NP-MRD: Showing NP-Card for Xanthorrhizol (NP0049050)

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Record Information

Version

2.0

Created at

2022-03-17 21:06:20 UTC

Updated at

2022-03-17 21:06:20 UTC

NP-MRD ID

NP0049050

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Xanthorrhizol

Description

Xanthorrhizol belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. Xanthorrhizol is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Xanthorrhizol is found, on average, in the highest concentration within gingers. Xanthorrhizol has also been detected, but not quantified in, a few different foods, such as beverages, herbs and spices, and root vegetables. Xanthorrhizol is found in Cinnamomum iners, Commiphora kua, Curcuma aromatica , Curcuma longa , Curcuma xanthorrhiza and Iostephane heterophylla. Xanthorrhizol was first documented in 2007 (PMID: 17465228). This could make xanthorrhizol a potential biomarker for the consumption of these foods (PMID: 21478819) (PMID: 18810881).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05061310172D          

 16 16  0  0  0  0            999 V2000
   -1.4289    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    4.9500    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
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    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
    1.4289    0.8250    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
   -0.7145    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    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
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   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
  9  8  2  0  0  0  0
 11  1  1  0  0  0  0
 11  2  1  0  0  0  0
 11  6  2  0  0  0  0
 12  3  1  0  0  0  0
 12  7  1  0  0  0  0
 13  4  1  0  0  0  0
 13  8  1  0  0  0  0
 14  9  1  0  0  0  0
 14 10  2  0  0  0  0
 14 12  1  0  0  0  0
 15 10  1  0  0  0  0
 15 13  2  0  0  0  0
 16 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0049050

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(CCC=C(C)C)C1=CC(O)=C(C)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C15H22O/c1-11(2)6-5-7-12(3)14-9-8-13(4)15(16)10-14/h6,8-10,12,16H,5,7H2,1-4H3

> <INCHI_KEY>
FKWGCEDRLNNZOZ-UHFFFAOYSA-N

> <FORMULA>
C15H22O

> <MOLECULAR_WEIGHT>
218.3346

> <EXACT_MASS>
218.167065326

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
27.063389183292504

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-methyl-5-(6-methylhept-5-en-2-yl)phenol

> <ALOGPS_LOGP>
5.64

> <JCHEM_LOGP>
5.0878253093333345

> <ALOGPS_LOGS>
-3.88

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.41717718532451

> <JCHEM_PKA_STRONGEST_BASIC>
-5.466329342299741

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
71.0735

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.89e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-methyl-5-(6-methylhept-5-en-2-yl)phenol

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0      -2.667   9.240   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   9.240   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       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334   6.930   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   4.620   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       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.334   8.470   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
CONECT    1   11                                                            
CONECT    2   11                                                            
CONECT    3   12                                                            
CONECT    4   13                                                            
CONECT    5    6    7                                                       
CONECT    6    5   11                                                       
CONECT    7    5   12                                                       
CONECT    8    9   13                                                       
CONECT    9    8   14                                                       
CONECT   10   14   15                                                       
CONECT   11    1    2    6                                                  
CONECT   12    3    7   14                                                  
CONECT   13    4    8   15                                                  
CONECT   14    9   10   12                                                  
CONECT   15   10   13   16                                                  
CONECT   16   15                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

View in JSmol

Synonyms

Value	Source
(-)-5-(1,5-Dimethyl-4-hexenyl)-2-methylphenol	HMDB
(R)-(-)-Xanthorrhizol	HMDB
(R)-5-(1,5-Dimethyl-4-hexenyl)-O-cresol	HMDB
(R)-5-(1-5-Dimethyl-4-hexenyl)-2-methylphenol	HMDB
5-(1,5-Dimethyl-4-hexenyl)-(-)-O-cresol	HMDB
5-(1,5-Dimethyl-4-hexenyl)-2-methyl-(-)-phenol	HMDB
5-(1,5-Dimethyl-4-hexenyl)-2-methylphenol	HMDB
5-(1,5-Dimethyl-4-hexenyl)-2-methylphenol, 9ci	HMDB
5-[(1R)-1,5-Dimethyl-4-hexenyl]-2-methyl-phenol	HMDB

Chemical Formula

C₁₅H₂₂O

Average Mass

218.3346 Da

Monoisotopic Mass

218.16707 Da

IUPAC Name

2-methyl-5-(6-methylhept-5-en-2-yl)phenol

Traditional Name

2-methyl-5-(6-methylhept-5-en-2-yl)phenol

CAS Registry Number

30199-26-9

SMILES

CC(CCC=C(C)C)C1=CC(O)=C(C)C=C1

InChI Identifier

InChI=1S/C15H22O/c1-11(2)6-5-7-12(3)14-9-8-13(4)15(16)10-14/h6,8-10,12,16H,5,7H2,1-4H3

InChI Key

FKWGCEDRLNNZOZ-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Cinnamomum iners	LOTUS Database	35616633
Commiphora kua	LOTUS Database	35616633
Curcuma aromatica	Plant	KNApSAcK
Curcuma longa	Plant	KNApSAcK
Curcuma xanthorrhiza	Plant	KNApSAcK
Iostephane heterophylla	LOTUS Database	35616633
Zingiber officinale	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases

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

Bisabolane sesquiterpenoid
Sesquiterpenoid
P-cymene
O-cresol
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Toluene
Phenol
Benzenoid
Monocyclic benzene moiety
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	5.64	ALOGPS
logP	5.09	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Acidic)	10.42	ChemAxon
pKa (Strongest Basic)	-5.5	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	71.07 m³·mol⁻¹	ChemAxon
Polarizability	27.06 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0038195

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB017434

KNApSAcK ID

C00011622

Chemspider ID

453998

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

520468

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Mustaffa F, Indurkar J, Ismail S, Shah M, Mansor SM: An antimicrobial compound isolated from Cinnamomum iners leaves with activity against methicillin-resistant Staphylococcus aureus. Molecules. 2011 Apr 8;16(4):3037-47. doi: 10.3390/molecules16043037. [PubMed:21478819 ]
Handayani T, Sakinah S, Nallappan M, Pihie AH: Regulation of p53-, Bcl-2- and caspase-dependent signaling pathway in xanthorrhizol-induced apoptosis of HepG2 hepatoma cells. Anticancer Res. 2007 Mar-Apr;27(2):965-71. [PubMed:17465228 ]
Lee LY, Shim JS, Rukayadi Y, Hwang JK: Antibacterial activity of xanthorrhizol isolated from Curcuma xanthorrhiza Roxb. against foodborne pathogens. J Food Prot. 2008 Sep;71(9):1926-30. doi: 10.4315/0362-028x-71.9.1926. [PubMed:18810881 ]

Showing NP-Card for Xanthorrhizol (NP0049050)

MOL for NP0049050 (Xanthorrhizol)

3D MOL for NP0049050 (Xanthorrhizol)

3D SDF for NP0049050 (Xanthorrhizol)

3D-SDF for NP0049050 (Xanthorrhizol)

PDB for NP0049050 (Xanthorrhizol)

3D PDB for NP0049050 (Xanthorrhizol)

SMILES for NP0049050 (Xanthorrhizol)

INCHI for NP0049050 (Xanthorrhizol)

Structure for NP0049050 (Xanthorrhizol)

3D Structure for NP0049050 (Xanthorrhizol)