NP-MRD: Showing NP-Card for desmethylxanthohumol (NP0221276)

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Record Information

Version

2.0

Created at

2022-09-05 22:48:45 UTC

Updated at

2022-09-05 22:48:45 UTC

NP-MRD ID

NP0221276

Secondary Accession Numbers

None

Natural Product Identification

Common Name

desmethylxanthohumol

Description

Desmethylxanthohumol belongs to the class of organic compounds known as 3-prenylated chalcones. These are chalcones featuring a C5-isoprenoid unit at the 3-position. Desmethylxanthohumol is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Desmethylxanthohumol has been detected, but not quantified in, alcoholic beverages. This could make desmethylxanthohumol a potential biomarker for the consumption of these foods. Cinnamic acid is oxidized by cinnamate-4-hydroxylase and loaded onto Coenzyme A (CoA) by 4-coumarate CoA ligase to yield 4-hydroxy-cinnamoyl CoA, the starter unit for PKS extension. This molecule is extended three times with malonyl CoA, cyclized through a Claisen condensation, and aromatized through tautomerization to form naringenin chalcone (chalconaringenin). Xanthohumol can be extracted with pressurized hot water. L-Phenylalanine serves as the starting material, which is converted to cinnamic acid by the PLP-dependent phenylalanine ammonia lyase. During the brewing process, xanthohumol and other prenylated flavonoids are lost as they are converted to the corresponding flavanones. Xanthohumol is a prenylated chalconoid derived from a plant type III PKS, and is synthesized in the glandular trichromes of hop cones. Total syntheses of xanthohumol and derivatives have been achieved, though extraction from hops remains a primary source. desmethylxanthohumol is found in Helichrysum felinum, Helichrysum forskahlii, Humulus lupulus and Sophora flavescens. desmethylxanthohumol was first documented in 2012 (PMID: 21912858). In the case of xanthohumol, a prenyltransferase called Humulus lupulus prenyltransferase 1 (HlPT-1) attaches a molecule of dimethylallyl pyrophosphate from the DXP pathway (PMID: 23947133).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05061305232D          

 25 26  0  0  0  0            999 V2000
   -3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -1.6500    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
   -2.1434    3.7125    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    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    4.5375    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
   -2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -0.4125    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
   -4.2868    0.0000    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
   -2.8579    0.8250    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
   -1.4289    5.7750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    2.0625    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
  7  4  1  0  0  0  0
  8  5  2  0  0  0  0
  9  3  1  0  0  0  0
 10  6  2  0  0  0  0
 12  1  1  0  0  0  0
 12  2  1  0  0  0  0
 12  3  2  0  0  0  0
 13  4  2  0  0  0  0
 13  5  1  0  0  0  0
 13  6  1  0  0  0  0
 14  7  2  0  0  0  0
 14  8  1  0  0  0  0
 15  9  1  0  0  0  0
 16 10  1  0  0  0  0
 17 11  2  0  0  0  0
 17 15  1  0  0  0  0
 18 11  1  0  0  0  0
 19 16  1  0  0  0  0
 19 18  2  0  0  0  0
 20 15  2  0  0  0  0
 20 19  1  0  0  0  0
 21 14  1  0  0  0  0
 22 16  2  0  0  0  0
 23 17  1  0  0  0  0
 24 18  1  0  0  0  0
 25 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0221276

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC1=C(O)C(C(=O)\C=C\C2=CC=C(O)C=C2)=C(O)C=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C20H20O5/c1-12(2)3-9-15-17(23)11-18(24)19(20(15)25)16(22)10-6-13-4-7-14(21)8-5-13/h3-8,10-11,21,23-25H,9H2,1-2H3/b10-6+

> <INCHI_KEY>
FUSADYLVRMROPL-UXBLZVDNSA-N

> <FORMULA>
C20H20O5

> <MOLECULAR_WEIGHT>
340.3698

> <EXACT_MASS>
340.13107375

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
36.789705685530066

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2E)-3-(4-hydroxyphenyl)-1-[2,4,6-trihydroxy-3-(3-methylbut-2-en-1-yl)phenyl]prop-2-en-1-one

> <ALOGPS_LOGP>
3.53

> <JCHEM_LOGP>
5.704631021666667

> <ALOGPS_LOGS>
-4.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.62830977434329

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.613358303148392

> <JCHEM_PKA_STRONGEST_BASIC>
-5.6197614617885

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
99.04339999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.08e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
desmethylxanthohumol

