NP-MRD: Showing NP-Card for Dendronobiloside B (NP0025869)

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Record Information

Version

2.0

Created at

2021-06-19 17:52:54 UTC

Updated at

2021-06-29 23:51:04 UTC

NP-MRD ID

NP0025869

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Dendronobiloside B

Provided By

JEOL Database JEOL Logo

Description

CHEMBL458760 belongs to the class of organic compounds known as terpene glycosides. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone. Dendronobiloside B is found in Dendrobium nobile. Dendronobiloside B was first documented in 2001 (Zhao, W., et al.). Based on a literature review very few articles have been published on CHEMBL458760.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306192119523D          

 67 69  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652306192119523D          

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M  END
> <DATABASE_ID>
NP0025869

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C21H38O8/c1-11(2)12-4-6-20(3)14(5-7-21(20,27)10-23)13(12)9-28-19-18(26)17(25)16(24)15(8-22)29-19/h11-19,22-27H,4-10H2,1-3H3/t12-,13-,14-,15-,16-,17+,18-,19-,20+,21+/m1/s1

> <INCHI_KEY>
NSBVLCNEJFYMMI-MQXSHROSSA-N

> <FORMULA>
C21H38O8

> <MOLECULAR_WEIGHT>
418.527

> <EXACT_MASS>
418.256668184

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
45.198430148062904

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R,3R,4S,5S,6R)-2-{[(1R,3aR,4R,5R,7aS)-1-hydroxy-1-(hydroxymethyl)-7a-methyl-5-(propan-2-yl)-octahydro-1H-inden-4-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
-0.22

> <JCHEM_LOGP>
-0.2987388786666657

> <ALOGPS_LOGS>
-2.10

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.058333341598935

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.191387157073418

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810834118093865

> <JCHEM_POLAR_SURFACE_AREA>
139.84

> <JCHEM_REFRACTIVITY>
104.1863

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.36e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S,5S,6R)-2-{[(1R,3aR,4R,5R,7aS)-1-hydroxy-1-(hydroxymethyl)-5-isopropyl-7a-methyl-hexahydro-2H-inden-4-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

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 11 49  1  0
 14 51  1  0
 14 52  1  0
  8 42  1  0
  8 43  1  0
  8 44  1  0
  2 33  1  1
 17 55  1  0
 17 56  1  0
  1 30  1  0
  1 31  1  0
  1 32  1  0
  3 34  1  0
  3 35  1  0
  3 36  1  0
 13 50  1  0
 15 53  1  0
M  END

