MiMeDB: Showing metabocard for Isotuberculosino (MMDBc0007301)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 00:32:15 UTC

Update Date

2022-08-31 06:26:56 UTC

Metabolite ID

MMDBc0007301

Metabolite Identification

Common Name

Isotuberculosino

Description

isotuberculosinol, also known as nosyberkol or edaxadiene, 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 ). Maturation of the phagosome would enable it to kill the bacterium. Nosyberkol was originally isolated in 2004 from a marine sponge in the ocean near island of Nosy Be after which it was named. isotuberculosinol is an extremely weak basic (essentially neutral) compound (based on its pKa). These biosynthetic genes include isotuberculosinol synthase. Isotuberculosinol functions by preventing maturation of the host-cell phagosome in which the bacterium lives. Mutations in genes involved in the biosynthetic pathway of nosyberkol result in normal development of the phagosome and reduction of mycobacterial infection. Isotuberculosinol, also called nosyberkol or edaxadiene is a diterpene molecule produced by the bacterium Mycobacterium tuberculosis, the causative agent of TB, which aids in its pathogenesis. The molecule was characterised as a triterpene but the structure was revised following its chemical synthesis in 2010.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152102322D          

 23 24  0  0  1  0            999 V2000
    0.3565   -2.0219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6131    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6737    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0673   -1.0029    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1027   -1.0445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1690   -2.1652    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
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    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
    2.2296   -0.9012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0421   -1.0445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6993   -1.5332    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3313   -2.0635    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.8250    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
 11 10  1  0  0  0  0
 12  8  1  0  0  0  0
 14 13  1  0  0  0  0
 15  2  1  6  0  0  0
 15 10  1  0  0  0  0
 16 11  2  0  0  0  0
 17  9  1  0  0  0  0
 17 16  1  0  0  0  0
 18  3  1  0  0  0  0
 18  4  1  0  0  0  0
 18 12  1  0  0  0  0
 18 16  1  0  0  0  0
 19  5  1  0  0  0  0
 19  7  1  0  0  0  0
 19 13  1  0  0  0  0
 20  6  1  6  0  0  0
 20 14  1  1  0  0  0
 20 15  1  0  0  0  0
 20 17  1  0  0  0  0
 21 19  1  0  0  0  0
 15 22  1  1  0  0  0
 17 23  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0007301

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(C)CC=C2[C@@]([H])(CCCC2(C)C)[C@]1(C)CCC(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-AIQOQHTRSA-N

> <FORMULA>
C20H34O

> <MOLECULAR_WEIGHT>
290.491

> <EXACT_MASS>
290.260965715

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
55

> <JCHEM_AVERAGE_POLARIZABILITY>
36.26589278952406

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
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>
92.15079999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.42e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
edaxadiene

> <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       0.666  -3.774   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.011   3.490   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.991   3.490   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.992  -1.872   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.658  -1.950   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.182  -4.042   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.162  -1.682   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.679  -1.950   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.172  -2.862   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       4.352  -3.852   0.000  0.00  0.00           O+0
HETATM   22  H   UNK     0       8.002  -1.540   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       5.335  -1.540   0.000  0.00  0.00           H+0
CONECT    1    7                                                            
CONECT    2   15                                                            
CONECT    3   18                                                            
CONECT    4   18                                                            
CONECT    5   19                                                            
CONECT    6   20                                                            
CONECT    7    1   19                                                       
CONECT    8    9   12                                                       
CONECT    9    8   17                                                       
CONECT   10   11   15                                                       
CONECT   11   10   16                                                       
CONECT   12    8   18                                                       
CONECT   13   14   19                                                       
CONECT   14   13   20                                                       
CONECT   15    2   10   20   22                                             
CONECT   16   11   17   18                                                  
CONECT   17    9   16   20   23                                             
CONECT   18    3    4   12   16                                             
CONECT   19    5    7   13   21                                             
CONECT   20    6   14   15   17                                             
CONECT   21   19                                                            
CONECT   22   15                                                            
CONECT   23   17                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

Synonyms

Value	Source
Nosyberkol	ChEBI
Edaxadiene	MeSH

Molecular Formula

C₂₀H₃₄O

Average Mass

290.491

Monoisotopic Mass

290.260965715

IUPAC Name

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

edaxadiene

CAS Registry Number

Not Available

SMILES

[H][C@]1(C)CC=C2[C@@]([H])(CCCC2(C)C)[C@]1(C)CCC(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-AIQOQHTRSA-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

tertiary alcohol (CHEBI:59685 )
carbobicyclic compound (CHEBI:59685 )
halimane diterpenoid (CHEBI:59685 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

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	36.27 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

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

Metabolic Reactions

Not Available

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	Actinobacteria	1	Human	Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	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

26331708

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Isotuberculosinol

METLIN ID

Not Available

PubChem Compound

46224604

PDB ID

Not Available

ChEBI ID

59685

Food Biomarker Ontology

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 Isotuberculosino (MMDBc0007301)

MOL for #<Metabolite:0x00007fece616efd8>

3D MOL for #<Metabolite:0x00007fece616efd8>

3D SDF for #<Metabolite:0x00007fece616efd8>

3D-SDF for #<Metabolite:0x00007fece616efd8>

PDB for #<Metabolite:0x00007fece616efd8>

3D PDB for #<Metabolite:0x00007fece616efd8>

SMILES for #<Metabolite:0x00007fece616efd8>

INCHI for #<Metabolite:0x00007fece616efd8>

Structure for #<Metabolite:0x00007fece616efd8>

3D Structure for #<Metabolite:0x00007fece616efd8>