NP-MRD: Showing NP-Card for (2s,3r,4s,5s,6r)-2-(5,7-dihydroxy-2-isopropyl-4-oxochromen-6-yl)-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,4,5-trihydroxybenzoate (NP0198150)

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Record Information

Version

2.0

Created at

2022-09-04 16:32:37 UTC

Updated at

2022-09-04 16:32:37 UTC

NP-MRD ID

NP0198150

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3r,4s,5s,6r)-2-(5,7-dihydroxy-2-isopropyl-4-oxochromen-6-yl)-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,4,5-trihydroxybenzoate

Description

CHEMBL465541 belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose. (2s,3r,4s,5s,6r)-2-(5,7-dihydroxy-2-isopropyl-4-oxochromen-6-yl)-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,4,5-trihydroxybenzoate is found in Baeckea frutescens and Kunzea ambigua. Based on a literature review very few articles have been published on CHEMBL465541.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309042218322D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309042218322D          

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 11 34  2  0  0  0  0
 34 35  1  0  0  0  0
 34 36  1  0  0  0  0
 36 37  2  0  0  0  0
  8 37  1  0  0  0  0
 37 38  1  0  0  0  0
  4 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0198150

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)C1=CC(=O)C2=C(O)C([C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3OC(=O)C3=CC(O)=C(O)C(O)=C3)=C(O)C=C2O1

> <INCHI_IDENTIFIER>
InChI=1S/C25H26O13/c1-8(2)14-5-10(27)17-15(36-14)6-11(28)18(21(17)33)23-24(22(34)20(32)16(7-26)37-23)38-25(35)9-3-12(29)19(31)13(30)4-9/h3-6,8,16,20,22-24,26,28-34H,7H2,1-2H3/t16-,20-,22+,23+,24-/m1/s1

> <INCHI_KEY>
SKFNXFFWGBHKGW-DONDVOMOSA-N

> <FORMULA>
C25H26O13

> <MOLECULAR_WEIGHT>
534.47

> <EXACT_MASS>
534.137340897

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
51.20191472131292

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5S,6R)-2-[5,7-dihydroxy-4-oxo-2-(propan-2-yl)-4H-chromen-6-yl]-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,4,5-trihydroxybenzoate

> <JCHEM_LOGP>
1.629200826

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.609258748429282

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.148375223140728

> <JCHEM_PKA_STRONGEST_BASIC>
-2.979193257148009

> <JCHEM_POLAR_SURFACE_AREA>
223.66999999999996

> <JCHEM_REFRACTIVITY>
128.94759999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5S,6R)-2-(5,7-dihydroxy-2-isopropyl-4-oxochromen-6-yl)-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,4,5-trihydroxybenzoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  -2.310   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       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667   1.540   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       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       8.002   1.540   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      10.669   4.620   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      10.669   1.540   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      12.003   2.310   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      10.669  -0.000   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      12.003  -0.770   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       9.336  -2.310   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      12.003  -2.310   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      12.003  -5.390   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      12.003  -6.930   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      13.337  -7.700   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      10.669  -7.700   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      10.669  -9.240   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       8.002  -7.700   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   38                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   37                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   34                                                  
CONECT   12   11   13   21                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15                                                            
CONECT   17   14   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   12   22                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   33                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   25                                                       
CONECT   34   11   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   37                                                       
CONECT   37   36    8   38                                                  
CONECT   38   37    4                                                       
MASTER        0    0    0    0    0    0    0    0   38    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₂₆O₁₃

Average Mass

534.4700 Da

Monoisotopic Mass

534.13734 Da

IUPAC Name

(2S,3R,4S,5S,6R)-2-[5,7-dihydroxy-4-oxo-2-(propan-2-yl)-4H-chromen-6-yl]-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,4,5-trihydroxybenzoate

Traditional Name

(2S,3R,4S,5S,6R)-2-(5,7-dihydroxy-2-isopropyl-4-oxochromen-6-yl)-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,4,5-trihydroxybenzoate

