NP-MRD: Showing NP-Card for Xanthomicrol (NP0048857)

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Record Information

Version

2.0

Created at

2022-03-17 21:03:17 UTC

Updated at

2022-03-17 21:03:17 UTC

NP-MRD ID

NP0048857

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Xanthomicrol

Description

Xanthomicrol belongs to the class of organic compounds known as 8-o-methylated flavonoids. These are flavonoids with methoxy groups attached to the C8 atom of the flavonoid backbone. Thus, xanthomicrol is considered to be a flavonoid lipid molecule. Xanthomicrol is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Outside of the human body, Xanthomicrol is found, on average, in the highest concentration within sweet basils. Xanthomicrol has also been detected, but not quantified in, several different foods, such as citrus, herbs and spices, peppermints, and winter savories. This could make xanthomicrol a potential biomarker for the consumption of these foods. Xanthomicrol is found in Ambrosia deltoidea, Baccharis patens, Baccharis quitensis, Baccharis tucumanensis, Bellardia trixago, Bombax ceiba, Bracteantha viscosa, Brickellia paniculata, Cheilanthes argentea, Citrus medica, Citrus sudachi , Citrus sudachii, Clinopodium douglasii, Cunila angustifolia, Cunila incana, Dracocephalum kotschyi, Dracocephalum multicaule, Ficus lyrata, Helichrysum spp., Hymenoxys scaposa, Lavandula mairei, Lavandula pubescens, Mentha piperita, Nepeta spp., Ocimum americanum, Ocimum americanum L.var.americanum , Ocimum gratissimum , Olearia heterocarpa, Ononis natrix , Origanum calcaratum, Origanum dictamnus , Origanum floribundum, Origanum dubium, Origanum microphyllum, Origanum onites , Origanum syriacum , Origanum vulgare subsp. Glandulosum , Origanum vulgare subsp. Hirtum , Phytolacca americana , Satureja cuneifolia, Satureja douglasii, Sideritis dasygnaphala, Sideritis leucantha, Sideritis spp., Stachys aegyptiaca, Stachys chrysantha, Stachys schtschegleevii, Thymus herba-barona , Thymus saturejoides, Thymus spp., Thymus vulgaris, Varthemia iphionoides and Wilkesia hobdyi. Xanthomicrol was first documented in 2005 (PMID: 15949825). A trimethoxyflavone that is flavone substituted by methoxy groups at positions 6, 7 and 8 and hydroxy groups at positions 5 and 4' (PMID: 23768339) (PMID: 24895220) (PMID: 25138085).

Structure

MOL SDF PDB SMILES InChI

  Mrv0541 05061309532D          

 25 27  0  0  0  0            999 V2000
    2.8579    0.0000    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
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.0625    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
   -2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    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
   -2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    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
   -1.4289    0.8250    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 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
    1.4289    0.0000    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    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    2.4750    0.0000 O   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
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   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
  6  4  1  0  0  0  0
  7  5  2  0  0  0  0
  9  4  2  0  0  0  0
  9  5  1  0  0  0  0
 10  6  2  0  0  0  0
 10  7  1  0  0  0  0
 11  8  1  0  0  0  0
 12  8  2  0  0  0  0
 12  9  1  0  0  0  0
 13 11  1  0  0  0  0
 14 13  2  0  0  0  0
 15 13  1  0  0  0  0
 16 14  1  0  0  0  0
 17 15  2  0  0  0  0
 18 16  2  0  0  0  0
 18 17  1  0  0  0  0
 19 10  1  0  0  0  0
 20 11  2  0  0  0  0
 21 14  1  0  0  0  0
 22  1  1  0  0  0  0
 22 16  1  0  0  0  0
 23  2  1  0  0  0  0
 23 17  1  0  0  0  0
 24  3  1  0  0  0  0
 24 18  1  0  0  0  0
 25 12  1  0  0  0  0
 25 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0048857

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(OC)C(OC)=C2OC(=CC(=O)C2=C1O)C1=CC=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C18H16O7/c1-22-16-14(21)13-11(20)8-12(9-4-6-10(19)7-5-9)25-15(13)17(23-2)18(16)24-3/h4-8,19,21H,1-3H3

> <INCHI_KEY>
SAMBWAJRKKEEOR-UHFFFAOYSA-N

> <FORMULA>
C18H16O7

> <MOLECULAR_WEIGHT>
344.3154

> <EXACT_MASS>
344.089602866

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
34.64078963877199

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-hydroxy-2-(4-hydroxyphenyl)-6,7,8-trimethoxy-4H-chromen-4-one

