NP-MRD: Showing NP-Card for Verbascoside B (NP0057559)

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Record Information

Version

2.0

Created at

2022-04-28 02:58:31 UTC

Updated at

2022-04-28 02:58:32 UTC

NP-MRD ID

NP0057559

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Verbascoside B

Description

(2S,3R,4S,5S,6R)-2-{[(1S,4aS,5S,6S,7R,7aS)-6,7-dihydroxy-7-(hydroxymethyl)-1-{[(2R,3S,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-5-yl]oxy}-6-methyloxane-3,4,5-triol belongs to the class of organic compounds known as iridoid o-glycosides. These are iridoid monoterpenes containing a glycosyl (usually a pyranosyl) moiety linked to the iridoid skeleton. Verbascoside B is found in Gmelina arborea and Verbascum georgicum. Based on a literature review very few articles have been published on (2S,3R,4S,5S,6R)-2-{[(1S,4aS,5S,6S,7R,7aS)-6,7-dihydroxy-7-(hydroxymethyl)-1-{[(2R,3S,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-5-yl]oxy}-6-methyloxane-3,4,5-triol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282204582D          

 36 39  0  0  1  0            999 V2000
    0.6411   -1.1104    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.3556   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.3646    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0701    2.1896    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    2.6021    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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  8 13  1  0  0  0  0
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  2 19  1  0  0  0  0
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 34 35  1  0  0  0  0
 19 36  1  1  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304282204582D          

 36 39  0  0  1  0            999 V2000
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  2 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
  1 21  1  0  0  0  0
 21 22  1  6  0  0  0
 23 22  1  1  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 23 28  1  0  0  0  0
 27 29  1  1  0  0  0
 26 30  1  6  0  0  0
 25 31  1  1  0  0  0
 24 32  1  6  0  0  0
 20 33  1  6  0  0  0
 19 34  1  6  0  0  0
 34 35  1  0  0  0  0
 19 36  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0057559

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1O[C@@H](O[C@@H]2[C@H](O)[C@](O)(CO)[C@@H]3[C@@H]2C=CO[C@H]3O[C@H]2O[C@H](CO)[C@@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C21H34O15/c1-6-10(24)12(26)14(28)19(33-6)35-16-7-2-3-32-18(9(7)21(31,5-23)17(16)30)36-20-15(29)13(27)11(25)8(4-22)34-20/h2-3,6-20,22-31H,4-5H2,1H3/t6-,7+,8-,9-,10-,11-,12+,13-,14-,15+,16+,17+,18+,19+,20-,21+/m1/s1

> <INCHI_KEY>
QJMLIWAVRXZVOF-GTRUITRHSA-N

> <FORMULA>
C21H34O15

> <MOLECULAR_WEIGHT>
526.488

> <EXACT_MASS>
526.189770395

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
49.24260306959566

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4R,5S,6R)-2-{[(1S,4aS,5S,6S,7R,7aS)-6,7-dihydroxy-7-(hydroxymethyl)-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
-1.98

