NP-MRD: Showing NP-Card for Podorhizol beta-D-glucoside (NP0051517)

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Record Information

Version

2.0

Created at

2022-04-27 22:51:16 UTC

Updated at

2022-04-27 22:51:16 UTC

NP-MRD ID

NP0051517

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Podorhizol beta-D-glucoside

Description

(3S,4R)-4-[(2H-1,3-benzodioxol-5-yl)methyl]-3-[(S)-{[(2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}(3,4,5-trimethoxyphenyl)methyl]oxolan-2-one belongs to the class of organic compounds known as lignan glycosides. These are aromatic polycyclic compounds containing a carbohydrate component glycosidically linked to a lignan moiety. They include 1-aryltetralin lactones. Podorhizol beta-D-glucoside is found in Podophyllum emodii, Podophyllum hexandrum and Podophyllum peltatum . Based on a literature review very few articles have been published on (3S,4R)-4-[(2H-1,3-benzodioxol-5-yl)methyl]-3-[(S)-{[(2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}(3,4,5-trimethoxyphenyl)methyl]oxolan-2-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282200512D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304282200512D          

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    5.6903   -1.7710    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4750   -1.5160    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.6465   -0.7090    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.4311   -0.4541    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.0442   -1.0061    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.8727   -1.8131    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.0881   -2.0680    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.4858   -2.3651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2704   -2.1102    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.8288   -0.7512    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6026    0.3529    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0334   -0.1570    0.0000 O   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
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  1  9  1  0  0  0  0
  4 10  1  0  0  0  0
 11 10  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 11 16  1  0  0  0  0
 12 17  1  1  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 18 23  1  0  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 21 26  1  0  0  0  0
 26 27  1  0  0  0  0
 20 28  1  0  0  0  0
 28 29  1  0  0  0  0
 17 30  1  6  0  0  0
 31 30  1  1  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 31 36  1  0  0  0  0
 35 37  1  1  0  0  0
 37 38  1  0  0  0  0
 34 39  1  6  0  0  0
 33 40  1  1  0  0  0
 32 41  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0051517

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(=CC(OC)=C1OC)[C@@H](O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1O)[C@@H]1[C@@H](CC2=CC=C3OCOC3=C2)COC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C28H34O13/c1-34-18-8-14(9-19(35-2)26(18)36-3)25(41-28-24(32)23(31)22(30)20(10-29)40-28)21-15(11-37-27(21)33)6-13-4-5-16-17(7-13)39-12-38-16/h4-5,7-9,15,20-25,28-32H,6,10-12H2,1-3H3/t15-,20+,21-,22+,23-,24-,25+,28-/m0/s1

> <INCHI_KEY>
IETDTZKBVWFSKR-ZKQCBYHXSA-N

> <FORMULA>
C28H34O13

> <MOLECULAR_WEIGHT>
578.567

> <EXACT_MASS>
578.199941155

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
57.68944253406739

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4R)-4-[(2H-1,3-benzodioxol-5-yl)methyl]-3-[(S)-{[(2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}(3,4,5-trimethoxyphenyl)methyl]oxolan-2-one

