NP-MRD: Showing NP-Card for Naringenin 5,7-dimethyl ether 4'-O-xylosyl-(1->4)-arabinoside (NP0055564)

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Record Information

Version

2.0

Created at

2022-04-28 01:34:42 UTC

Updated at

2022-04-28 01:34:42 UTC

NP-MRD ID

NP0055564

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Naringenin 5,7-dimethyl ether 4'-O-xylosyl-(1->4)-arabinoside

Description

(2R)-2-(4-{[(2S,3S,4R,5R)-3,4-dihydroxy-5-{[(2R,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}phenyl)-5,7-dimethoxy-3,4-dihydro-2H-1-benzopyran-4-one belongs to the class of organic compounds known as flavonoid o-glycosides. Flavonoid O-glycosides are compounds containing a carbohydrate moiety which is O-glycosidically linked to the 2-phenylchromen-4-one flavonoid backbone. Naringenin 5,7-dimethyl ether 4'-O-xylosyl-(1->4)-arabinoside is found in Hibiscus mutabilis . Based on a literature review very few articles have been published on (2R)-2-(4-{[(2S,3S,4R,5R)-3,4-dihydroxy-5-{[(2R,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}phenyl)-5,7-dimethoxy-3,4-dihydro-2H-1-benzopyran-4-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282203342D          

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M  END

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  Mrv1652304282203342D          

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    7.8592    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 O   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
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  4 10  1  0  0  0  0
 10 11  2  0  0  0  0
  8 12  1  1  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 12 17  1  0  0  0  0
 15 18  1  0  0  0  0
 19 18  1  1  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 19 24  1  0  0  0  0
 22 25  1  6  0  0  0
 26 25  1  6  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 26 31  1  0  0  0  0
 29 32  1  1  0  0  0
 28 33  1  1  0  0  0
 27 34  1  6  0  0  0
 21 35  1  1  0  0  0
 20 36  1  1  0  0  0
  3 37  1  0  0  0  0
 37 38  1  0  0  0  0
  1 39  1  0  0  0  0
 39 40  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0055564

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(OC)=C2C(=O)C[C@@H](OC2=C1)C1=CC=C(O[C@@H]2OC[C@@H](O[C@H]3OC[C@H](O)[C@H](O)[C@H]3O)[C@H](O)[C@@H]2O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C27H32O13/c1-34-14-7-18(35-2)21-15(28)9-17(39-19(21)8-14)12-3-5-13(6-4-12)38-26-25(33)23(31)20(11-37-26)40-27-24(32)22(30)16(29)10-36-27/h3-8,16-17,20,22-27,29-33H,9-11H2,1-2H3/t16-,17+,20+,22-,23-,24+,25-,26-,27+/m0/s1

> <INCHI_KEY>
SVNWACIHAFUKAJ-UATUJUEYSA-N

> <FORMULA>
C27H32O13

> <MOLECULAR_WEIGHT>
564.54

> <EXACT_MASS>
564.18429109

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
56.36074759666102

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-(4-{[(2S,3S,4R,5R)-3,4-dihydroxy-5-{[(2R,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}phenyl)-5,7-dimethoxy-3,4-dihydro-2H-1-benzopyran-4-one

> <ALOGPS_LOGP>
0.46

> <JCHEM_LOGP>
-0.3013376926666658

> <ALOGPS_LOGS>
-2.85

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.512374188821465

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.953243688316453

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5265806595271325

> <JCHEM_POLAR_SURFACE_AREA>
182.82999999999998

> <JCHEM_REFRACTIVITY>
132.88709999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.89e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-(4-{[(2S,3S,4R,5R)-3,4-dihydroxy-5-{[(2R,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}phenyl)-5,7-dimethoxy-2,3-dihydro-1-benzopyran-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  -3.080   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       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       4.001  -0.770   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       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      10.669   1.540   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      12.003   2.310   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      13.337   1.540   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      13.337  -0.000   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      12.003  -0.770   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      10.669  -0.000   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      14.670  -0.770   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      14.670  -2.310   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      16.004  -3.080   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      16.004  -4.620   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      14.670  -5.390   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      13.337  -4.620   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      13.337  -3.080   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      14.670  -6.930   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      17.338  -5.390   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      17.338  -2.310   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      14.670   2.310   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      12.003   3.850   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
CONECT    1    2    6   39                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   37                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9   12                                                  
CONECT    9    8   10                                                       
CONECT   10    9    4   11                                                  
CONECT   11   10                                                            
CONECT   12    8   13   17                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   18                                                  
CONECT   16   15   17                                                       
CONECT   17   16   12                                                       
CONECT   18   15   19                                                       
CONECT   19   18   20   24                                                  
CONECT   20   19   21   36                                                  
CONECT   21   20   22   35                                                  
CONECT   22   21   23   25                                                  
CONECT   23   22   24                                                       
CONECT   24   23   19                                                       
CONECT   25   22   26                                                       
CONECT   26   25   27   31                                                  
CONECT   27   26   28   34                                                  
CONECT   28   27   29   33                                                  
CONECT   29   28   30   32                                                  
CONECT   30   29   31                                                       
CONECT   31   30   26                                                       
CONECT   32   29                                                            
CONECT   33   28                                                            
CONECT   34   27                                                            
CONECT   35   21                                                            
CONECT   36   20                                                            
CONECT   37    3   38                                                       
CONECT   38   37                                                            
CONECT   39    1   40                                                       
CONECT   40   39                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   88    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₂O₁₃