CAS Registry Number

Not Available

SMILES

CC(C)C1=CC(=O)C2=C(O)C([C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3OC(=O)C3=CC(O)=C(O)C(O)=C3)=C(O)C=C2O1

InChI Identifier

InChI=1S/C25H26O13/c1-8(2)14-5-10(27)17-15(36-14)6-11(28)18(21(17)33)23-24(22(34)20(32)16(7-26)37-23)38-25(35)9-3-12(29)19(31)13(30)4-9/h3-6,8,16,20,22-24,26,28-34H,7H2,1-2H3/t16-,20-,22+,23+,24-/m1/s1

InChI Key

SKFNXFFWGBHKGW-DONDVOMOSA-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
Baeckea frutescens	LOTUS Database	35616633
Kunzea ambigua	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Phenolic glycosides

Alternative Parents

Substituents

Phenolic glycoside
Galloyl ester
Gallic acid or derivatives
Hexose monosaccharide
P-hydroxybenzoic acid alkyl ester
M-hydroxybenzoic acid ester
P-hydroxybenzoic acid ester
Chromone
C-glycosyl compound
Benzopyran
1-benzopyran
Benzoate ester
Benzenetriol
Pyrogallol derivative
Benzoic acid or derivatives
Benzoyl
Pyranone
Phenol
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Pyran
Oxane
Monosaccharide
Monocyclic benzene moiety
Benzenoid
Heteroaromatic compound
Vinylogous acid
Secondary alcohol
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Polyol
Ether
Carboxylic acid derivative
Dialkyl ether
Primary alcohol
Organic oxide
Hydrocarbon derivative
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	1.63	ChemAxon
pKa (Strongest Acidic)	6.15	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	223.67 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	128.95 m³·mol⁻¹	ChemAxon
Polarizability	51.2 Å³	ChemAxon
Number of Rings	4	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

23339476

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5317461

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s,3r,4s,5s,6r)-2-(5,7-dihydroxy-2-isopropyl-4-oxochromen-6-yl)-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,4,5-trihydroxybenzoate (NP0198150)

MOL for NP0198150 ((2s,3r,4s,5s,6r)-2-(5,7-dihydroxy-2-isopropyl-4-oxochromen-6-yl)-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,4,5-trihydroxybenzoate)

3D MOL for NP0198150 ((2s,3r,4s,5s,6r)-2-(5,7-dihydroxy-2-isopropyl-4-oxochromen-6-yl)-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,4,5-trihydroxybenzoate)

3D SDF for NP0198150 ((2s,3r,4s,5s,6r)-2-(5,7-dihydroxy-2-isopropyl-4-oxochromen-6-yl)-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,4,5-trihydroxybenzoate)

3D-SDF for NP0198150 ((2s,3r,4s,5s,6r)-2-(5,7-dihydroxy-2-isopropyl-4-oxochromen-6-yl)-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,4,5-trihydroxybenzoate)

PDB for NP0198150 ((2s,3r,4s,5s,6r)-2-(5,7-dihydroxy-2-isopropyl-4-oxochromen-6-yl)-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,4,5-trihydroxybenzoate)

3D PDB for NP0198150 ((2s,3r,4s,5s,6r)-2-(5,7-dihydroxy-2-isopropyl-4-oxochromen-6-yl)-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,4,5-trihydroxybenzoate)

SMILES for NP0198150 ((2s,3r,4s,5s,6r)-2-(5,7-dihydroxy-2-isopropyl-4-oxochromen-6-yl)-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,4,5-trihydroxybenzoate)

INCHI for NP0198150 ((2s,3r,4s,5s,6r)-2-(5,7-dihydroxy-2-isopropyl-4-oxochromen-6-yl)-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,4,5-trihydroxybenzoate)

Structure for NP0198150 ((2s,3r,4s,5s,6r)-2-(5,7-dihydroxy-2-isopropyl-4-oxochromen-6-yl)-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,4,5-trihydroxybenzoate)

3D Structure for NP0198150 ((2s,3r,4s,5s,6r)-2-(5,7-dihydroxy-2-isopropyl-4-oxochromen-6-yl)-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,4,5-trihydroxybenzoate)