MiMeDB: Showing metabocard for Gamma-Patchoulene (MMDBc0017073)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 07:32:34 UTC

Update Date

2025-10-07 16:06:37 UTC

Metabolite ID

MMDBc0017073

Metabolite Identification

Common Name

Gamma-Patchoulene

Description

Gamma-Patchoulene is a sesquiterpene hydrocarbon, classified within the chemical class of terpenes. Its chemical structure features a complex arrangement of carbon atoms, typically comprising 15 carbons, which contributes to its unique properties and interactions. In the context of plant metabolism, gamma-patchoulene is synthesized through the mevalonate pathway, where it is derived from farnesyl pyrophosphate, a key precursor in the biosynthesis of various terpenes. It is notably present in the essential oils of certain plants, such as those analyzed in a study where gamma-patchoulene constituted 11.0% of the leaf oil composition (PMID:22224304 ). This compound plays a role in the aromatic profile of these oils, which can attract pollinators or deter herbivores. Additionally, gamma-patchoulene may participate in various biochemical pathways, contributing to the plant's defense mechanisms and ecological interactions. Its presence in essential oils highlights its potential applications in fragrance and flavor industries, as well as its significance in understanding plant secondary metabolite production.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152109322D          

 18 20  0  0  1  0            999 V2000
   -0.5052    0.4914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7615    3.2195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5854    1.5324    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2237    2.0547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7697    2.1676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9136    1.3280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1351    1.9192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5799    2.3467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4754    0.3953    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0428    1.1081    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9336    2.4127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2454    0.7787    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8674    1.0272    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7785    1.3601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2471    1.8280    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3436    0.3399    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6940    0.0863    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6816    1.1600    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0  0  0  0
  8  7  1  0  0  0  0
 10  1  1  6  0  0  0
 10  7  1  0  0  0  0
 11  2  2  0  0  0  0
 11  5  1  0  0  0  0
 12  6  1  0  0  0  0
 12  9  1  0  0  0  0
 13  9  1  0  0  0  0
 13 10  1  0  0  0  0
 14  3  1  0  0  0  0
 14  4  1  0  0  0  0
 14 12  1  0  0  0  0
 15  8  1  6  0  0  0
 15 11  1  0  0  0  0
 15 13  1  0  0  0  0
 15 14  1  0  0  0  0
 10 16  1  1  0  0  0
 12 17  1  1  0  0  0
 13 18  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0017073

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(C)CC[C@@]23C(=C)CC[C@]([H])(C[C@]12[H])C3(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C15H24/c1-10-7-8-15-11(2)5-6-12(9-13(10)15)14(15,3)4/h10,12-13H,2,5-9H2,1,3-4H3/t10-,12-,13-,15-/m1/s1

> <INCHI_KEY>
SLTLKLCDQWGISZ-BPGGGUHBSA-N

> <FORMULA>
C15H24

> <MOLECULAR_WEIGHT>
204.357

> <EXACT_MASS>
204.187800773

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
148.32317858934744

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,4R,5R,7R)-4,11,11-trimethyl-10-methylidenetricyclo[5.3.1.0^{1,5}]undecane

> <ALOGPS_LOGP>
5.35

> <JCHEM_LOGP>
4.159091856666667

> <ALOGPS_LOGS>
-5.20

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
64.6219

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.29e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,4R,5R,7R)-4,11,11-trimethyl-10-methylidenetricyclo[5.3.1.0^{1,5}]undecane

> <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      -0.943   0.917   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.288   6.010   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.826   2.860   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.151   3.836   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.170   4.046   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.439   2.479   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.252   3.583   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.082   4.381   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.754   0.738   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.080   2.069   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.609   4.504   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.191   1.454   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.619   1.917   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.320   2.539   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.328   3.412   0.000  0.00  0.00           C+0
HETATM   16  H   UNK     0       0.641   0.635   0.000  0.00  0.00           H+0
HETATM   17  H   UNK     0       5.029   0.161   0.000  0.00  0.00           H+0
HETATM   18  H   UNK     0       3.139   2.165   0.000  0.00  0.00           H+0
CONECT    1   10                                                            
CONECT    2   11                                                            
CONECT    3   14                                                            
CONECT    4   14                                                            
CONECT    5    6   11                                                       
CONECT    6    5   12                                                       
CONECT    7    8   10                                                       
CONECT    8    7   15                                                       
CONECT    9   12   13                                                       
CONECT   10    1    7   13   16                                             
CONECT   11    2    5   15                                                  
CONECT   12    6    9   14   17                                             
CONECT   13    9   10   15   18                                             
CONECT   14    3    4   12   15                                             
CONECT   15    8   11   13   14                                             
CONECT   16   10                                                            
CONECT   17   12                                                            
CONECT   18   13                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

Synonyms

Value	Source
g-Patchoulene	Generator
Γ-patchoulene	Generator

Molecular Formula

C₁₅H₂₄

Average Mass

204.357

Monoisotopic Mass

204.187800773

IUPAC Name

(1S,4R,5R,7R)-4,11,11-trimethyl-10-methylidenetricyclo[5.3.1.0^{1,5}]undecane

Traditional Name

(1S,4R,5R,7R)-4,11,11-trimethyl-10-methylidenetricyclo[5.3.1.0^{1,5}]undecane

CAS Registry Number

Not Available

SMILES

[H][C@@]1(C)CC[C@@]23C(=C)CC[C@]([H])(C[C@]12[H])C3(C)C

InChI Identifier

InChI=1S/C15H24/c1-10-7-8-15-11(2)5-6-12(9-13(10)15)14(15,3)4/h10,12-13H,2,5-9H2,1,3-4H3/t10-,12-,13-,15-/m1/s1

InChI Key

SLTLKLCDQWGISZ-BPGGGUHBSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Sesquiterpenoids

Alternative Parents

Substituents

Patchoulane sesquiterpenoid
Sesquiterpenoid
Branched unsaturated hydrocarbon
Polycyclic hydrocarbon
Cyclic olefin
Unsaturated aliphatic hydrocarbon
Unsaturated hydrocarbon
Olefin
Hydrocarbon
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.0013 g/L	ALOGPS
logP	5.35	ALOGPS
logP	4.16	ChemAxon
logS	-5.2	ALOGPS
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	0 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	64.62 m³·mol⁻¹	ChemAxon
Polarizability	148.32 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-10	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	View Spectrum

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
Eukaryota/Fungi	Ascomycota	1	Human feces	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

C00055858

Chemspider ID

78439817

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139587800

PDB ID

Not Available

ChEBI ID

Not Available

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 Gamma-Patchoulene (MMDBc0017073)

MOL for #<Metabolite:0x00007f8de861d118>

3D MOL for #<Metabolite:0x00007f8de861d118>

3D SDF for #<Metabolite:0x00007f8de861d118>

3D-SDF for #<Metabolite:0x00007f8de861d118>

PDB for #<Metabolite:0x00007f8de861d118>

3D PDB for #<Metabolite:0x00007f8de861d118>

SMILES for #<Metabolite:0x00007f8de861d118>

INCHI for #<Metabolite:0x00007f8de861d118>

Structure for #<Metabolite:0x00007f8de861d118>

3D Structure for #<Metabolite:0x00007f8de861d118>