NP-MRD: Showing NP-Card for 5,7-dihydroxy-2-(4-hydroxyphenyl)-3,8-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})chromen-4-one (NP0164005)

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Record Information

Version

2.0

Created at

2022-09-02 22:48:03 UTC

Updated at

2022-09-02 22:48:04 UTC

NP-MRD ID

NP0164005

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5,7-dihydroxy-2-(4-hydroxyphenyl)-3,8-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})chromen-4-one

Description

Herbacetin 3,8-diglucoside belongs to the class of organic compounds known as flavonoid-8-o-glycosides. These are phenolic compounds containing a flavonoid moiety which is O-glycosidically linked to carbohydrate moiety at the C8-position. 5,7-dihydroxy-2-(4-hydroxyphenyl)-3,8-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})chromen-4-one is found in Citrus sinensis. Herbacetin 3,8-diglucoside is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 05061311472D          

 44 48  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv0541 05061311472D          

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    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
   -2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    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    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    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    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
  3  1  1  0  0  0  0
  4  2  2  0  0  0  0
  8  1  2  0  0  0  0
  8  2  1  0  0  0  0
  9  3  2  0  0  0  0
  9  4  1  0  0  0  0
 10  5  2  0  0  0  0
 11  5  1  0  0  0  0
 12  6  1  0  0  0  0
 13  7  1  0  0  0  0
 14 10  1  0  0  0  0
 15 12  1  0  0  0  0
 16 13  1  0  0  0  0
 17 14  1  0  0  0  0
 18 15  1  0  0  0  0
 19 16  1  0  0  0  0
 20 18  1  0  0  0  0
 21 19  1  0  0  0  0
 22  8  1  0  0  0  0
 23 11  2  0  0  0  0
 24 14  2  0  0  0  0
 24 23  1  0  0  0  0
 25 17  1  0  0  0  0
 25 22  2  0  0  0  0
 26 20  1  0  0  0  0
 27 21  1  0  0  0  0
 28  6  1  0  0  0  0
 29  7  1  0  0  0  0
 30  9  1  0  0  0  0
 31 10  1  0  0  0  0
 32 11  1  0  0  0  0
 33 15  1  0  0  0  0
 34 16  1  0  0  0  0
 35 17  2  0  0  0  0
 36 18  1  0  0  0  0
 37 19  1  0  0  0  0
 38 20  1  0  0  0  0
 39 21  1  0  0  0  0
 40 12  1  0  0  0  0
 40 26  1  0  0  0  0
 41 13  1  0  0  0  0
 41 27  1  0  0  0  0
 42 22  1  0  0  0  0
 42 24  1  0  0  0  0
 43 23  1  0  0  0  0
 43 26  1  0  0  0  0
 44 25  1  0  0  0  0
 44 27  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0164005

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(OC2=C(O)C=C(O)C3=C2OC(C2=CC=C(O)C=C2)=C(OC2OC(CO)C(O)C(O)C2O)C3=O)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C27H30O17/c28-6-12-15(33)18(36)20(38)26(40-12)43-23-11(32)5-10(31)14-17(35)25(22(42-24(14)23)8-1-3-9(30)4-2-8)44-27-21(39)19(37)16(34)13(7-29)41-27/h1-5,12-13,15-16,18-21,26-34,36-39H,6-7H2

> <INCHI_KEY>
VMOKZQAQPBUNRW-UHFFFAOYSA-N

> <FORMULA>
C27H30O17

> <MOLECULAR_WEIGHT>
626.5169

> <EXACT_MASS>
626.148299534

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
59.03079024098043

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5,7-dihydroxy-2-(4-hydroxyphenyl)-3,8-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})-4H-chromen-4-one

> <ALOGPS_LOGP>
-0.81

> <JCHEM_LOGP>
-2.412903389333334

> <ALOGPS_LOGS>
-2.00

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.502809658235991

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.819461851778007

> <JCHEM_PKA_STRONGEST_BASIC>
-3.648395395250552

> <JCHEM_POLAR_SURFACE_AREA>
285.75

> <JCHEM_REFRACTIVITY>
141.41989999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.30e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5,7-dihydroxy-2-(4-hydroxyphenyl)-3,8-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})chromen-4-one

