NP-MRD: Showing NP-Card for (-)-Tetracentronside B (NP0075834)

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Record Information

Version

2.0

Created at

2022-04-28 21:03:37 UTC

Updated at

2022-04-28 21:03:37 UTC

NP-MRD ID

NP0075834

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Tetracentronside B

Description

CHEMBL3290507 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. (-)-Tetracentronside B is found in Tetracentron sinense . Based on a literature review very few articles have been published on CHEMBL3290507.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282223032D          

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 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
  1 34  1  0  0  0  0
 32 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 31 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0075834

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H](CC1=CC2=C(OCO2)C=C1)[C@H](CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)CC1=CC2=C(OCO2)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C26H32O11/c27-9-16(5-14-1-3-18-20(7-14)35-12-33-18)17(6-15-2-4-19-21(8-15)36-13-34-19)11-32-26-25(31)24(30)23(29)22(10-28)37-26/h1-4,7-8,16-17,22-31H,5-6,9-13H2/t16-,17-,22+,23+,24-,25+,26+/m0/s1

> <INCHI_KEY>
RYQGXMHEFILHCV-DNABOVRESA-N

> <FORMULA>
C26H32O11

> <MOLECULAR_WEIGHT>
520.531

> <EXACT_MASS>
520.19446185

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
53.43850731306006

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5S,6R)-2-[(2R,3R)-2,3-bis[(2H-1,3-benzodioxol-5-yl)methyl]-4-hydroxybutoxy]-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
0.63

> <JCHEM_LOGP>
0.7309655470000005

> <ALOGPS_LOGS>
-3.06

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.198050507184906

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.2107213360493

> <JCHEM_PKA_STRONGEST_BASIC>
-2.6032158759522774

> <JCHEM_POLAR_SURFACE_AREA>
156.53

> <JCHEM_REFRACTIVITY>
126.3459

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.49e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S,5S,6R)-2-[(2R,3R)-2,3-bis(2H-1,3-benzodioxol-5-ylmethyl)-4-hydroxybutoxy]-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       6.258 -11.313   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.591 -12.083   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.925 -11.313   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.259 -12.083   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.259 -13.623   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.592 -14.393   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.926 -13.623   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      14.260 -14.393   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.260 -15.933   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.926 -16.703   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      11.592 -15.933   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      15.724 -16.409   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      16.629 -15.163   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      15.724 -13.917   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      11.592 -11.313   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      12.926 -12.083   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      14.260 -11.313   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      14.260  -9.773   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      15.593  -9.003   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      16.927  -9.773   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      16.927 -11.313   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      15.593 -12.083   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      18.261 -12.083   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      19.594 -11.313   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      18.261  -9.003   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      15.593  -7.463   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      12.926  -9.003   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       8.925  -9.773   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      10.259  -9.003   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       4.924 -12.083   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       3.590 -11.313   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       3.590  -9.773   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       4.924  -9.003   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.258  -9.773   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       2.126  -9.297   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       1.220 -10.543   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       2.126 -11.789   0.000  0.00  0.00           O+0
CONECT    1    2   30   34                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   28                                                  
CONECT    4    3    5   15                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   14                                                  
CONECT    9    8   10   12                                                  
CONECT   10    9   11                                                       
CONECT   11   10    6                                                       
CONECT   12    9   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13    8                                                       
CONECT   15    4   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   22                                                  
CONECT   18   17   19   27                                                  
CONECT   19   18   20   26                                                  
CONECT   20   19   21   25                                                  
CONECT   21   20   22   23                                                  
CONECT   22   21   17                                                       
CONECT   23   21   24                                                       
CONECT   24   23                                                            
CONECT   25   20                                                            
CONECT   26   19                                                            
CONECT   27   18                                                            
CONECT   28    3   29                                                       
CONECT   29   28                                                            
CONECT   30    1   31                                                       
CONECT   31   30   32   37                                                  
CONECT   32   31   33   35                                                  
CONECT   33   32   34                                                       
CONECT   34   33    1                                                       
CONECT   35   32   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   31                                                       
MASTER        0    0    0    0    0    0    0    0   37    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₃₂O₁₁

Average Mass

520.5310 Da

Monoisotopic Mass

520.19446 Da

IUPAC Name

(2R,3R,4S,5S,6R)-2-[(2R,3R)-2,3-bis[(2H-1,3-benzodioxol-5-yl)methyl]-4-hydroxybutoxy]-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

(2R,3R,4S,5S,6R)-2-[(2R,3R)-2,3-bis(2H-1,3-benzodioxol-5-ylmethyl)-4-hydroxybutoxy]-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

OC[C@H](CC1=CC2=C(OCO2)C=C1)[C@H](CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)CC1=CC2=C(OCO2)C=C1

InChI Identifier

InChI=1S/C26H32O11/c27-9-16(5-14-1-3-18-20(7-14)35-12-33-18)17(6-15-2-4-19-21(8-15)36-13-34-19)11-32-26-25(31)24(30)23(29)22(10-28)37-26/h1-4,7-8,16-17,22-31H,5-6,9-13H2/t16-,17-,22+,23+,24-,25+,26+/m0/s1

InChI Key

RYQGXMHEFILHCV-DNABOVRESA-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
Tetracentron sinense	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
Dibenzylbutane lignan skeleton
Fatty acyl glycoside
Fatty acyl glycoside of mono- or disaccharide
Alkyl glycoside
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Benzodioxole
Oxane
Monosaccharide
Benzenoid
Fatty acyl
Secondary alcohol
Polyol
Organoheterocyclic compound
Acetal
Oxacycle
Organooxygen compound
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Primary 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	0.63	ALOGPS
logP	0.73	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	-2.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	156.53 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	126.35 m³·mol⁻¹	ChemAxon
Polarizability	53.44 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

34216779

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

90682210

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for (-)-Tetracentronside B (NP0075834)

MOL for NP0075834 ((-)-Tetracentronside B)

3D MOL for NP0075834 ((-)-Tetracentronside B)

3D SDF for NP0075834 ((-)-Tetracentronside B)

3D-SDF for NP0075834 ((-)-Tetracentronside B)

PDB for NP0075834 ((-)-Tetracentronside B)

3D PDB for NP0075834 ((-)-Tetracentronside B)

SMILES for NP0075834 ((-)-Tetracentronside B)

INCHI for NP0075834 ((-)-Tetracentronside B)

Structure for NP0075834 ((-)-Tetracentronside B)

3D Structure for NP0075834 ((-)-Tetracentronside B)