NP-MRD: Showing NP-Card for Gambiriin B3 (NP0056166)

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Record Information

Version

2.0

Created at

2022-04-28 02:01:24 UTC

Updated at

2022-04-28 02:01:24 UTC

NP-MRD ID

NP0056166

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Gambiriin B3

Description

Gambiriin B3 belongs to the class of organic compounds known as catechins. Catechins are compounds containing a catechin moiety, which is a 3,4-dihydro-2-chromene-3,5.7-Tiol. Gambiriin B3 is found in Sanguisorba officinalis and Uncaria gambir . Based on a literature review a small amount of articles have been published on Gambiriin B3.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282204012D          

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  8 10  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 11 16  1  0  0  0  0
 16 17  1  0  0  0  0
 14 18  1  0  0  0  0
 12 19  1  0  0  0  0
  7 20  1  1  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 20 25  1  0  0  0  0
 23 26  1  0  0  0  0
 22 27  1  0  0  0  0
  3 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
  2 31  1  0  0  0  0
 30 32  1  1  0  0  0
 29 33  1  6  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
 33 38  1  0  0  0  0
 37 39  1  0  0  0  0
 36 40  1  0  0  0  0
  1 41  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0056166

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H]1CC2=C(O)C3=C(O[C@H](CC4=C(O)C=C(O)C=C4O)[C@@H]3C3=CC(O)=C(O)C=C3)C=C2O[C@@H]1C1=CC=C(O)C(O)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C30H26O11/c31-14-7-19(34)15(20(35)8-14)10-25-27(12-1-3-17(32)21(36)5-12)28-26(40-25)11-24-16(29(28)39)9-23(38)30(41-24)13-2-4-18(33)22(37)6-13/h1-8,11,23,25,27,30-39H,9-10H2/t23-,25+,27-,30+/m0/s1

> <INCHI_KEY>
FFCVTFZKQFEUKL-YJRUHBOJSA-N

> <FORMULA>
C30H26O11

> <MOLECULAR_WEIGHT>
562.527

> <EXACT_MASS>
562.147511657

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
56.24022033526009

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{[(5R,6R,11S,12R)-6,12-bis(3,4-dihydroxyphenyl)-8,11-dihydroxy-4,13-dioxatricyclo[7.4.0.0^{3,7}]trideca-1,3(7),8-trien-5-yl]methyl}benzene-1,3,5-triol

> <ALOGPS_LOGP>
2.74

> <JCHEM_LOGP>
4.034741160666666

> <ALOGPS_LOGS>
-4.38

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.18604201936915

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.742811317224247

> <JCHEM_PKA_STRONGEST_BASIC>
-5.270449784131515

> <JCHEM_POLAR_SURFACE_AREA>
200.52999999999997

> <JCHEM_REFRACTIVITY>
145.30050000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.34e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-{[(5R,6R,11S,12R)-6,12-bis(3,4-dihydroxyphenyl)-8,11-dihydroxy-4,13-dioxatricyclo[7.4.0.0^{3,7}]trideca-1,3(7),8-trien-5-yl]methyl}benzene-1,3,5-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  -5.153   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.530  -4.383   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.530  -2.843   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.197  -2.073   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.137  -2.843   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.137  -4.383   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.602  -4.859   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.507  -3.613   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.602  -2.367   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -4.047  -3.613   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -4.817  -2.279   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -6.357  -2.279   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -7.127  -0.945   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -6.357   0.388   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -4.817   0.388   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -4.047  -0.945   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -2.507  -0.945   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -7.127   1.722   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -7.127  -3.613   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -2.077  -6.323   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -3.584  -6.644   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -4.060  -8.108   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -3.029  -9.253   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -1.523  -8.932   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.047  -7.468   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -3.505 -10.717   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -5.566  -8.428   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       3.864  -2.073   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       5.198  -2.843   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.198  -4.383   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       3.864  -5.153   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       6.531  -5.153   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       6.531  -2.073   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.531  -0.533   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       7.865   0.237   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       9.199  -0.533   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       9.199  -2.073   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       7.865  -2.843   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      10.533  -2.843   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0      10.533   0.237   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0       1.197  -6.693   0.000  0.00  0.00           O+0
CONECT    1    2    6   41                                                  
CONECT    2    1    3   31                                                  
CONECT    3    2    4   28                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    9                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8   20                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8    5                                                       
CONECT   10    8   11                                                       
CONECT   11   10   12   16                                                  
CONECT   12   11   13   19                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   18                                                  
CONECT   15   14   16                                                       
CONECT   16   15   11   17                                                  
CONECT   17   16                                                            
CONECT   18   14                                                            
CONECT   19   12                                                            
CONECT   20    7   21   25                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   27                                                  
CONECT   23   22   24   26                                                  
CONECT   24   23   25                                                       
CONECT   25   24   20                                                       
CONECT   26   23                                                            
CONECT   27   22                                                            
CONECT   28    3   29                                                       
CONECT   29   28   30   33                                                  
CONECT   30   29   31   32                                                  
CONECT   31   30    2                                                       
CONECT   32   30                                                            
CONECT   33   29   34   38                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37   40                                                  
CONECT   37   36   38   39                                                  
CONECT   38   37   33                                                       
CONECT   39   37                                                            
CONECT   40   36                                                            
CONECT   41    1                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   92    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₂₆O₁₁

