NP-MRD: Showing NP-Card for Gambiriin C (NP0051674)

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Record Information

Version

2.0

Created at

2022-04-27 22:57:08 UTC

Updated at

2022-04-27 22:57:08 UTC

NP-MRD ID

NP0051674

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Gambiriin C

Description

Gambiriin c belongs to the class of organic compounds known as biflavonoids and polyflavonoids. These are organic compounds containing at least two flavan/flavone units. These units are usually linked through CC or C-O-C bonds. Some examples include C2-O-C3, C2-O-C4, C3'-C3''', and C6-C8''. Thus, gambiriin c is considered to be a flavonoid. Gambiriin C is found in Thujopsis dolabrata and Uncaria gambir . Gambiriin C was first documented in 2007 (PMID: 17268100). Based on a literature review a small amount of articles have been published on Gambiriin c (PMID: 34467724).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282200572D          

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M  END

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  3 11  1  0  0  0  0
 10 12  1  6  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 12 17  1  0  0  0  0
 15 18  1  0  0  0  0
  9 19  1  6  0  0  0
  8 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
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 24 29  1  0  0  0  0
 28 30  1  1  0  0  0
 27 31  1  6  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 31 36  1  0  0  0  0
 34 37  1  0  0  0  0
 33 38  1  0  0  0  0
 23 39  1  0  0  0  0
 21 40  1  0  0  0  0
  1 41  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0051674

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H]1CC2=C(O[C@@H]1C1=CC(O)=C(O)C=C1)C([C@@H]1[C@@H](O)[C@H](OC3=C1C(O)=CC(O)=C3)C1=CC=C(O)C=C1)=C(O)C=C2O

> <INCHI_IDENTIFIER>
InChI=1S/C30H26O11/c31-14-4-1-12(2-5-14)29-27(39)26(24-20(36)8-15(32)9-23(24)40-29)25-21(37)11-18(34)16-10-22(38)28(41-30(16)25)13-3-6-17(33)19(35)7-13/h1-9,11,22,26-29,31-39H,10H2/t22-,26+,27+,28+,29+/m0/s1

> <INCHI_KEY>
KUODBSWFMJMVJV-UKWJTHFESA-N

> <FORMULA>
C30H26O11

> <MOLECULAR_WEIGHT>
562.527

> <EXACT_MASS>
562.147511657

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
54.27385689473036

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R)-4-[(2R,3S)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2H-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3,5,7-triol

> <ALOGPS_LOGP>
2.39

> <JCHEM_LOGP>
3.419310335333334

> <ALOGPS_LOGS>
-3.78

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.193602284175489

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.758127682890152

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4601834882350033

> <JCHEM_POLAR_SURFACE_AREA>
200.52999999999997

> <JCHEM_REFRACTIVITY>
144.52710000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.35e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4R)-4-[(2R,3S)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2H-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3,5,7-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      -4.001   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -2.667  -0.000   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       6.668   6.930   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0      -2.865  -0.931   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0      -5.335   4.620   0.000  0.00  0.00           O+0
CONECT    1    2    6   41                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   11                                                  
CONECT    4    3    5    8                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5                                                            
CONECT    8    4    9   20                                                  
CONECT    9    8   10   19                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10    3                                                       
CONECT   12   10   13   17                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   18                                                  
CONECT   16   15   17                                                       
CONECT   17   16   12                                                       
CONECT   18   15                                                            
CONECT   19    9                                                            
CONECT   20    8   21   25                                                  
CONECT   21   20   22   40                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   39                                                  
CONECT   24   23   25   29                                                  
CONECT   25   24   20   26                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   31                                                  
CONECT   28   27   29   30                                                  
CONECT   29   28   24                                                       
CONECT   30   28                                                            
CONECT   31   27   32   36                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34   38                                                  
CONECT   34   33   35   37                                                  
CONECT   35   34   36                                                       
CONECT   36   35   31                                                       
CONECT   37   34                                                            
CONECT   38   33                                                            
CONECT   39   23                                                            
CONECT   40   21                                                            
CONECT   41    1                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   92    0
END

View in JSmol

Synonyms

Value	Source
Epiafzelechin-(4beta->8)-catechin	Kegg
Epiafzelechin-(4b->8)-catechin	Generator
Epiafzelechin-(4β->8)-catechin	Generator