HEADER    PROTEIN                                 19-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-JUN-21         0                                  
HETATM    1  C   UNK     0      -2.917   1.061  -2.717  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.901   1.563  -1.683  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.696   3.070  -1.860  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.581   0.730  -1.707  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.144   0.809  -3.066  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.394  -0.070  -3.112  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.413   0.226  -1.978  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.095   1.575  -2.267  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.701   0.235  -0.604  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.538  -1.255  -0.254  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.610  -2.014  -1.039  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.426  -0.957  -1.803  0.00  0.00           C+0
HETATM   13  O   UNK     0       3.816  -1.484  -3.074  0.00  0.00           O+0
HETATM   14  C   UNK     0       4.729  -0.642  -1.028  0.00  0.00           C+0
HETATM   15  O   UNK     0       5.609   0.124  -1.856  0.00  0.00           O+0
HETATM   16  C   UNK     0       0.408   1.091  -0.557  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.226   1.050   0.849  0.00  0.00           C+0
HETATM   18  O   UNK     0      -0.921  -0.177   1.048  0.00  0.00           O+0
HETATM   19  C   UNK     0      -1.551  -0.244   2.330  0.00  0.00           C+0
HETATM   20  O   UNK     0      -0.577  -0.284   3.371  0.00  0.00           O+0
HETATM   21  C   UNK     0      -1.176  -0.367   4.671  0.00  0.00           C+0
HETATM   22  C   UNK     0      -0.075  -0.297   5.737  0.00  0.00           C+0
HETATM   23  O   UNK     0      -0.610  -0.163   7.049  0.00  0.00           O+0
HETATM   24  C   UNK     0      -1.991  -1.666   4.802  0.00  0.00           C+0
HETATM   25  O   UNK     0      -2.628  -1.753   6.081  0.00  0.00           O+0
HETATM   26  C   UNK     0      -3.047  -1.719   3.697  0.00  0.00           C+0
HETATM   27  O   UNK     0      -3.728  -2.981   3.764  0.00  0.00           O+0
HETATM   28  C   UNK     0      -2.396  -1.532   2.330  0.00  0.00           C+0
HETATM   29  O   UNK     0      -3.422  -1.489   1.327  0.00  0.00           O+0
HETATM   30  H   UNK     0      -2.608   1.292  -3.741  0.00  0.00           H+0
HETATM   31  H   UNK     0      -3.059  -0.021  -2.632  0.00  0.00           H+0
HETATM   32  H   UNK     0      -3.892   1.536  -2.555  0.00  0.00           H+0
HETATM   33  H   UNK     0      -2.377   1.412  -0.706  0.00  0.00           H+0
HETATM   34  H   UNK     0      -1.037   3.482  -1.091  0.00  0.00           H+0
HETATM   35  H   UNK     0      -1.274   3.312  -2.840  0.00  0.00           H+0
HETATM   36  H   UNK     0      -2.653   3.597  -1.778  0.00  0.00           H+0
HETATM   37  H   UNK     0      -0.884  -0.317  -1.573  0.00  0.00           H+0
HETATM   38  H   UNK     0       0.414   1.844  -3.299  0.00  0.00           H+0
HETATM   39  H   UNK     0      -0.523   0.477  -3.870  0.00  0.00           H+0
HETATM   40  H   UNK     0       1.877   0.054  -4.090  0.00  0.00           H+0
HETATM   41  H   UNK     0       1.064  -1.116  -3.075  0.00  0.00           H+0
HETATM   42  H   UNK     0       3.751   1.884  -1.446  0.00  0.00           H+0
HETATM   43  H   UNK     0       3.693   1.524  -3.183  0.00  0.00           H+0
HETATM   44  H   UNK     0       2.371   2.385  -2.397  0.00  0.00           H+0
HETATM   45  H   UNK     0       2.390   0.662   0.140  0.00  0.00           H+0
HETATM   46  H   UNK     0       1.659  -1.413   0.824  0.00  0.00           H+0
HETATM   47  H   UNK     0       0.555  -1.648  -0.528  0.00  0.00           H+0
HETATM   48  H   UNK     0       2.137  -2.724  -1.730  0.00  0.00           H+0
HETATM   49  H   UNK     0       3.230  -2.619  -0.368  0.00  0.00           H+0
HETATM   50  H   UNK     0       4.541  -0.898  -3.375  0.00  0.00           H+0
HETATM   51  H   UNK     0       5.261  -1.570  -0.793  0.00  0.00           H+0
HETATM   52  H   UNK     0       4.545  -0.099  -0.097  0.00  0.00           H+0
HETATM   53  H   UNK     0       6.427   0.258  -1.345  0.00  0.00           H+0
HETATM   54  H   UNK     0       0.734   2.128  -0.709  0.00  0.00           H+0
HETATM   55  H   UNK     0       0.554   1.166   1.611  0.00  0.00           H+0
HETATM   56  H   UNK     0      -0.925   1.886   0.967  0.00  0.00           H+0
HETATM   57  H   UNK     0      -2.200   0.635   2.445  0.00  0.00           H+0
HETATM   58  H   UNK     0      -1.838   0.497   4.822  0.00  0.00           H+0
HETATM   59  H   UNK     0       0.579   0.561   5.549  0.00  0.00           H+0
HETATM   60  H   UNK     0       0.560  -1.190   5.705  0.00  0.00           H+0
HETATM   61  H   UNK     0      -1.360  -0.793   7.118  0.00  0.00           H+0
HETATM   62  H   UNK     0      -1.331  -2.538   4.712  0.00  0.00           H+0
HETATM   63  H   UNK     0      -3.270  -2.490   5.992  0.00  0.00           H+0
HETATM   64  H   UNK     0      -3.819  -0.958   3.868  0.00  0.00           H+0
HETATM   65  H   UNK     0      -4.249  -3.034   2.936  0.00  0.00           H+0
HETATM   66  H   UNK     0      -1.769  -2.402   2.095  0.00  0.00           H+0
HETATM   67  H   UNK     0      -2.956  -1.263   0.496  0.00  0.00           H+0
CONECT    1    2   30   31   32                                             
CONECT    2    4    1    3   33                                             
CONECT    3    2   34   35   36                                             
CONECT    4    5   16    2   37                                             
CONECT    5    4    6   38   39                                             
CONECT    6    7    5   40   41                                             
CONECT    7    6    9   12    8                                             
CONECT    8    7   42   43   44                                             
CONECT    9   16    7   10   45                                             
CONECT   10    9   11   46   47                                             
CONECT   11   10   12   48   49                                             
CONECT   12   11    7   14   13                                             
CONECT   13   12   50                                                       
CONECT   14   12   15   51   52                                             
CONECT   15   14   53                                                       
CONECT   16    4    9   17   54                                             
CONECT   17   16   18   55   56                                             
CONECT   18   19   17                                                       
CONECT   19   18   28   20   57                                             
CONECT   20   21   19                                                       
CONECT   21   20   24   22   58                                             
CONECT   22   23   21   59   60                                             
CONECT   23   22   61                                                       
CONECT   24   21   26   25   62                                             
CONECT   25   24   63                                                       
CONECT   26   27   24   28   64                                             
CONECT   27   26   65                                                       
CONECT   28   29   26   19   66                                             
CONECT   29   28   67                                                       
CONECT   30    1                                                            
CONECT   31    1                                                            
CONECT   32    1                                                            
CONECT   33    2                                                            
CONECT   34    3                                                            
CONECT   35    3                                                            
CONECT   36    3                                                            
CONECT   37    4                                                            
CONECT   38    5                                                            
CONECT   39    5                                                            
CONECT   40    6                                                            
CONECT   41    6                                                            
CONECT   42    8                                                            
CONECT   43    8                                                            
CONECT   44    8                                                            
CONECT   45    9                                                            
CONECT   46   10                                                            
CONECT   47   10                                                            
CONECT   48   11                                                            
CONECT   49   11                                                            
CONECT   50   13                                                            
CONECT   51   14                                                            
CONECT   52   14                                                            
CONECT   53   15                                                            
CONECT   54   16                                                            
CONECT   55   17                                                            
CONECT   56   17                                                            
CONECT   57   19                                                            
CONECT   58   21                                                            
CONECT   59   22                                                            
CONECT   60   22                                                            
CONECT   61   23                                                            
CONECT   62   24                                                            
CONECT   63   25                                                            
CONECT   64   26                                                            
CONECT   65   27                                                            
CONECT   66   28                                                            
CONECT   67   29                                                            
MASTER        0    0    0    0    0    0    0    0   67    0  138    0
END