Average Mass

562.5270 Da

Monoisotopic Mass

562.14751 Da

IUPAC Name

2-{[(5R,6R,11S,12R)-6,12-bis(3,4-dihydroxyphenyl)-8,11-dihydroxy-4,13-dioxatricyclo[7.4.0.0^{3,7}]trideca-1,3(7),8-trien-5-yl]methyl}benzene-1,3,5-triol

Traditional Name

2-{[(5R,6R,11S,12R)-6,12-bis(3,4-dihydroxyphenyl)-8,11-dihydroxy-4,13-dioxatricyclo[7.4.0.0^{3,7}]trideca-1,3(7),8-trien-5-yl]methyl}benzene-1,3,5-triol

CAS Registry Number

Not Available

SMILES

O[C@H]1CC2=C(O)C3=C(O[C@H](CC4=C(O)C=C(O)C=C4O)[C@@H]3C3=CC(O)=C(O)C=C3)C=C2O[C@@H]1C1=CC=C(O)C(O)=C1

InChI Identifier

InChI=1S/C30H26O11/c31-14-7-19(34)15(20(35)8-14)10-25-27(12-1-3-17(32)21(36)5-12)28-26(40-25)11-24-16(29(28)39)9-23(38)30(41-24)13-2-4-18(33)22(37)6-13/h1-8,11,23,25,27,30-39H,9-10H2/t23-,25+,27-,30+/m0/s1

InChI Key

FFCVTFZKQFEUKL-YJRUHBOJSA-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
Sanguisorba officinalis	Plant	KNApSAcK
Uncaria gambir	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as catechins. Catechins are compounds containing a catechin moiety, which is a 3,4-dihydro-2-chromene-3,5.7-Tiol.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavans

Direct Parent

Catechins

Alternative Parents

Substituents

Catechin
Furanoflavonoid or dihydroflavonoid
Linear 1,7-diphenylheptane skeleton
3'-hydroxyflavonoid
3-hydroxyflavonoid
4'-hydroxyflavonoid
5-hydroxyflavonoid
Hydroxyflavonoid
1-phenylcoumaran
Chromane
Benzopyran
1-benzopyran
Coumaran
Benzenetriol
Phloroglucinol derivative
Catechol
Phenol
1-hydroxy-4-unsubstituted benzenoid
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
Monocyclic benzene moiety
Benzenoid
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Polyol
Ether
Hydrocarbon derivative
Organic oxygen compound
Organooxygen compound
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

catechin (CHEBI:81330 )

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	2.74	ALOGPS
logP	4.03	ChemAxon
logS	-4.4	ALOGPS
pKa (Strongest Acidic)	8.74	ChemAxon
pKa (Strongest Basic)	-5.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	200.53 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	145.3 m³·mol⁻¹	ChemAxon
Polarizability	56.24 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00008933

Chemspider ID

30791573

KEGG Compound ID

C17777

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

46173996

PDB ID

Not Available

ChEBI ID

81330

Good Scents ID

Not Available

References

General References

Showing NP-Card for Gambiriin B3 (NP0056166)

MOL for NP0056166 (Gambiriin B3)

3D MOL for NP0056166 (Gambiriin B3)

3D SDF for NP0056166 (Gambiriin B3)

3D-SDF for NP0056166 (Gambiriin B3)

PDB for NP0056166 (Gambiriin B3)

3D PDB for NP0056166 (Gambiriin B3)

SMILES for NP0056166 (Gambiriin B3)

INCHI for NP0056166 (Gambiriin B3)

Structure for NP0056166 (Gambiriin B3)

3D Structure for NP0056166 (Gambiriin B3)