> <ALOGPS_LOGP>
2.89

> <JCHEM_LOGP>
2.5372406583333333

> <ALOGPS_LOGS>
-3.91

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.71204236478852

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.67398531709772

> <JCHEM_PKA_STRONGEST_BASIC>
-4.2915477595730005

> <JCHEM_POLAR_SURFACE_AREA>
94.45000000000002

> <JCHEM_REFRACTIVITY>
90.3226

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.21e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
xanthomicrol

> <JCHEM_VEBER_RULE>
0

$$$$

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       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.001   3.850   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      -5.335   4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -6.668   2.310   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      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -6.668   3.850   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   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       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -8.002   4.620   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1   22                                                            
CONECT    2   23                                                            
CONECT    3   24                                                            
CONECT    4    6    9                                                       
CONECT    5    7    9                                                       
CONECT    6    4   10                                                       
CONECT    7    5   10                                                       
CONECT    8   11   12                                                       
CONECT    9    4    5   12                                                  
CONECT   10    6    7   19                                                  
CONECT   11    8   13   20                                                  
CONECT   12    8    9   25                                                  
CONECT   13   11   14   15                                                  
CONECT   14   13   16   21                                                  
CONECT   15   13   17   25                                                  
CONECT   16   14   18   22                                                  
CONECT   17   15   18   23                                                  
CONECT   18   16   17   24                                                  
CONECT   19   10                                                            
CONECT   20   11                                                            
CONECT   21   14                                                            
CONECT   22    1   16                                                       
CONECT   23    2   17                                                       
CONECT   24    3   18                                                       
CONECT   25   12   15                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   54    0
END

View in JSmol

Synonyms

Value	Source
4',5-Dihydroxy-6,7,8-trimethoxyflavone	ChEBI
5-Hydroxy-2-(4-hydroxyphenyl)-6,7,8-trimethoxy-4H-1-benzopyran-4-one	HMDB

Chemical Formula

C₁₈H₁₆O₇

Average Mass

344.3154 Da

Monoisotopic Mass

344.08960 Da

IUPAC Name

5-hydroxy-2-(4-hydroxyphenyl)-6,7,8-trimethoxy-4H-chromen-4-one

Traditional Name

xanthomicrol

CAS Registry Number

16545-23-6

SMILES

COC1=C(OC)C(OC)=C2OC(=CC(=O)C2=C1O)C1=CC=C(O)C=C1

InChI Identifier

InChI=1S/C18H16O7/c1-22-16-14(21)13-11(20)8-12(9-4-6-10(19)7-5-9)25-15(13)17(23-2)18(16)24-3/h4-8,19,21H,1-3H3

InChI Key

SAMBWAJRKKEEOR-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Ambrosia deltoidea	Plant	KNApSAcK
Baccharis patens	Plant	KNApSAcK
Baccharis quitensis	LOTUS Database	35616633
Baccharis tucumanensis	LOTUS Database	35616633
Bartsia trixago	LOTUS Database	35616633
Bombax ceiba	LOTUS Database	35616633
Bracteantha viscosa	Plant	KNApSAcK
Brickellia paniculata	LOTUS Database	35616633
Cheilanthes argentea	Plant	KNApSAcK
Citrus medica	LOTUS Database	35616633
Citrus sudachi	Plant	KNApSAcK
Citrus sudachii	Plant	KNApSAcK
Clinopodium douglasii	LOTUS Database	35616633
Cunila angustifolia	Plant	KNApSAcK
Cunila incana	Plant	KNApSAcK
Dracocephalum kotschyi	LOTUS Database	35616633
Dracocephalum multicaule	LOTUS Database	35616633
Ficus lyrata	LOTUS Database	35616633
Helichrysum spp.	Plant	KNApSAcK
Hymenoxys scaposa	Plant	KNApSAcK
Lavandula mairei var. mairei	LOTUS Database	35616633
Lavandula pubescens	LOTUS Database	35616633
Mentha piperita	LOTUS Database	35616633
Mentha x piperita	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Nepeta spp.	Plant	KNApSAcK
Ocimum americanum	LOTUS Database	35616633
Ocimum americanum L.var.americanum	Plant	KNApSAcK
Ocimum basilicum	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Ocimum gratissimum	Plant	KNApSAcK
Olearia heterocarpa	LOTUS Database	35616633
Ononis natrix	Plant	KNApSAcK
Origanum calcaratum	Plant	KNApSAcK
Origanum dictamnus	Plant	KNApSAcK
Origanum floribundum	Plant	KNApSAcK
Origanum majorana	Plant	KNApSAcK
Origanum microphyllum	Plant	KNApSAcK
Origanum onites	Plant	KNApSAcK
Origanum syriacum	Plant	KNApSAcK
Origanum vulgare subsp. Glandulosum	Plant	KNApSAcK
Origanum vulgare subsp. Hirtum	Plant	KNApSAcK
Phytolacca americana	Plant	KNApSAcK
Satureja cuneifolia	LOTUS Database	35616633
Satureja douglasii	Plant	KNApSAcK
Satureja montana	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Sideritis dasygnaphala	Plant	KNApSAcK
Sideritis leucantha	LOTUS Database	35616633
Sideritis spp.	Plant	KNApSAcK
Stachys aegyptiaca	LOTUS Database	35616633
Stachys chrysantha	LOTUS Database	35616633
Stachys schtschegleevii	LOTUS Database	35616633
Thymus herba-barona	Plant	KNApSAcK
Thymus satureioides	LOTUS Database	35616633
Thymus spp.	Plant	KNApSAcK
Thymus vulgaris	LOTUS Database	35616633
Varthemia iphionoides	Plant	KNApSAcK
Wilkesia hobdyi	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 8-o-methylated flavonoids. These are flavonoids with methoxy groups attached to the C8 atom of the flavonoid backbone.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

