NP-MRD: Showing NP-Card for Gambiriin B1 (NP0056165)

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Record Information

Version

2.0

Created at

2022-04-28 02:01:22 UTC

Updated at

2022-04-28 02:01:22 UTC

NP-MRD ID

NP0056165

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Gambiriin B1

Description

2-{[(3S,4R,11S,12R)-3,12-bis(3,4-dihydroxyphenyl)-8,11-dihydroxy-5,13-dioxatricyclo[7.4.0.0²,⁶]Trideca-1(9),2(6),7-trien-4-yl]methyl}benzene-1,3,5-triol 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 B1 is found in Uncaria gambir . Based on a literature review very few articles have been published on 2-{[(3S,4R,11S,12R)-3,12-bis(3,4-dihydroxyphenyl)-8,11-dihydroxy-5,13-dioxatricyclo[7.4.0.0²,⁶]Trideca-1(9),2(6),7-trien-4-yl]methyl}benzene-1,3,5-triol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282204012D          

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M  END

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  Mrv1652304282204012D          

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  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
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  1  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 10 15  1  0  0  0  0
 14 16  1  0  0  0  0
 13 17  1  0  0  0  0
  8 18  1  6  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 19 24  1  0  0  0  0
 24 25  1  0  0  0  0
 22 26  1  0  0  0  0
 20 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
 36 39  1  0  0  0  0
 35 40  1  0  0  0  0
  1 41  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0056165

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H]1CC2=C(O)C=C3O[C@H](CC4=C(O)C=C(O)C=C4O)[C@H](C3=C2O[C@@H]1C1=CC(O)=C(O)C=C1)C1=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)22(37)5-12)28-26(40-25)11-21(36)16-9-24(39)29(41-30(16)28)13-2-4-18(33)23(38)6-13/h1-8,11,24-25,27,29,31-39H,9-10H2/t24-,25+,27+,29+/m0/s1

> <INCHI_KEY>
HLOYODWMNGTCGH-HLBHGXTFSA-N

> <FORMULA>
C30H26O11

> <MOLECULAR_WEIGHT>
562.527

> <EXACT_MASS>
562.147511657

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
55.763790677962035

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
2.73

> <JCHEM_LOGP>
4.034741160666666

> <ALOGPS_LOGS>
-4.36

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.180706326744227

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.739197777408847

> <JCHEM_PKA_STRONGEST_BASIC>
-5.332420740269547

> <JCHEM_POLAR_SURFACE_AREA>
200.52999999999997

> <JCHEM_REFRACTIVITY>
145.3005

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.45e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-{[(3S,4R,11S,12R)-3,12-bis(3,4-dihydroxyphenyl)-8,11-dihydroxy-5,13-dioxatricyclo[7.4.0.0^{2,6}]trideca-1,6,8-trien-4-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       0.369  -4.158   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.180  -2.849   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.452  -1.492   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.087  -1.444   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.898  -2.753   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.170  -4.110   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -3.394  -2.386   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -3.507  -0.850   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.081  -0.268   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.714   1.228   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.826   2.294   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.459   3.789   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.980   4.219   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.132   3.153   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.235   1.658   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.610   3.583   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -0.613   5.715   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -4.816  -0.039   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -6.173  -0.767   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -6.221  -2.306   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -7.578  -3.034   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -8.887  -2.223   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -8.839  -0.683   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -7.482   0.045   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -7.434   1.584   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0     -10.244  -2.951   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -4.912  -3.117   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       1.263  -0.183   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       2.803  -0.231   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       3.531  -1.588   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       2.719  -2.897   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       5.070  -1.636   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       3.614   1.078   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.886   2.435   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       3.697   3.744   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       5.237   3.696   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       5.965   2.339   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       5.153   1.030   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0       6.048   5.005   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0       2.969   5.101   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0       1.097  -5.515   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    9                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9   18                                                  
CONECT    9    8    4   10                                                  
CONECT   10    9   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   17                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14   10                                                       
CONECT   16   14                                                            
CONECT   17   13                                                            
CONECT   18    8   19                                                       
CONECT   19   18   20   24                                                  
CONECT   20   19   21   27                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   26                                                  
CONECT   23   22   24                                                       
CONECT   24   23   19   25                                                  
CONECT   25   24                                                            
CONECT   26   22                                                            
CONECT   27   20                                                            
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   40                                                  
CONECT   36   35   37   39                                                  
CONECT   37   36   38                                                       
CONECT   38   37   33                                                       
CONECT   39   36                                                            
CONECT   40   35                                                            
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-{[(3S,4R,11S,12R)-3,12-bis(3,4-dihydroxyphenyl)-8,11-dihydroxy-5,13-dioxatricyclo[7.4.0.0^{2,6}]trideca-1,6,8-trien-4-yl]methyl}benzene-1,3,5-triol

Traditional Name

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

CAS Registry Number

Not Available

SMILES

O[C@H]1CC2=C(O)C=C3O[C@H](CC4=C(O)C=C(O)C=C4O)[C@H](C3=C2O[C@@H]1C1=CC(O)=C(O)C=C1)C1=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)22(37)5-12)28-26(40-25)11-21(36)16-9-24(39)29(41-30(16)28)13-2-4-18(33)23(38)6-13/h1-8,11,24-25,27,29,31-39H,9-10H2/t24-,25+,27+,29+/m0/s1

InChI Key

HLOYODWMNGTCGH-HLBHGXTFSA-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
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
Linear 1,7-diphenylheptane skeleton
Hydroxyflavonoid
5-hydroxyflavonoid
4'-hydroxyflavonoid
3-hydroxyflavonoid
3'-hydroxyflavonoid
1-phenylcoumaran
1-benzopyran
Benzopyran
Chromane
Coumaran
Phloroglucinol derivative
Benzenetriol
Catechol
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Alkyl aryl ether
Benzenoid
Monocyclic benzene moiety
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Polyol
Ether
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
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	2.73	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	55.76 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

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

163014086

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Gambiriin B1 (NP0056165)

MOL for NP0056165 (Gambiriin B1)

3D MOL for NP0056165 (Gambiriin B1)

3D SDF for NP0056165 (Gambiriin B1)

3D-SDF for NP0056165 (Gambiriin B1)

PDB for NP0056165 (Gambiriin B1)

3D PDB for NP0056165 (Gambiriin B1)

SMILES for NP0056165 (Gambiriin B1)

INCHI for NP0056165 (Gambiriin B1)

Structure for NP0056165 (Gambiriin B1)

3D Structure for NP0056165 (Gambiriin B1)