MiMeDB: Showing metabocard for 1(10)E,5E-germacradiene-3,11-diol (MMDBc0013693)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 04:57:28 UTC

Update Date

2025-10-07 16:06:10 UTC

Metabolite ID

MMDBc0013693

Metabolite Identification

Common Name

1(10)E,5E-germacradiene-3,11-diol

Description

1(10)E,5E-germacradiene-3,11-diol is a sesquiterpenoid, a class of chemical compounds known for their diverse biological activities and roles in plant metabolism. This compound has been characterized through extensive NMR studies, revealing its structure alongside related metabolites such as 1(10)E,5E-germacradiene-11-ol and 1(10)E,5E-germacradiene-2,11-diol (PMID:16170856 ). Sesquiterpenoids, including 1(10)E,5E-germacradiene-3,11-diol, are often involved in plant defense mechanisms and can exhibit antimicrobial, anti-inflammatory, and anticancer properties, making them of significant interest in both chemistry and biology. The presence of hydroxyl groups in its structure suggests potential for hydrogen bonding, which may influence its solubility and reactivity, further impacting its biological functions. Understanding the properties and mechanisms of action of such metabolites can provide insights into their potential therapeutic applications and ecological roles.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152106572D          

 23 23  0  0  1  0            999 V2000
    3.5724   -0.4125    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    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6039    1.6500    0.0000 C   0  0  0  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
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  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
    0.7145    1.2375    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
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  5  1  0  0  0  0
  9  7  2  0  0  0  0
 10  6  1  0  0  0  0
 11  1  1  0  0  0  0
 11  5  1  0  0  0  0
 11  6  2  0  0  0  0
 12  2  1  6  0  0  0
 12  7  1  0  0  0  0
 13  8  1  0  0  0  0
 13  9  1  0  0  0  0
 14 10  1  0  0  0  0
 14 12  1  0  0  0  0
 15  3  1  0  0  0  0
 15  4  1  0  0  0  0
 13 15  1  1  0  0  0
 14 16  1  1  0  0  0
 17 15  1  0  0  0  0
 18  6  1  0  0  0  0
 19  7  1  0  0  0  0
 20  9  1  0  0  0  0
 12 21  1  1  0  0  0
 13 22  1  1  0  0  0
 14 23  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0013693

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C1=C(C)\CC[C@]([H])(C([H])=C([H])[C@@]([H])(C)[C@]([H])(O)C1)C(C)(C)O

> <INCHI_IDENTIFIER>
InChI=1S/C15H26O2/c1-11-5-8-13(15(3,4)17)9-7-12(2)14(16)10-6-11/h6-7,9,12-14,16-17H,5,8,10H2,1-4H3/b9-7+,11-6-/t12-,13-,14-/m1/s1

> <INCHI_KEY>
RBBWQOZTCXYKSH-KGZIOKJRSA-N

> <FORMULA>
C15H26O2

> <MOLECULAR_WEIGHT>
238.371

> <EXACT_MASS>
238.193280077

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
28.03962638660316

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2R,3Z,5R,8Z)-5-(2-hydroxypropan-2-yl)-2,8-dimethylcyclodeca-3,8-dien-1-ol

> <ALOGPS_LOGP>
3.08

> <JCHEM_LOGP>
2.568904810333332

> <ALOGPS_LOGS>
-2.83

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.296474671843164

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.885835820041425

> <JCHEM_PKA_STRONGEST_BASIC>
-0.6990786728443242

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
74.1236

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.53e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,3Z,5R,8Z)-5-(2-hydroxypropan-2-yl)-2,8-dimethylcyclodeca-3,8-dien-1-ol

> <JCHEM_VEBER_RULE>
0

$$$$

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       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.127   3.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334   2.310   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       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.667   3.080   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       4.207   3.080   0.000  0.00  0.00           O+0
HETATM   18  H   UNK     0       4.001  -2.310   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0      -1.334   2.310   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       1.334   0.770   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0      -1.334   0.770   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       4.001   0.770   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0      -0.000  -1.540   0.000  0.00  0.00           H+0
CONECT    1   11                                                            
CONECT    2   12                                                            
CONECT    3   15                                                            
CONECT    4   15                                                            
CONECT    5    8   11                                                       
CONECT    6   10   11   18                                                  
CONECT    7    9   12   19                                                  
CONECT    8    5   13                                                       
CONECT    9    7   13   20                                                  
CONECT   10    6   14                                                       
CONECT   11    1    5    6                                                  
CONECT   12    2    7   14   21                                             
CONECT   13    8    9   15   22                                             
CONECT   14   10   12   16   23                                             
CONECT   15    3    4   13   17                                             
CONECT   16   14                                                            
CONECT   17   15                                                            
CONECT   18    6                                                            
CONECT   19    7                                                            
CONECT   20    9                                                            
CONECT   21   12                                                            
CONECT   22   13                                                            
CONECT   23   14                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   46    0
END

Synonyms

Not Available

Molecular Formula

C₁₅H₂₆O₂

Average Mass

238.371

Monoisotopic Mass

238.193280077

IUPAC Name

(1R,2R,3Z,5R,8Z)-5-(2-hydroxypropan-2-yl)-2,8-dimethylcyclodeca-3,8-dien-1-ol

Traditional Name

(1R,2R,3Z,5R,8Z)-5-(2-hydroxypropan-2-yl)-2,8-dimethylcyclodeca-3,8-dien-1-ol

CAS Registry Number

Not Available

SMILES

[H]\C1=C(C)\CC[C@]([H])(C([H])=C([H])[C@@]([H])(C)[C@]([H])(O)C1)C(C)(C)O

InChI Identifier

InChI=1S/C15H26O2/c1-11-5-8-13(15(3,4)17)9-7-12(2)14(16)10-6-11/h6-7,9,12-14,16-17H,5,8,10H2,1-4H3/b9-7+,11-6-/t12-,13-,14-/m1/s1

InChI Key

RBBWQOZTCXYKSH-KGZIOKJRSA-N

Chemical Taxonomy

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.35 g/L	ALOGPS
logP	3.08	ALOGPS
logP	2.57	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	18.89	ChemAxon
pKa (Strongest Basic)	-0.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	40.46 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	74.12 m³·mol⁻¹	ChemAxon
Polarizability	28.04 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	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
Bacteria/Eubacteria	Actinobacteria	1		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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

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 1(10)E,5E-germacradiene-3,11-diol (MMDBc0013693)

MOL for #<Metabolite:0x00007f2ac90e2ae0>

3D MOL for #<Metabolite:0x00007f2ac90e2ae0>

3D SDF for #<Metabolite:0x00007f2ac90e2ae0>

3D-SDF for #<Metabolite:0x00007f2ac90e2ae0>

PDB for #<Metabolite:0x00007f2ac90e2ae0>

3D PDB for #<Metabolite:0x00007f2ac90e2ae0>

SMILES for #<Metabolite:0x00007f2ac90e2ae0>

INCHI for #<Metabolite:0x00007f2ac90e2ae0>

Structure for #<Metabolite:0x00007f2ac90e2ae0>

3D Structure for #<Metabolite:0x00007f2ac90e2ae0>