> <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      -6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -9.336  -5.390   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -8.002  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.334   6.930   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.001   6.930   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.334   8.470   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.001   8.470   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.001   3.850   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -8.002   1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.667   6.160   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.667   9.240   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -8.002   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -2.667  10.780   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -9.336  -0.770   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -6.668   3.850   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      -4.001  -0.770   0.000  0.00  0.00           O+0
CONECT    1   12                                                            
CONECT    2   12                                                            
CONECT    3    9   12                                                       
CONECT    4    7   13                                                       
CONECT    5    8   13                                                       
CONECT    6   10   13                                                       
CONECT    7    4   14                                                       
CONECT    8    5   14                                                       
CONECT    9    3   15                                                       
CONECT   10    6   16                                                       
CONECT   11   17   18                                                       
CONECT   12    1    2    3                                                  
CONECT   13    4    5    6                                                  
CONECT   14    7    8   21                                                  
CONECT   15    9   17   20                                                  
CONECT   16   10   19   22                                                  
CONECT   17   11   15   23                                                  
CONECT   18   11   19   24                                                  
CONECT   19   16   18   20                                                  
CONECT   20   15   19   25                                                  
CONECT   21   14                                                            
CONECT   22   16                                                            
CONECT   23   17                                                            
CONECT   24   18                                                            
CONECT   25   20                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   52    0
END

View in JSmol

Synonyms

Value	Source
3-(4-Hydroxyphenyl)-1-[2,4,6-trihydroxy-3-(3-methyl-2-butenyl)phenyl]-2-propen-1-one	HMDB
1-(2,4-Dihydroxy-6-methoxy-3-(3-methyl-2-butenyl)phenyl)-3-(4-hydroxyphenyl)-2-propen-1-one	MeSH
Xanthohumol	MeSH

Chemical Formula

C₂₀H₂₀O₅

Average Mass

340.3698 Da

Monoisotopic Mass

340.13107 Da

IUPAC Name

(2E)-3-(4-hydroxyphenyl)-1-[2,4,6-trihydroxy-3-(3-methylbut-2-en-1-yl)phenyl]prop-2-en-1-one

Traditional Name

desmethylxanthohumol

CAS Registry Number

Not Available

SMILES

CC(C)=CCC1=C(O)C(C(=O)\C=C\C2=CC=C(O)C=C2)=C(O)C=C1O

InChI Identifier

InChI=1S/C20H20O5/c1-12(2)3-9-15-17(23)11-18(24)19(20(15)25)16(22)10-6-13-4-7-14(21)8-5-13/h3-8,10-11,21,23-25H,9H2,1-2H3/b10-6+

InChI Key

FUSADYLVRMROPL-UXBLZVDNSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Helichrysum felinum	LOTUS Database	35616633
Helichrysum forskahlii	LOTUS Database	35616633
Humulus lupulus	LOTUS Database	35616633
Sophora flavescens	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 3-prenylated chalcones. These are chalcones featuring a C5-isoprenoid unit at the 3-position.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Linear 1,3-diarylpropanoids

Sub Class

Chalcones and dihydrochalcones

Direct Parent

3-prenylated chalcones

Alternative Parents

Substituents

3-prenylated chalcone
2'-hydroxychalcone
Cinnamylphenol
Hydroxycinnamic acid or derivatives
Acylphloroglucinol derivative
Benzenetriol
Phloroglucinol derivative
Benzoyl
Aryl ketone
Styrene
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Monocyclic benzene moiety
Benzenoid
Acryloyl-group
Vinylogous acid
Enone
Alpha,beta-unsaturated ketone
Ketone
Polyol
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

benzenetriol (CHEBI:80489 )
chalcones (CHEBI:80489 )
chalcones (C16416 )

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	3.53	ALOGPS
logP	5.7	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Acidic)	7.61	ChemAxon
pKa (Strongest Basic)	-5.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	97.99 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	99.04 m³·mol⁻¹	ChemAxon
Polarizability	36.79 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0030610

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

Xanthohumol

METLIN ID

Not Available

PubChem Compound

6443339

PDB ID

Not Available

ChEBI ID

80489

Good Scents ID

Not Available

References

General References

Zhang WK, Wang SB, Fu CY, Li P, Xu JK: [Flavonoids from Humulus lupulus]. Zhongguo Zhong Yao Za Zhi. 2013 May;38(10):1539-42. [PubMed:23947133 ]
Gatica-Arias A, Farag MA, Stanke M, Matousek J, Wessjohann L, Weber G: Flavonoid production in transgenic hop (Humulus lupulus L.) altered by PAP1/MYB75 from Arabidopsis thaliana L. Plant Cell Rep. 2012 Jan;31(1):111-9. doi: 10.1007/s00299-011-1144-5. Epub 2011 Sep 13. [PubMed:21912858 ]
LOTUS database [Link]

Showing NP-Card for desmethylxanthohumol (NP0221276)

MOL for NP0221276 (desmethylxanthohumol)

3D MOL for NP0221276 (desmethylxanthohumol)

3D SDF for NP0221276 (desmethylxanthohumol)

3D-SDF for NP0221276 (desmethylxanthohumol)

PDB for NP0221276 (desmethylxanthohumol)

3D PDB for NP0221276 (desmethylxanthohumol)

SMILES for NP0221276 (desmethylxanthohumol)

INCHI for NP0221276 (desmethylxanthohumol)

Structure for NP0221276 (desmethylxanthohumol)

3D Structure for NP0221276 (desmethylxanthohumol)