O-methylated flavonoids

Direct Parent

8-O-methylated flavonoids

Alternative Parents

Substituents

6-methoxyflavonoid-skeleton
8-methoxyflavonoid-skeleton
7-methoxyflavonoid-skeleton
4'-hydroxyflavonoid
5-hydroxyflavonoid
Flavone
Hydroxyflavonoid
Chromone
Benzopyran
1-benzopyran
Anisole
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
Phenol
Pyranone
Benzenoid
Pyran
Monocyclic benzene moiety
Vinylogous acid
Heteroaromatic compound
Ether
Organoheterocyclic compound
Oxacycle
Organic oxygen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

dihydroxyflavone (CHEBI:35047 )
trimethoxyflavone (CHEBI:35047 )
Flavones and Flavonols (C14476 )
Flavones and Flavonols (LMPK12111447 )

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	2.89	ALOGPS
logP	2.54	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Acidic)	8.67	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	94.45 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	90.32 m³·mol⁻¹	ChemAxon
Polarizability	34.64 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0037600

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

73207

PDB ID

Not Available

ChEBI ID

35047

Good Scents ID

Not Available

References

General References

Jahaniani F, Ebrahimi SA, Rahbar-Roshandel N, Mahmoudian M: Xanthomicrol is the main cytotoxic component of Dracocephalum kotschyii and a potential anti-cancer agent. Phytochemistry. 2005 Jul;66(13):1581-92. doi: 10.1016/j.phytochem.2005.04.035. [PubMed:15949825 ]
Fattahi M, Nazeri V, Torras-Claveria L, Sefidkon F, Cusido RM, Zamani Z, Palazon J: Identification and quantification of leaf surface flavonoids in wild-growing populations of Dracocephalum kotschyi by LC-DAD-ESI-MS. Food Chem. 2013 Nov 1;141(1):139-46. doi: 10.1016/j.foodchem.2013.03.019. Epub 2013 Mar 13. [PubMed:23768339 ]
Abbaszadeh H, Ebrahimi SA, Akhavan MM: Antiangiogenic activity of xanthomicrol and calycopterin, two polymethoxylated hydroxyflavones in both in vitro and ex vivo models. Phytother Res. 2014 Nov;28(11):1661-70. doi: 10.1002/ptr.5179. Epub 2014 Jun 3. [PubMed:24895220 ]
Fattahi M, Cusido RM, Khojasteh A, Bonfill M, Palazon J: Xanthomicrol: a comprehensive review of its chemistry, distribution, biosynthesis and pharmacological activity. Mini Rev Med Chem. 2014;14(9):725-33. doi: 10.2174/1389557514666140820122818. [PubMed:25138085 ]

Showing NP-Card for Xanthomicrol (NP0048857)

MOL for NP0048857 (Xanthomicrol)

3D MOL for NP0048857 (Xanthomicrol)

3D SDF for NP0048857 (Xanthomicrol)

3D-SDF for NP0048857 (Xanthomicrol)

PDB for NP0048857 (Xanthomicrol)

3D PDB for NP0048857 (Xanthomicrol)

SMILES for NP0048857 (Xanthomicrol)

INCHI for NP0048857 (Xanthomicrol)

Structure for NP0048857 (Xanthomicrol)

3D Structure for NP0048857 (Xanthomicrol)