Chemical Formula

C₃₀H₂₆O₁₁

Average Mass

562.5270 Da

Monoisotopic Mass

562.14751 Da

IUPAC Name

(2R,3R,4R)-4-[(2R,3S)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2H-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3,5,7-triol

Traditional Name

(2R,3R,4R)-4-[(2R,3S)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2H-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3,5,7-triol

CAS Registry Number

Not Available

SMILES

O[C@H]1CC2=C(O[C@@H]1C1=CC(O)=C(O)C=C1)C([C@@H]1[C@@H](O)[C@H](OC3=C1C(O)=CC(O)=C3)C1=CC=C(O)C=C1)=C(O)C=C2O

InChI Identifier

InChI=1S/C30H26O11/c31-14-4-1-12(2-5-14)29-27(39)26(24-20(36)8-15(32)9-23(24)40-29)25-21(37)11-18(34)16-10-22(38)28(41-30(16)25)13-3-6-17(33)19(35)7-13/h1-9,11,22,26-29,31-39H,10H2/t22-,26+,27+,28+,29+/m0/s1

InChI Key

KUODBSWFMJMVJV-UKWJTHFESA-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
Thujopsis dolabrata	LOTUS Database	35616633
Uncaria gambir	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as biflavonoids and polyflavonoids. These are organic compounds containing at least two flavan/flavone units. These units are usually linked through CC or C-O-C bonds. Some examples include C2-O-C3, C2-O-C4, C3'-C3''', and C6-C8''.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Biflavonoids and polyflavonoids

Direct Parent

Biflavonoids and polyflavonoids

Alternative Parents

Substituents

B-type proanthocyanidin
Bi- and polyflavonoid skeleton
Proanthocyanidin
Catechin
Flavan-3-ol
Hydroxyflavonoid
3'-hydroxyflavonoid
7-hydroxyflavonoid
5-hydroxyflavonoid
4'-hydroxyflavonoid
3-hydroxyflavonoid
Flavan
Chromane
1-benzopyran
Benzopyran
Catechol
Phenol
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
1-hydroxy-4-unsubstituted benzenoid
Benzenoid
Monocyclic benzene moiety
Secondary alcohol
Polyol
Organoheterocyclic compound
Oxacycle
Ether
Hydrocarbon derivative
Alcohol
Organic oxygen compound
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

proanthocyanidin (CHEBI:5271 )
Proanthocyanidins (C10228 )
Condensed tannins (Proanthocyanidins) (C10228 )
Proanthocyanidins (LMPK12030011 )

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	2.39	ALOGPS
logP	3.42	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	8.76	ChemAxon
pKa (Strongest Basic)	-3.5	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	3	ChemAxon
Refractivity	144.53 m³·mol⁻¹	ChemAxon
Polarizability	54.27 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

C00002924

Chemspider ID

137941

KEGG Compound ID

C10228

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

156680

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Zhang YF, Zhu ZX, Wang WX, Zhang H, Liu L, Zhang SL, Zhao YF, Song YL, Zheng J, Tu PF, Huo HX, Li J: [Condensed tannins from roots of Indigofera stachyodes]. Zhongguo Zhong Yao Za Zhi. 2021 Aug;46(16):4131-4138. doi: 10.19540/j.cnki.cjcmm.20210518.201. [PubMed:34467724 ]
Taniguchi S, Kuroda K, Doi K, Tanabe M, Shibata T, Yoshida T, Hatano T: Revised structures of gambiriins A1, A2, B1, and B2, chalcane-flavan dimers from gambir (Uncaria gambir extract). Chem Pharm Bull (Tokyo). 2007 Feb;55(2):268-72. doi: 10.1248/cpb.55.268. [PubMed:17268100 ]

Showing NP-Card for Gambiriin C (NP0051674)

MOL for NP0051674 (Gambiriin C)

3D MOL for NP0051674 (Gambiriin C)

3D SDF for NP0051674 (Gambiriin C)

3D-SDF for NP0051674 (Gambiriin C)

PDB for NP0051674 (Gambiriin C)

3D PDB for NP0051674 (Gambiriin C)

SMILES for NP0051674 (Gambiriin C)

INCHI for NP0051674 (Gambiriin C)

Structure for NP0051674 (Gambiriin C)

3D Structure for NP0051674 (Gambiriin C)