MiMeDB: Showing metabocard for Germacrene A (MMDBc0009222)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 01:48:05 UTC

Update Date

2022-08-31 06:29:46 UTC

Metabolite ID

MMDBc0009222

Metabolite Identification

Common Name

Germacrene A

Description

germacrene a belongs to the class of organic compounds known as germacrane sesquiterpenoids. These are sesquiterpenoids having the germacrane skeleton, with a structure characterized by a cyclodecane ring substituted with an isopropyl and two methyl groups. Based on a literature review a significant number of articles have been published on germacrene a.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152103482D          

 17 17  0  0  0  0            999 V2000
    0.8889   -1.3025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1913   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3488    2.4393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5893   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6990    0.7243    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.5039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5091    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0787    1.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2391   -0.8348    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3488    0.2566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.6789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6188   -0.5230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6188    1.6598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7792   -0.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1589    0.1007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9690    2.1275    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5091   -1.6143    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0  0  0  0
  7  5  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12  1  2  0  0  0  0
 12  2  1  0  0  0  0
 13  3  1  0  0  0  0
 13  6  2  0  0  0  0
 13  8  1  0  0  0  0
 14  4  1  0  0  0  0
 14  7  1  0  0  0  0
 14  9  2  0  0  0  0
 15 10  1  0  0  0  0
 15 11  1  0  0  0  0
 15 12  1  0  0  0  0
 16  6  1  0  0  0  0
 17  9  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0009222

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C1=C(C)\CCC(C\C([H])=C(C)/CC1)C(C)=C

> <INCHI_IDENTIFIER>
InChI=1S/C15H24/c1-12(2)15-10-8-13(3)6-5-7-14(4)9-11-15/h6,9,15H,1,5,7-8,10-11H2,2-4H3/b13-6-,14-9-

> <INCHI_KEY>
XMRKUJJDDKYUHV-OMQMMEOVSA-N

> <FORMULA>
C15H24

> <MOLECULAR_WEIGHT>
204.357

> <EXACT_MASS>
204.187800773

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
25.801563996367264

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1Z,5Z)-1,5-dimethyl-8-(prop-1-en-2-yl)cyclodeca-1,5-diene

> <ALOGPS_LOGP>
6.02

> <JCHEM_LOGP>
4.879526926666667

> <ALOGPS_LOGS>
-4.38

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
70.2829

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.46e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1Z,5Z)-1,5-dimethyl-8-(prop-1-en-2-yl)cyclodeca-1,5-diene

> <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       1.659  -2.431   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.357  -0.685   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.651   4.553   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.700  -0.685   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.171   1.352   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   2.807   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.684   1.061   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.147   1.934   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.180  -1.558   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.651   0.479   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667  -1.267   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.155  -0.976   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.155   3.098   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.188  -0.394   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.163   0.188   0.000  0.00  0.00           C+0
HETATM   16  H   UNK     0       3.676   3.971   0.000  0.00  0.00           H+0
HETATM   17  H   UNK     0       4.684  -3.013   0.000  0.00  0.00           H+0
CONECT    1   12                                                            
CONECT    2   12                                                            
CONECT    3   13                                                            
CONECT    4   14                                                            
CONECT    5    6    7                                                       
CONECT    6    5   13   16                                                  
CONECT    7    5   14                                                       
CONECT    8   10   13                                                       
CONECT    9   11   14   17                                                  
CONECT   10    8   15                                                       
CONECT   11    9   15                                                       
CONECT   12    1    2   15                                                  
CONECT   13    3    6    8                                                  
CONECT   14    4    7    9                                                  
CONECT   15   10   11   12                                                  
CONECT   16    6                                                            
CONECT   17    9                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END

Synonyms

Not Available

Molecular Formula

C₁₅H₂₄

Average Mass

204.357

Monoisotopic Mass

204.187800773

IUPAC Name

(1Z,5Z)-1,5-dimethyl-8-(prop-1-en-2-yl)cyclodeca-1,5-diene

Traditional Name

(1Z,5Z)-1,5-dimethyl-8-(prop-1-en-2-yl)cyclodeca-1,5-diene

CAS Registry Number

Not Available

SMILES

[H]\C1=C(C)\CCC(C\C([H])=C(C)/CC1)C(C)=C

InChI Identifier

InChI=1S/C15H24/c1-12(2)15-10-8-13(3)6-5-7-14(4)9-11-15/h6,9,15H,1,5,7-8,10-11H2,2-4H3/b13-6-,14-9-

InChI Key

XMRKUJJDDKYUHV-OMQMMEOVSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as germacrane sesquiterpenoids. These are sesquiterpenoids having the germacrane skeleton, with a structure characterized by a cyclodecane ring substituted with an isopropyl and two methyl groups.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Germacrane sesquiterpenoids

Alternative Parents

Substituents

Germacrane sesquiterpenoid
Branched unsaturated hydrocarbon
Cyclic olefin
Unsaturated aliphatic hydrocarbon
Unsaturated hydrocarbon
Olefin
Hydrocarbon
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	0.0085 g/L	ALOGPS
logP	6.02	ALOGPS
logP	4.88	ChemAxon
logS	-4.4	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	70.28 m³·mol⁻¹	ChemAxon
Polarizability	25.8 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

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0013125	Farnesyl pyrophosphate	Germacrene A	Alpha-muurolene synthase	Synthesis	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
Eukaryota/Fungi	Basidiomycota	1
Eukaryota/Fungi	Ascomycota	2		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

C00011719

Chemspider ID

20122171

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5353644

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

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 Germacrene A (MMDBc0009222)

MOL for #<Metabolite:0x00007fa48ed63be0>

3D MOL for #<Metabolite:0x00007fa48ed63be0>

3D SDF for #<Metabolite:0x00007fa48ed63be0>

3D-SDF for #<Metabolite:0x00007fa48ed63be0>

PDB for #<Metabolite:0x00007fa48ed63be0>

3D PDB for #<Metabolite:0x00007fa48ed63be0>

SMILES for #<Metabolite:0x00007fa48ed63be0>

INCHI for #<Metabolite:0x00007fa48ed63be0>

Structure for #<Metabolite:0x00007fa48ed63be0>

3D Structure for #<Metabolite:0x00007fa48ed63be0>