> <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   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -6.668   3.850   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -5.335   4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -5.335   6.160   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -4.001   6.930   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -2.667   6.160   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -8.002   4.620   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       8.002   4.620   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -4.001   2.310   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -6.668   6.930   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      -4.001   8.470   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      -1.334   6.930   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0      -4.001   3.850   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
CONECT    1    3    8                                                       
CONECT    2    4    8                                                       
CONECT    3    1    9                                                       
CONECT    4    2    9                                                       
CONECT    5   10   11                                                       
CONECT    6   12   28                                                       
CONECT    7   13   29                                                       
CONECT    8    1    2   22                                                  
CONECT    9    3    4   30                                                  
CONECT   10    5   14   31                                                  
CONECT   11    5   23   32                                                  
CONECT   12    6   15   40                                                  
CONECT   13    7   16   41                                                  
CONECT   14   10   17   24                                                  
CONECT   15   12   18   33                                                  
CONECT   16   13   19   34                                                  
CONECT   17   14   25   35                                                  
CONECT   18   15   20   36                                                  
CONECT   19   16   21   37                                                  
CONECT   20   18   26   38                                                  
CONECT   21   19   27   39                                                  
CONECT   22    8   25   42                                                  
CONECT   23   11   24   43                                                  
CONECT   24   14   23   42                                                  
CONECT   25   17   22   44                                                  
CONECT   26   20   40   43                                                  
CONECT   27   21   41   44                                                  
CONECT   28    6                                                            
CONECT   29    7                                                            
CONECT   30    9                                                            
CONECT   31   10                                                            
CONECT   32   11                                                            
CONECT   33   15                                                            
CONECT   34   16                                                            
CONECT   35   17                                                            
CONECT   36   18                                                            
CONECT   37   19                                                            
CONECT   38   20                                                            
CONECT   39   21                                                            
CONECT   40   12   26                                                       
CONECT   41   13   27                                                       
CONECT   42   22   24                                                       
CONECT   43   23   26                                                       
CONECT   44   25   27                                                       
MASTER        0    0    0    0    0    0    0    0   44    0   96    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₀O₁₇

Average Mass

626.5169 Da

Monoisotopic Mass

626.14830 Da

IUPAC Name

5,7-dihydroxy-2-(4-hydroxyphenyl)-3,8-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})-4H-chromen-4-one

Traditional Name

5,7-dihydroxy-2-(4-hydroxyphenyl)-3,8-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})chromen-4-one

CAS Registry Number

Not Available

SMILES

OCC1OC(OC2=C(O)C=C(O)C3=C2OC(C2=CC=C(O)C=C2)=C(OC2OC(CO)C(O)C(O)C2O)C3=O)C(O)C(O)C1O

InChI Identifier

InChI=1S/C27H30O17/c28-6-12-15(33)18(36)20(38)26(40-12)43-23-11(32)5-10(31)14-17(35)25(22(42-24(14)23)8-1-3-9(30)4-2-8)44-27-21(39)19(37)16(34)13(7-29)41-27/h1-5,12-13,15-16,18-21,26-34,36-39H,6-7H2

InChI Key

VMOKZQAQPBUNRW-UHFFFAOYSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Citrus sinensis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavonoid-8-o-glycosides. These are phenolic compounds containing a flavonoid moiety which is O-glycosidically linked to carbohydrate moiety at the C8-position.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Flavonoid-8-O-glycosides

Alternative Parents

Substituents

Flavonoid-3-o-glycoside
Flavonoid-8-o-glycoside
Hydroxyflavonoid
4'-hydroxyflavonoid
5-hydroxyflavonoid
7-hydroxyflavonoid
Flavone
Phenolic glycoside
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Chromone
Benzopyran
1-benzopyran
Pyranone
1-hydroxy-2-unsubstituted benzenoid
Phenol
Benzenoid
Monocyclic benzene moiety
Pyran
Oxane
Monosaccharide
Heteroaromatic compound
Vinylogous acid
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Acetal
Polyol
Primary alcohol
Organic oxide
Organic oxygen compound
Alcohol
Hydrocarbon derivative
Organooxygen compound
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	-0.81	ALOGPS
logP	-2.4	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	6.82	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	17	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	285.75 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	141.42 m³·mol⁻¹	ChemAxon
Polarizability	59.03 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

HMDB0040371

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB020102

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

14375133

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 5,7-dihydroxy-2-(4-hydroxyphenyl)-3,8-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})chromen-4-one (NP0164005)

MOL for NP0164005 (5,7-dihydroxy-2-(4-hydroxyphenyl)-3,8-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})chromen-4-one)

3D MOL for NP0164005 (5,7-dihydroxy-2-(4-hydroxyphenyl)-3,8-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})chromen-4-one)

3D SDF for NP0164005 (5,7-dihydroxy-2-(4-hydroxyphenyl)-3,8-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})chromen-4-one)

3D-SDF for NP0164005 (5,7-dihydroxy-2-(4-hydroxyphenyl)-3,8-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})chromen-4-one)

PDB for NP0164005 (5,7-dihydroxy-2-(4-hydroxyphenyl)-3,8-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})chromen-4-one)

3D PDB for NP0164005 (5,7-dihydroxy-2-(4-hydroxyphenyl)-3,8-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})chromen-4-one)

SMILES for NP0164005 (5,7-dihydroxy-2-(4-hydroxyphenyl)-3,8-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})chromen-4-one)

INCHI for NP0164005 (5,7-dihydroxy-2-(4-hydroxyphenyl)-3,8-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})chromen-4-one)

Structure for NP0164005 (5,7-dihydroxy-2-(4-hydroxyphenyl)-3,8-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})chromen-4-one)

3D Structure for NP0164005 (5,7-dihydroxy-2-(4-hydroxyphenyl)-3,8-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})chromen-4-one)