

Tertiary alcohols

Alternative Parents

Hydrocarbon derivatives

Substituents

Tertiary alcohol
Hydrocarbon derivative
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

edaxadiene (CHEBI:63178 )

Functional Ontology

Not Available

Physical Properties

State

Not Available

Predicted Properties

Property	Value	Source
Water Solubility	0.00084 g/L	ALOGPS
logP	6.28	ALOGPS
logP	5.25	ChemAxon
logS	-5.5	ALOGPS
pKa (Strongest Acidic)	18.2	ChemAxon
pKa (Strongest Basic)	-1.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	20.23 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	92.15 m³·mol⁻¹	ChemAxon
Polarizability	36.06 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	Yes	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)	2025-10-24	159.7
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (void)	2025-10-24	31.5
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-24	495.9
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	813.8
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	811.3
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-24	492.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	2846.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-24	93.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	300.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	736.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-24	600.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	213.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	228.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (void)	2025-10-24	8.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	408.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	310.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	421.5
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	1404.0
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	1584.6

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	(13R)-Edaxadiene_TMS_1	C=C[C@@](C)(CC[C@]1(C)[C@@H](C)CC=C2[C@H]1CCCC2(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	1600.54
Gas Chromatography	(13R)-Edaxadiene_TMS_1	C=C[C@@](C)(CC[C@]1(C)[C@@H](C)CC=C2[C@H]1CCCC2(C)C)O[Si](C)(C)C	standard polar	2025-10-24	2139.79

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
MMDBr0024878	tuberculosinyl diphosphate	(13R)-Edaxadiene	Tuberculosinyl adenosine transferase	Transfer of adenosine	RHEA	34755880

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

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

26333002

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

56927769

PDB ID

Not Available

ChEBI ID

63178

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for (13R)-Edaxadiene (MMDBc0057114)

MOL for #<Metabolite:0x00007f9ac3cf8ae0>

3D MOL for #<Metabolite:0x00007f9ac3cf8ae0>

3D SDF for #<Metabolite:0x00007f9ac3cf8ae0>

3D-SDF for #<Metabolite:0x00007f9ac3cf8ae0>

PDB for #<Metabolite:0x00007f9ac3cf8ae0>

3D PDB for #<Metabolite:0x00007f9ac3cf8ae0>

SMILES for #<Metabolite:0x00007f9ac3cf8ae0>

INCHI for #<Metabolite:0x00007f9ac3cf8ae0>

Structure for #<Metabolite:0x00007f9ac3cf8ae0>

3D Structure for #<Metabolite:0x00007f9ac3cf8ae0>