NP-MRD: Showing NP-Card for Daphneticin 4''-beta-D-glucopyranoside (NP0076397)

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Record Information

Version

2.0

Created at

2022-04-28 21:32:35 UTC

Updated at

2022-04-28 21:32:35 UTC

NP-MRD ID

NP0076397

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Daphneticin 4''-beta-D-glucopyranoside

Description

CHEMBL575616 belongs to the class of organic compounds known as coumarinolignans. These are lignans with a structure characterized by the presence of a 1,4-dioxane bridge substituted by a phenyl group, and fused to a coumarin. Daphneticin 4''-beta-D-glucopyranoside is found in Daphne feddei. Based on a literature review very few articles have been published on CHEMBL575616.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282223322D          

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M  END

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M  END


  Mrv1652304282223322D          

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 21 26  1  6  0  0  0
 20 27  1  1  0  0  0
 27 28  1  0  0  0  0
 11 29  1  0  0  0  0
 29 30  1  0  0  0  0
  3 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
  2 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  2  0  0  0  0
 36 38  1  0  0  0  0
 38 39  2  0  0  0  0
 33 39  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0076397

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(=CC(OC)=C1O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)[C@H]1OC2=CC=C3C=CC(=O)OC3=C2O[C@@H]1CO

> <INCHI_IDENTIFIER>
InChI=1S/C26H28O13/c1-33-14-7-12(8-15(34-2)24(14)39-26-21(32)20(31)19(30)16(9-27)37-26)22-17(10-28)36-25-13(35-22)5-3-11-4-6-18(29)38-23(11)25/h3-8,16-17,19-22,26-28,30-32H,9-10H2,1-2H3/t16-,17-,19-,20+,21-,22-,26+/m1/s1

> <INCHI_KEY>
UFNILYRCPSTPHP-BPCUWKSQSA-N

> <FORMULA>
C26H28O13

> <MOLECULAR_WEIGHT>
548.497

> <EXACT_MASS>
548.152990962

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
53.976082838824176

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R)-3-(3,5-dimethoxy-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2-(hydroxymethyl)-2H,3H,9H-[1,4]dioxino[2,3-h]chromen-9-one

> <ALOGPS_LOGP>
0.69

> <JCHEM_LOGP>
-0.4365785603333333

> <ALOGPS_LOGS>
-2.96

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.17956251289499

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.198003481556457

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810923662076965

> <JCHEM_POLAR_SURFACE_AREA>
182.82999999999998

> <JCHEM_REFRACTIVITY>
129.80299999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.96e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R)-3-(3,5-dimethoxy-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2-(hydroxymethyl)-2H,3H-[1,4]dioxino[2,3-h]chromen-9-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  O   UNK     0       5.184  -0.564   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.414   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.184   2.104   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       6.724   2.104   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       7.494   0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.724  -0.564   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.494  -1.897   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       6.724  -3.231   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       9.034   0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.804   2.104   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      11.344   2.104   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.114   0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      11.344  -0.564   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.804  -0.564   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      12.114  -1.897   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      11.344  -3.231   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      13.654   0.770   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      14.424  -0.564   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      13.654  -1.897   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      14.424  -3.231   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      15.964  -3.231   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      16.734  -1.897   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      15.964  -0.564   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      16.734   0.770   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      18.274  -1.897   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      16.734  -4.565   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      13.654  -4.565   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      14.424  -5.898   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      12.114   3.437   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      13.654   3.437   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.414   3.437   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.874   3.437   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.104   2.104   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       2.104  -0.564   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       0.564  -0.564   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      -0.206  -1.897   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      -0.206   0.770   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       0.564   2.104   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3   34                                                  
CONECT    3    2    4   31                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    9                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7                                                            
CONECT    9    5   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   29                                                  
CONECT   12   11   13   17                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13    9                                                       
CONECT   15   13   16                                                       
CONECT   16   15                                                            
CONECT   17   12   18                                                       
CONECT   18   17   19   23                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   27                                                  
CONECT   21   20   22   26                                                  
CONECT   22   21   23   25                                                  
CONECT   23   22   18   24                                                  
CONECT   24   23                                                            
CONECT   25   22                                                            
CONECT   26   21                                                            
CONECT   27   20   28                                                       
CONECT   28   27                                                            
CONECT   29   11   30                                                       
CONECT   30   29                                                            
CONECT   31    3   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34   39                                                  
CONECT   34   33    2   35                                                  
CONECT   35   34   36                                                       
CONECT   36   35   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   39                                                       
CONECT   39   38   33                                                       
MASTER        0    0    0    0    0    0    0    0   39    0   86    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₂₈O₁₃