Average Mass

564.5400 Da

Monoisotopic Mass

564.18429 Da

IUPAC Name

(2R)-2-(4-{[(2S,3S,4R,5R)-3,4-dihydroxy-5-{[(2R,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}phenyl)-5,7-dimethoxy-3,4-dihydro-2H-1-benzopyran-4-one

Traditional Name

(2R)-2-(4-{[(2S,3S,4R,5R)-3,4-dihydroxy-5-{[(2R,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}phenyl)-5,7-dimethoxy-2,3-dihydro-1-benzopyran-4-one

CAS Registry Number

Not Available

SMILES

COC1=CC(OC)=C2C(=O)C[C@@H](OC2=C1)C1=CC=C(O[C@@H]2OC[C@@H](O[C@H]3OC[C@H](O)[C@H](O)[C@H]3O)[C@H](O)[C@@H]2O)C=C1

InChI Identifier

InChI=1S/C27H32O13/c1-34-14-7-18(35-2)21-15(28)9-17(39-19(21)8-14)12-3-5-13(6-4-12)38-26-25(33)23(31)20(11-37-26)40-27-24(32)22(30)16(29)10-36-27/h3-8,16-17,20,22-27,29-33H,9-11H2,1-2H3/t16-,17+,20+,22-,23-,24+,25-,26-,27+/m0/s1

InChI Key

SVNWACIHAFUKAJ-UATUJUEYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Hibiscus mutabilis	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavonoid o-glycosides. Flavonoid O-glycosides are compounds containing a carbohydrate moiety which is O-glycosidically linked to the 2-phenylchromen-4-one flavonoid backbone.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Flavonoid O-glycosides

Alternative Parents

Substituents

Flavonoid o-glycoside
Flavonoid-4p-o-glycoside
7-methoxyflavonoid-skeleton
5-methoxyflavonoid-skeleton
Flavanone
Flavan
Phenolic glycoside
O-glycosyl compound
Glycosyl compound
Disaccharide
Chromone
1-benzopyran
Benzopyran
Chromane
Phenoxy compound
Aryl alkyl ketone
Aryl ketone
Phenol ether
Anisole
Alkyl aryl ether
Benzenoid
Oxane
Monocyclic benzene moiety
Secondary alcohol
Ketone
Oxacycle
Organoheterocyclic compound
Polyol
Ether
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	0.46	ALOGPS
logP	-0.3	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	11.95	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	182.83 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	132.89 m³·mol⁻¹	ChemAxon
Polarizability	56.36 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

163068106

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Naringenin 5,7-dimethyl ether 4'-O-xylosyl-(1->4)-arabinoside (NP0055564)

MOL for NP0055564 (Naringenin 5,7-dimethyl ether 4'-O-xylosyl-(1->4)-arabinoside)

3D MOL for NP0055564 (Naringenin 5,7-dimethyl ether 4'-O-xylosyl-(1->4)-arabinoside)

3D SDF for NP0055564 (Naringenin 5,7-dimethyl ether 4'-O-xylosyl-(1->4)-arabinoside)

3D-SDF for NP0055564 (Naringenin 5,7-dimethyl ether 4'-O-xylosyl-(1->4)-arabinoside)

PDB for NP0055564 (Naringenin 5,7-dimethyl ether 4'-O-xylosyl-(1->4)-arabinoside)

3D PDB for NP0055564 (Naringenin 5,7-dimethyl ether 4'-O-xylosyl-(1->4)-arabinoside)

SMILES for NP0055564 (Naringenin 5,7-dimethyl ether 4'-O-xylosyl-(1->4)-arabinoside)

INCHI for NP0055564 (Naringenin 5,7-dimethyl ether 4'-O-xylosyl-(1->4)-arabinoside)

Structure for NP0055564 (Naringenin 5,7-dimethyl ether 4'-O-xylosyl-(1->4)-arabinoside)

3D Structure for NP0055564 (Naringenin 5,7-dimethyl ether 4'-O-xylosyl-(1->4)-arabinoside)