RDKit          3D

67 69  0  0  0  0  0  0  0  0999 V2000
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  1 30  1  0
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  1 32  1  0
  3 34  1  0
  3 35  1  0
  3 36  1  0
 13 50  1  0
 15 53  1  0
M  END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₁H₃₈O₈

Average Mass

418.5270 Da

Monoisotopic Mass

418.25667 Da

IUPAC Name

(2R,3R,4S,5S,6R)-2-{[(1R,3aR,4R,5R,7aS)-1-hydroxy-1-(hydroxymethyl)-7a-methyl-5-(propan-2-yl)-octahydro-1H-inden-4-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

(2R,3R,4S,5S,6R)-2-{[(1R,3aR,4R,5R,7aS)-1-hydroxy-1-(hydroxymethyl)-5-isopropyl-7a-methyl-hexahydro-2H-inden-4-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

[H]OC([H])([H])[C@@]1([H])O[C@@]([H])(OC([H])([H])[C@@]2([H])[C@@]3([H])C([H])([H])C([H])([H])[C@](O[H])(C([H])([H])O[H])[C@@]3(C([H])([H])[H])C([H])([H])C([H])([H])[C@]2([H])C([H])(C([H])([H])[H])C([H])([H])[H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@]1([H])O[H]

InChI Identifier

InChI=1S/C21H38O8/c1-11(2)12-4-6-20(3)14(5-7-21(20,27)10-23)13(12)9-28-19-18(26)17(25)16(24)15(8-22)29-19/h11-19,22-27H,4-10H2,1-3H3/t12-,13-,14-,15-,16-,17+,18-,19-,20+,21+/m1/s1

InChI Key

NSBVLCNEJFYMMI-MQXSHROSSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Dendrobium nobile	JEOL database	Zhao, W., et al, J. Nat. Prod. 64, 1196 (2001)

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene glycosides. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Terpene glycosides

Alternative Parents

Substituents

Terpene glycoside
Sesquiterpenoid
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Monosaccharide
Oxane
Cyclic alcohol
Tertiary alcohol
Secondary alcohol
Polyol
Organoheterocyclic compound
Oxacycle
Acetal
Alcohol
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
Primary 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	-0.22	ALOGPS
logP	-0.3	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	12.19	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	139.84 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	104.19 m³·mol⁻¹	ChemAxon
Polarizability	45.2 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	Yes	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

9936253

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11761556

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Zhao, W., et al. (2001). Zhao, W., et al, J. Nat. Prod. 64, 1196 (2001). J. Nat. Prod..

Showing NP-Card for Dendronobiloside B (NP0025869)

MOL for NP0025869 (Dendronobiloside B)

3D MOL for NP0025869 (Dendronobiloside B)

3D SDF for NP0025869 (Dendronobiloside B)

3D-SDF for NP0025869 (Dendronobiloside B)

PDB for NP0025869 (Dendronobiloside B)

3D PDB for NP0025869 (Dendronobiloside B)

SMILES for NP0025869 (Dendronobiloside B)

INCHI for NP0025869 (Dendronobiloside B)

Structure for NP0025869 (Dendronobiloside B)

3D Structure for NP0025869 (Dendronobiloside B)