> <JCHEM_LOGP>
-5.317432861

> <ALOGPS_LOGS>
-0.40

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.258539150944369

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.807650772829163

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6121825921061017

> <JCHEM_POLAR_SURFACE_AREA>
248.44999999999996

> <JCHEM_REFRACTIVITY>
111.57119999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.08e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4R,5S,6R)-2-{[(1S,4aS,5S,6S,7R,7aS)-6,7-dihydroxy-7-(hydroxymethyl)-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}-1H,4aH,5H,6H,7aH-cyclopenta[c]pyran-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <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       1.197  -2.073   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.197  -0.533   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.530   0.237   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       3.864  -0.533   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       3.864  -2.073   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.530  -2.843   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.530   1.777   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       3.864   2.547   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       3.864   4.087   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       5.198   4.857   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.531   4.087   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.531   2.547   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.198   1.777   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       5.198   0.237   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       7.865   1.777   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       7.865   4.857   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       5.198   6.397   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       6.531   7.167   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -0.268  -0.057   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -1.173  -1.303   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -0.268  -2.549   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -0.744  -4.013   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -2.250  -4.334   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.726  -5.798   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -4.232  -6.118   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -5.263  -4.974   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -4.787  -3.509   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -3.281  -3.189   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -5.817  -2.365   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -6.769  -5.294   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -4.708  -7.583   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -1.696  -6.943   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -2.713  -1.303   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       0.037   1.453   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -1.119   2.471   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      -1.401   0.985   0.000  0.00  0.00           O+0
CONECT    1    2    6   21                                                  
CONECT    2    1    3   19                                                  
CONECT    3    2    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
CONECT    7    3    8                                                       
CONECT    8    7    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   17                                                  
CONECT   11   10   12   16                                                  
CONECT   12   11   13   15                                                  
CONECT   13   12    8   14                                                  
CONECT   14   13                                                            
CONECT   15   12                                                            
CONECT   16   11                                                            
CONECT   17   10   18                                                       
CONECT   18   17                                                            
CONECT   19    2   20   34   36                                             
CONECT   20   19   21   33                                                  
CONECT   21   20    1   22                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   28                                                  
CONECT   24   23   25   32                                                  
CONECT   25   24   26   31                                                  
CONECT   26   25   27   30                                                  
CONECT   27   26   28   29                                                  
CONECT   28   27   23                                                       
CONECT   29   27                                                            
CONECT   30   26                                                            
CONECT   31   25                                                            
CONECT   32   24                                                            
CONECT   33   20                                                            
CONECT   34   19   35                                                       
CONECT   35   34                                                            
CONECT   36   19                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₁H₃₄O₁₅

Average Mass

526.4880 Da

Monoisotopic Mass

526.18977 Da

IUPAC Name

(2R,3S,4R,5S,6R)-2-{[(1S,4aS,5S,6S,7R,7aS)-6,7-dihydroxy-7-(hydroxymethyl)-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

(2R,3S,4R,5S,6R)-2-{[(1S,4aS,5S,6S,7R,7aS)-6,7-dihydroxy-7-(hydroxymethyl)-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}-1H,4aH,5H,6H,7aH-cyclopenta[c]pyran-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

C[C@H]1O[C@@H](O[C@@H]2[C@H](O)[C@](O)(CO)[C@@H]3[C@@H]2C=CO[C@H]3O[C@H]2O[C@H](CO)[C@@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C21H34O15/c1-6-10(24)12(26)14(28)19(33-6)35-16-7-2-3-32-18(9(7)21(31,5-23)17(16)30)36-20-15(29)13(27)11(25)8(4-22)34-20/h2-3,6-20,22-31H,4-5H2,1H3/t6-,7+,8-,9-,10-,11-,12+,13-,14-,15+,16+,17+,18+,19+,20-,21+/m1/s1

InChI Key

QJMLIWAVRXZVOF-GTRUITRHSA-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
Gmelina arborea	Plant	KNApSAcK
Verbascum georgicum	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as iridoid o-glycosides. These are iridoid monoterpenes containing a glycosyl (usually a pyranosyl) moiety linked to the iridoid skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Iridoid O-glycosides

Alternative Parents

Substituents

Iridoid o-glycoside
O-glycosyl compound
Iridoid-skeleton
Glycosyl compound
Monoterpenoid
Bicyclic monoterpenoid
Oxane
Monosaccharide
Tertiary alcohol
Cyclic alcohol
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Polyol
Acetal
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	-2	ALOGPS
logP	-5.3	ChemAxon
logS	-0.4	ALOGPS
pKa (Strongest Acidic)	11.81	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	248.45 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	111.57 m³·mol⁻¹	ChemAxon
Polarizability	49.24 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

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

162982422

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Verbascoside B (NP0057559)

MOL for NP0057559 (Verbascoside B)

3D MOL for NP0057559 (Verbascoside B)

3D SDF for NP0057559 (Verbascoside B)

3D-SDF for NP0057559 (Verbascoside B)

PDB for NP0057559 (Verbascoside B)

3D PDB for NP0057559 (Verbascoside B)

SMILES for NP0057559 (Verbascoside B)

INCHI for NP0057559 (Verbascoside B)

Structure for NP0057559 (Verbascoside B)

3D Structure for NP0057559 (Verbascoside B)