Average Mass

548.4970 Da

Monoisotopic Mass

548.15299 Da

IUPAC Name

(2R,3R)-3-(3,5-dimethoxy-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2-(hydroxymethyl)-2H,3H,9H-[1,4]dioxino[2,3-h]chromen-9-one

Traditional Name

(2R,3R)-3-(3,5-dimethoxy-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2-(hydroxymethyl)-2H,3H-[1,4]dioxino[2,3-h]chromen-9-one

CAS Registry Number

Not Available

SMILES

COC1=CC(=CC(OC)=C1O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)[C@H]1OC2=CC=C3C=CC(=O)OC3=C2O[C@@H]1CO

InChI Identifier

InChI=1S/C26H28O13/c1-33-14-7-12(8-15(34-2)24(14)39-26-21(32)20(31)19(30)16(9-27)37-26)22-17(10-28)36-25-13(35-22)5-3-11-4-6-18(29)38-23(11)25/h3-8,16-17,19-22,26-28,30-32H,9-10H2,1-2H3/t16-,17-,19-,20+,21-,22-,26+/m1/s1

InChI Key

UFNILYRCPSTPHP-BPCUWKSQSA-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
Daphne feddei	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as coumarinolignans. These are lignans with a structure characterized by the presence of a 1,4-dioxane bridge substituted by a phenyl group, and fused to a coumarin.

Kingdom

Organic compounds

Super Class

Lignans, neolignans and related compounds

Class

Coumarinolignans

Sub Class

Not Available

Direct Parent

Coumarinolignans

Alternative Parents

Substituents

Angular-fused coumarolignan skeleton
2-phenylbenzo-1,4-dioxane
Phenylbenzodioxane
Phenolic glycoside
P-dioxolo[2,3-h]coumarin
Hexose monosaccharide
Coumarin
Glycosyl compound
O-glycosyl compound
Dimethoxybenzene
M-dimethoxybenzene
1-benzopyran
Benzo-1,4-dioxane
Benzodioxane
Benzopyran
Methoxybenzene
Anisole
Phenoxy compound
Phenol ether
Pyranone
Alkyl aryl ether
Benzenoid
Monocyclic benzene moiety
Pyran
Monosaccharide
Oxane
Para-dioxin
Heteroaromatic compound
Lactone
Secondary alcohol
Ether
Acetal
Oxacycle
Organoheterocyclic compound
Polyol
Organic oxygen compound
Alcohol
Primary alcohol
Hydrocarbon derivative
Organooxygen compound
Organic oxide
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	0.69	ALOGPS
logP	-0.44	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	12.2	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	182.83 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	129.8 m³·mol⁻¹	ChemAxon
Polarizability	53.98 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

24635728

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

45482326

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Daphneticin 4''-beta-D-glucopyranoside (NP0076397)

MOL for NP0076397 (Daphneticin 4''-beta-D-glucopyranoside)

3D MOL for NP0076397 (Daphneticin 4''-beta-D-glucopyranoside)

3D SDF for NP0076397 (Daphneticin 4''-beta-D-glucopyranoside)

3D-SDF for NP0076397 (Daphneticin 4''-beta-D-glucopyranoside)

PDB for NP0076397 (Daphneticin 4''-beta-D-glucopyranoside)

3D PDB for NP0076397 (Daphneticin 4''-beta-D-glucopyranoside)

SMILES for NP0076397 (Daphneticin 4''-beta-D-glucopyranoside)

INCHI for NP0076397 (Daphneticin 4''-beta-D-glucopyranoside)

Structure for NP0076397 (Daphneticin 4''-beta-D-glucopyranoside)

3D Structure for NP0076397 (Daphneticin 4''-beta-D-glucopyranoside)