NP-MRD: Showing NP-Card for Phellodendroside (NP0056000)

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Record Information

Version

2.0

Created at

2022-04-28 01:54:15 UTC

Updated at

2022-04-28 01:54:15 UTC

NP-MRD ID

NP0056000

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Phellodendroside

Description

(4S,5S)-8-hydroxy-4-(4-hydroxyphenyl)-12,12-dimethyl-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,11-dioxatricyclo[8.4.0.0²,⁷]Tetradeca-1(10),2(7),8-trien-6-one belongs to the class of organic compounds known as flavonoid-3-o-glycosides. These are phenolic compounds containing a flavonoid moiety which is O-glycosidically linked to carbohydrate moiety at the C3-position. Phellodendroside is found in Phellodendron amurense and Phellodendron japonicum. Based on a literature review very few articles have been published on (4S,5S)-8-hydroxy-4-(4-hydroxyphenyl)-12,12-dimethyl-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,11-dioxatricyclo[8.4.0.0²,⁷]Tetradeca-1(10),2(7),8-trien-6-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282203542D          

 37 41  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652304282203542D          

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 23 25  1  1  0  0  0
 25 26  1  0  0  0  0
 22 27  1  6  0  0  0
 21 28  1  1  0  0  0
 20 29  1  6  0  0  0
 14 30  1  1  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
 30 35  1  0  0  0  0
 33 36  1  0  0  0  0
  2 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0056000

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1(C)CCC2=C(O1)C=C(O)C1=C2O[C@H]([C@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C1=O)C1=CC=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C26H30O11/c1-26(2)8-7-13-15(37-26)9-14(29)17-19(31)24(22(35-23(13)17)11-3-5-12(28)6-4-11)36-25-21(33)20(32)18(30)16(10-27)34-25/h3-6,9,16,18,20-22,24-25,27-30,32-33H,7-8,10H2,1-2H3/t16-,18-,20+,21-,22+,24-,25+/m1/s1

> <INCHI_KEY>
BIXCRRQKYRPIOC-BMZPCTPXSA-N

> <FORMULA>
C26H30O11

> <MOLECULAR_WEIGHT>
518.515

> <EXACT_MASS>
518.178811786

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
53.061927076377096

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S,5S)-8-hydroxy-4-(4-hydroxyphenyl)-12,12-dimethyl-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,11-dioxatricyclo[8.4.0.0^{2,7}]tetradeca-1(10),2(7),8-trien-6-one

> <ALOGPS_LOGP>
0.97

> <JCHEM_LOGP>
1.676616864333332

> <ALOGPS_LOGS>
-2.67

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.590358841860777

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.85751885657194

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981083713221519

> <JCHEM_POLAR_SURFACE_AREA>
175.37

> <JCHEM_REFRACTIVITY>
126.49119999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.12e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4S,5S)-8-hydroxy-4-(4-hydroxyphenyl)-12,12-dimethyl-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,11-dioxatricyclo[8.4.0.0^{2,7}]tetradeca-1(10),2(7),8-trien-6-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       2.874  -1.897   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.414  -1.897   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.184  -0.564   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.414   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.104  -0.564   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.564  -0.564   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -0.206   0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.564   2.104   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.104   2.104   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.566   1.493   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.566   0.047   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       5.184   2.104   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       6.724   2.104   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.494   0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.724  -0.564   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       7.494  -1.897   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       9.034   0.770   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       9.804  -0.564   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      11.344  -0.564   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      12.114  -1.897   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      11.344  -3.231   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       9.804  -3.231   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       9.034  -1.897   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       9.034  -4.565   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       9.804  -5.898   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      12.114  -4.565   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      13.654  -1.897   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      12.114   0.770   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       7.494   3.437   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       6.724   4.771   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       7.494   6.105   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       9.034   6.105   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       9.804   4.771   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       9.034   3.437   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       9.804   7.438   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0       5.184  -3.231   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   37                                                  
CONECT    3    2    4   16                                                  
CONECT    4    3    5   13                                                  
CONECT    5    4    6   10                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   11   12                                             
CONECT    9    8   10                                                       
CONECT   10    9    5                                                       
CONECT   11    8                                                            
CONECT   12    8                                                            
CONECT   13    4   14                                                       
CONECT   14   13   15   30                                                  
CONECT   15   14   16   18                                                  
CONECT   16   15    3   17                                                  
CONECT   17   16                                                            
CONECT   18   15   19                                                       
CONECT   19   18   20   24                                                  
CONECT   20   19   21   29                                                  
CONECT   21   20   22   28                                                  
CONECT   22   21   23   27                                                  
CONECT   23   22   24   25                                                  
CONECT   24   23   19                                                       
CONECT   25   23   26                                                       
CONECT   26   25                                                            
CONECT   27   22                                                            
CONECT   28   21                                                            
CONECT   29   20                                                            
CONECT   30   14   31   35                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34   36                                                  
CONECT   34   33   35                                                       
CONECT   35   34   30                                                       
CONECT   36   33                                                            
CONECT   37    2                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₃₀O₁₁

