MiMeDB: Showing metabocard for cubebol (MMDBc0054405)

Xenobiotic

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:11:00 UTC

Update Date

2025-10-07 16:08:30 UTC

Metabolite ID

MMDBc0054405

Metabolite Identification

Common Name

cubebol

Description

Cubebol is a sesquiterpene metabolite characterized by its unique chemical structure, which includes a bicyclic framework typical of many terpenes. It is primarily synthesized through the cyclization of farnesyl pyrophosphate (FPP) by various enzymes, including sesquiterpene synthases, which exhibit cofactor-dependent catalysis, utilizing divalent metal ions such as Mn2+, Co2+, or Ni2+ (PMID:38527951 ). Cubebol is notable for its role in generating diverse aromatic compounds, contributing to the woody floral scent profile in certain plant extracts (PMID:39493592 ). It is also involved in complex biosynthetic pathways, where it is formed alongside other compounds like beta-myrcene and beta-phellandrene, enhancing the sensory characteristics of products such as tea (PMID:38540936 ). Additionally, cubebol has been identified as a major product in various essential oils, where it coexists with other oxygenated sesquiterpenes, indicating its significance in the chemical composition of these natural extracts (PMID:38929167 ). Its applications extend to the food industry, where it is valued for its long-lasting cooling and refreshing properties (PMID:40401765 ). Overall, cubebol exemplifies the intricate interplay between chemistry and biology in natural product synthesis.

Structure

MOL SDF PDB SMILES InChI


  Mrv1572004251600532D          

 20 22  0  0  1  0            999 V2000
    2.4747    3.2712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7452    2.6171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4105   -0.3565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0280    2.3698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6122    0.4166    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9899    1.1501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0509    0.7307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8199    0.4318    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9211    2.5774    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7882    0.3770    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5435    1.8439    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7194    1.8042    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8954    1.7645    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0976    1.5544    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3418    1.0708    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7264    1.5147    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2346   -0.3168    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3675    1.8836    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6797    2.6283    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7698    2.5799    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
  9  1  1  0  0  0  0
  9  2  1  0  0  0  0
 10  3  1  1  0  0  0
 10  5  1  0  0  0  0
 11  6  1  0  0  0  0
 11  9  1  6  0  0  0
 12 11  1  0  0  0  0
 13 12  1  0  0  0  0
 14  4  1  1  0  0  0
 14  7  1  0  0  0  0
 14 13  1  0  0  0  0
 15  8  1  6  0  0  0
 15 10  1  0  0  0  0
 15 12  1  0  0  0  0
 15 13  1  0  0  0  0
 14 16  1  6  0  0  0
 10 17  1  6  0  0  0
 11 18  1  1  0  0  0
 12 19  1  6  0  0  0
 13 20  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054405

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]12[C@]3([H])[C@]1(CC[C@]3(C)O)[C@]([H])(C)CC[C@@]2([H])C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C15H26O/c1-9(2)11-6-5-10(3)15-8-7-14(4,16)13(15)12(11)15/h9-13,16H,5-8H2,1-4H3/t10-,11+,12-,13+,14+,15-/m1/s1

> <INCHI_KEY>
KONGRWVLXLWGDV-BYGOPZEFSA-N

> <FORMULA>
C15H26O

> <MOLECULAR_WEIGHT>
222.372

> <EXACT_MASS>
222.198365457

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
27.446667116137462

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,4S,5R,6R,7S,10R)-4,10-dimethyl-7-(propan-2-yl)tricyclo[4.4.0.0¹,⁵]decan-4-ol

> <ALOGPS_LOGP>
2.93

> <JCHEM_LOGP>
3.1785024189999995

> <ALOGPS_LOGS>
-4.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
19.3935086763188

> <JCHEM_PKA_STRONGEST_BASIC>
-0.8770793049781566

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
66.60000000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.81e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(-)-cubebol

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 25-APR-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-16         0                                  
HETATM    1  C   UNK     0       4.619   6.106   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.991   4.885   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.633  -0.666   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.052   4.424   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.876   0.778   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.581   2.147   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.095   1.364   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.530   0.806   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.453   4.811   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.338   0.704   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.748   3.442   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.210   3.368   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.671   3.294   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.182   2.902   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.505   1.999   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -1.356   2.827   0.000  0.00  0.00           O+0
HETATM   17  H   UNK     0       4.171  -0.591   0.000  0.00  0.00           H+0
HETATM   18  H   UNK     0       6.286   3.516   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       3.136   4.906   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       1.437   4.816   0.000  0.00  0.00           H+0
CONECT    1    9                                                            
CONECT    2    9                                                            
CONECT    3   10                                                            
CONECT    4   14                                                            
CONECT    5    6   10                                                       
CONECT    6    5   11                                                       
CONECT    7    8   14                                                       
CONECT    8    7   15                                                       
CONECT    9    1    2   11                                                  
CONECT   10    3    5   15   17                                             
CONECT   11    6    9   12   18                                             
CONECT   12   11   13   15   19                                             
CONECT   13   12   14   15   20                                             
CONECT   14    4    7   13   16                                             
CONECT   15    8   10   12   13                                             
CONECT   16   14                                                            
CONECT   17   10                                                            
CONECT   18   11                                                            
CONECT   19   12                                                            
CONECT   20   13                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