> <ALOGPS_LOGP>
1.04

> <JCHEM_LOGP>
0.5187361036666664

> <ALOGPS_LOGS>
-2.96

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.199889667081347

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.21004785441589

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810836884355165

> <JCHEM_POLAR_SURFACE_AREA>
171.83

> <JCHEM_REFRACTIVITY>
137.67750000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.38e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,4R)-4-(2H-1,3-benzodioxol-5-ylmethyl)-3-[(S)-{[(2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}(3,4,5-trimethoxyphenyl)methyl]oxolan-2-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       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.126  -2.549   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.126  -0.057   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       7.591  -2.843   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.591  -4.383   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.837  -5.288   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.361  -6.753   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       9.266  -7.999   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       6.821  -6.753   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       6.345  -5.288   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.302  -4.812   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      11.446  -5.843   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      12.911  -5.367   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      14.055  -6.397   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      13.735  -7.904   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      12.270  -8.379   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      11.126  -7.349   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      11.950  -9.886   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      10.486 -10.362   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      14.880  -8.934   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      16.344  -8.458   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      15.520  -5.921   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      16.664  -6.952   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      10.622  -3.306   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      12.087  -2.830   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      12.407  -1.324   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      13.871  -0.848   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      15.016  -1.878   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      14.696  -3.384   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      13.231  -3.860   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      15.840  -4.415   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      17.305  -3.939   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      16.480  -1.402   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0      14.192   0.659   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0      11.262  -0.293   0.000  0.00  0.00           O+0
CONECT    1    2    6    9                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   10                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    1                                                       
CONECT   10    4   11                                                       
CONECT   11   10   12   16                                                  
CONECT   12   11   13   17                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   11                                                       
CONECT   17   12   18   30                                                  
CONECT   18   17   19   23                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   28                                                  
CONECT   21   20   22   26                                                  
CONECT   22   21   23   24                                                  
CONECT   23   22   18                                                       
CONECT   24   22   25                                                       
CONECT   25   24                                                            
CONECT   26   21   27                                                       
CONECT   27   26                                                            
CONECT   28   20   29                                                       
CONECT   29   28                                                            
CONECT   30   17   31                                                       
CONECT   31   30   32   36                                                  
CONECT   32   31   33   41                                                  
CONECT   33   32   34   40                                                  
CONECT   34   33   35   39                                                  
CONECT   35   34   36   37                                                  
CONECT   36   35   31                                                       
CONECT   37   35   38                                                       
CONECT   38   37                                                            
CONECT   39   34                                                            
CONECT   40   33                                                            
CONECT   41   32                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   90    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₄O₁₃

Average Mass

578.5670 Da

Monoisotopic Mass

578.19994 Da

IUPAC Name

(3S,4R)-4-[(2H-1,3-benzodioxol-5-yl)methyl]-3-[(S)-{[(2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}(3,4,5-trimethoxyphenyl)methyl]oxolan-2-one

Traditional Name

(3S,4R)-4-(2H-1,3-benzodioxol-5-ylmethyl)-3-[(S)-{[(2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}(3,4,5-trimethoxyphenyl)methyl]oxolan-2-one

CAS Registry Number

Not Available

SMILES

COC1=CC(=CC(OC)=C1OC)[C@@H](O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1O)[C@@H]1[C@@H](CC2=CC=C3OCOC3=C2)COC1=O

InChI Identifier

InChI=1S/C28H34O13/c1-34-18-8-14(9-19(35-2)26(18)36-3)25(41-28-24(32)23(31)22(30)20(10-29)40-28)21-15(11-37-27(21)33)6-13-4-5-16-17(7-13)39-12-38-16/h4-5,7-9,15,20-25,28-32H,6,10-12H2,1-3H3/t15-,20+,21-,22+,23-,24-,25+,28-/m0/s1

InChI Key

IETDTZKBVWFSKR-ZKQCBYHXSA-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
Podophyllum emodii	Plant	KNApSAcK
Podophyllum hexandrum	Plant	KNApSAcK
Podophyllum peltatum	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as lignan glycosides. These are aromatic polycyclic compounds containing a carbohydrate component glycosidically linked to a lignan moiety. They include 1-aryltetralin lactones.

Kingdom

Organic compounds

Super Class

Lignans, neolignans and related compounds

Class

Lignan glycosides

Sub Class

Not Available

Direct Parent

Lignan glycosides

Alternative Parents

Substituents

Lignan glycoside
Dibenzylbutyrolactone
Furanoid lignan
9,9p-epoxylignan
Tetrahydrofuran lignan
Lignan lactone
O-glycosyl compound
Glycosyl compound
Benzodioxole
Phenoxy compound
Methoxybenzene
Phenol ether
Anisole
Alkyl aryl ether
Benzenoid
Oxane
Monosaccharide
Gamma butyrolactone
Monocyclic benzene moiety
Tetrahydrofuran
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Polyol
Monocarboxylic acid or derivatives
Ether
Carboxylic acid derivative
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
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	1.04	ALOGPS
logP	0.52	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	171.83 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	137.68 m³·mol⁻¹	ChemAxon
Polarizability	57.69 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

163012631

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Podorhizol beta-D-glucoside (NP0051517)

MOL for NP0051517 (Podorhizol beta-D-glucoside)

3D MOL for NP0051517 (Podorhizol beta-D-glucoside)

3D SDF for NP0051517 (Podorhizol beta-D-glucoside)

3D-SDF for NP0051517 (Podorhizol beta-D-glucoside)

PDB for NP0051517 (Podorhizol beta-D-glucoside)

3D PDB for NP0051517 (Podorhizol beta-D-glucoside)

SMILES for NP0051517 (Podorhizol beta-D-glucoside)

INCHI for NP0051517 (Podorhizol beta-D-glucoside)

Structure for NP0051517 (Podorhizol beta-D-glucoside)

3D Structure for NP0051517 (Podorhizol beta-D-glucoside)