Average Mass

518.5150 Da

Monoisotopic Mass

518.17881 Da

IUPAC Name

(4S,5S)-8-hydroxy-4-(4-hydroxyphenyl)-12,12-dimethyl-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,11-dioxatricyclo[8.4.0.0^{2,7}]tetradeca-1(10),2(7),8-trien-6-one

Traditional Name

(4S,5S)-8-hydroxy-4-(4-hydroxyphenyl)-12,12-dimethyl-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,11-dioxatricyclo[8.4.0.0^{2,7}]tetradeca-1(10),2(7),8-trien-6-one

CAS Registry Number

Not Available

SMILES

CC1(C)CCC2=C(O1)C=C(O)C1=C2O[C@H]([C@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C1=O)C1=CC=C(O)C=C1

InChI Identifier

InChI=1S/C26H30O11/c1-26(2)8-7-13-15(37-26)9-14(29)17-19(31)24(22(35-23(13)17)11-3-5-12(28)6-4-11)36-25-21(33)20(32)18(30)16(10-27)34-25/h3-6,9,16,18,20-22,24-25,27-30,32-33H,7-8,10H2,1-2H3/t16-,18-,20+,21-,22+,24-,25+/m1/s1

InChI Key

BIXCRRQKYRPIOC-BMZPCTPXSA-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
Phellodendron amurense	Plant	KNApSAcK
Phellodendron japonicum	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavonoid-3-o-glycosides. These are phenolic compounds containing a flavonoid moiety which is O-glycosidically linked to carbohydrate moiety at the C3-position.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Flavonoid-3-O-glycosides

Alternative Parents

Substituents

Flavonoid-3-o-glycoside
8-prenylated flavanone
8-prenylated flavan
Pyranoflavonoid
Hydroxyflavonoid
Flavanonol
Flavanone
5-hydroxyflavonoid
4'-hydroxyflavonoid
Flavan
Pyranochromene
2,2-dimethyl-1-benzopyran
Hexose monosaccharide
O-glycosyl compound
Glycosyl compound
Chromone
1-benzopyran
Benzopyran
Chromane
Aryl alkyl ketone
Aryl ketone
1-hydroxy-2-unsubstituted benzenoid
Phenol
Alkyl aryl ether
Benzenoid
Oxane
Monosaccharide
Monocyclic benzene moiety
Vinylogous acid
Secondary alcohol
Ketone
Oxacycle
Organoheterocyclic compound
Polyol
Ether
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
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	0.97	ALOGPS
logP	1.68	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	8.86	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	175.37 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	126.49 m³·mol⁻¹	ChemAxon
Polarizability	53.06 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	No	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

162931845

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Phellodendroside (NP0056000)

MOL for NP0056000 (Phellodendroside)

3D MOL for NP0056000 (Phellodendroside)

3D SDF for NP0056000 (Phellodendroside)

3D-SDF for NP0056000 (Phellodendroside)

PDB for NP0056000 (Phellodendroside)

3D PDB for NP0056000 (Phellodendroside)

SMILES for NP0056000 (Phellodendroside)

INCHI for NP0056000 (Phellodendroside)

Structure for NP0056000 (Phellodendroside)

3D Structure for NP0056000 (Phellodendroside)