Synonyms

Value	Source
(-)-(1R,4S,5R,6R,7S,10R)-7-Isopropyl-4,10-dimethyl-tricyclo[4.4.0.0(1,5)]decan-4-ol	ChEBI
(1R,4S,5R,6R,7S,10R)-7-Isopropyl-4,10-dimethyl-tricyclo[4.4.0.0(1,5)]decan-4-ol	ChEBI
Cubeb camphor	ChEBI
Cubebol	ChEBI

Molecular Formula

C₁₅H₂₆O

Average Mass

222.372

Monoisotopic Mass

222.198365457

IUPAC Name

(1R,4S,5R,6R,7S,10R)-4,10-dimethyl-7-(propan-2-yl)tricyclo[4.4.0.0¹,⁵]decan-4-ol

Traditional Name

(-)-cubebol

CAS Registry Number

Not Available

SMILES

[H][C@@]12[C@]3([H])[C@]1(CC[C@]3(C)O)[C@]([H])(C)CC[C@@]2([H])C(C)C

InChI Identifier

InChI=1S/C15H26O/c1-9(2)11-6-5-10(3)15-8-7-14(4,16)13(15)12(11)15/h9-13,16H,5-8H2,1-4H3/t10-,11+,12-,13+,14+,15-/m1/s1

InChI Key

KONGRWVLXLWGDV-BYGOPZEFSA-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

Cubebane sesquiterpenoid
Sesquiterpenoid
Tertiary alcohol
Cyclic alcohol
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

tertiary alcohol (CHEBI:63446 )
sesquiterpenoid (CHEBI:63446 )
carbotricyclic compound (CHEBI:63446 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.0038 g/L	ALOGPS
logP	2.93	ALOGPS
logP	3.18	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	19.39	ChemAxon
pKa (Strongest Basic)	-0.88	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	1	ChemAxon
Refractivity	66.6 m³·mol⁻¹	ChemAxon
Polarizability	27.45 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 GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0ab9-0290000000-eaf17eb89a13ad5acfcc	2016-06-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0ab9-3960000000-fe1734227dde7b7a6078	2016-06-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0aor-9800000000-cc948286749db915ffd7	2016-06-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-0090000000-d8cf21e6ced5f3976005	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00di-0090000000-f4bee99b8262c5e6ba98	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0bvi-1940000000-e063c3ef8bf808a8820c	2016-08-03	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum

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	171.9
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	26.5
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-24	498.7
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	804.8
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	812.8
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-24	530.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	2463.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-24	88.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	414.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	645.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	557.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	248.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	203.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	9.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	395.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	416.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	423.4
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	1510.8
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	1333.1

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	cubebol_TMS_1	CC(C)[C@@H]1CC[C@@H](C)[C@@]23CC[C@](C)(O[Si](C)(C)C)[C@@H]2[C@@H]13	standard non polar	2025-10-24	1689.72
Gas Chromatography	cubebol_TMS_1	CC(C)[C@@H]1CC[C@@H](C)[C@@]23CC[C@](C)(O[Si](C)(C)C)[C@@H]2[C@@H]13	standard polar	2025-10-24	1886.63

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	Basidiomycota	1

Exposure Sources

Other Exposures

Source Type	Data Source	Reference
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox

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

11276107

PDB ID

Not Available

ChEBI ID

63446

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 cubebol (MMDBc0054405)

MOL for #<Metabolite:0x00007f9aa689f830>

3D MOL for #<Metabolite:0x00007f9aa689f830>

3D SDF for #<Metabolite:0x00007f9aa689f830>

3D-SDF for #<Metabolite:0x00007f9aa689f830>

PDB for #<Metabolite:0x00007f9aa689f830>

3D PDB for #<Metabolite:0x00007f9aa689f830>

SMILES for #<Metabolite:0x00007f9aa689f830>

INCHI for #<Metabolite:0x00007f9aa689f830>

Structure for #<Metabolite:0x00007f9aa689f830>

3D Structure for #<Metabolite:0x00007f9aa689f830>