NP-MRD: Showing NP-Card for Gambiriin A1 (NP0056161)

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Record Information

Version

2.0

Created at

2022-04-28 02:01:13 UTC

Updated at

2022-04-28 02:01:13 UTC

NP-MRD ID

NP0056161

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Gambiriin A1

Description

Gambriin A1 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 A1 is found in Sanguisorba officinalis and Uncaria gambir . Based on a literature review very few articles have been published on Gambriin A1.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282204012D          

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M  END

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  Mrv1652304282204012D          

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    3.5724    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  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
  8  4  1  1  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  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
  9 20  1  6  0  0  0
  8 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
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 21 26  1  0  0  0  0
 25 27  1  0  0  0  0
 24 28  1  0  0  0  0
  3 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
  2 32  1  0  0  0  0
 31 33  1  1  0  0  0
 30 34  1  6  0  0  0
 34 35  2  0  0  0  0
 35 36  1  0  0  0  0
 36 37  2  0  0  0  0
 37 38  1  0  0  0  0
 38 39  2  0  0  0  0
 34 39  1  0  0  0  0
 37 40  1  0  0  0  0
 36 41  1  0  0  0  0
  1 42  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0056161

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H](CC1=C(O)C=C(O)C=C1O)[C@@H](C1=CC=C(O)C(O)=C1)C1=C2O[C@@H]([C@@H](O)CC2=C(O)C=C1O)C1=CC(O)=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C30H28O12/c31-14-7-19(34)15(20(35)8-14)9-24(39)27(12-1-3-17(32)22(37)5-12)28-25(40)11-21(36)16-10-26(41)29(42-30(16)28)13-2-4-18(33)23(38)6-13/h1-8,11,24,26-27,29,31-41H,9-10H2/t24-,26-,27+,29+/m0/s1

> <INCHI_KEY>
AAOPKIFUFWCDQZ-VIUUMSQESA-N

> <FORMULA>
C30H28O12

> <MOLECULAR_WEIGHT>
580.542

> <EXACT_MASS>
580.158076342

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
55.15725102620627

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S)-2-(3,4-dihydroxyphenyl)-8-[(1S,2S)-1-(3,4-dihydroxyphenyl)-2-hydroxy-3-(2,4,6-trihydroxyphenyl)propyl]-3,4-dihydro-2H-1-benzopyran-3,5,7-triol

> <ALOGPS_LOGP>
2.11

> <JCHEM_LOGP>
3.3702700359999995

> <ALOGPS_LOGS>
-3.79

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.195085276647141

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.7545455759857

> <JCHEM_PKA_STRONGEST_BASIC>
-5.171413906479295

> <JCHEM_POLAR_SURFACE_AREA>
231.75999999999996

> <JCHEM_REFRACTIVITY>
149.07950000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.41e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S)-2-(3,4-dihydroxyphenyl)-8-[(1S,2S)-1-(3,4-dihydroxyphenyl)-2-hydroxy-3-(2,4,6-trihydroxyphenyl)propyl]-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      -0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334  -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      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -6.668   3.850   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -5.335   4.620   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -4.001   3.850   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -2.667   4.620   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -8.002   4.620   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -5.335  -0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       2.667   6.160   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       5.335   4.620   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0      -0.000  -4.620   0.000  0.00  0.00           O+0
CONECT    1    2    6   42                                                  
CONECT    2    1    3   32                                                  
CONECT    3    2    4   29                                                  
CONECT    4    3    5    8                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5                                                            
CONECT    8    4    9   21                                                  
CONECT    9    8   10   20                                                  
CONECT   10    9   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    9                                                            
CONECT   21    8   22   26                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   28                                                  
CONECT   25   24   26   27                                                  
CONECT   26   25   21                                                       
CONECT   27   25                                                            
CONECT   28   24                                                            
CONECT   29    3   30                                                       
CONECT   30   29   31   34                                                  
CONECT   31   30   32   33                                                  
CONECT   32   31    2                                                       
CONECT   33   31                                                            
CONECT   34   30   35   39                                                  
CONECT   35   34   36                                                       
CONECT   36   35   37   41                                                  
CONECT   37   36   38   40                                                  
CONECT   38   37   39                                                       
CONECT   39   38   34                                                       
CONECT   40   37                                                            
CONECT   41   36                                                            
CONECT   42    1                                                            
MASTER        0    0    0    0    0    0    0    0   42    0   92    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₂₈O₁₂

Average Mass

580.5420 Da

Monoisotopic Mass

580.15808 Da

IUPAC Name

(2R,3S)-2-(3,4-dihydroxyphenyl)-8-[(1S,2S)-1-(3,4-dihydroxyphenyl)-2-hydroxy-3-(2,4,6-trihydroxyphenyl)propyl]-3,4-dihydro-2H-1-benzopyran-3,5,7-triol

Traditional Name

(2R,3S)-2-(3,4-dihydroxyphenyl)-8-[(1S,2S)-1-(3,4-dihydroxyphenyl)-2-hydroxy-3-(2,4,6-trihydroxyphenyl)propyl]-3,4-dihydro-2H-1-benzopyran-3,5,7-triol

CAS Registry Number

Not Available

SMILES

O[C@@H](CC1=C(O)C=C(O)C=C1O)[C@@H](C1=CC=C(O)C(O)=C1)C1=C2O[C@@H]([C@@H](O)CC2=C(O)C=C1O)C1=CC(O)=C(O)C=C1

InChI Identifier

InChI=1S/C30H28O12/c31-14-7-19(34)15(20(35)8-14)9-24(39)27(12-1-3-17(32)22(37)5-12)28-25(40)11-21(36)16-10-26(41)29(42-30(16)28)13-2-4-18(33)23(38)6-13/h1-8,11,24,26-27,29,31-41H,9-10H2/t24-,26-,27+,29+/m0/s1

InChI Key

AAOPKIFUFWCDQZ-VIUUMSQESA-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
Linear 1,7-diphenylheptane skeleton
3'-hydroxyflavonoid
3-hydroxyflavonoid
4'-hydroxyflavonoid
5-hydroxyflavonoid
7-hydroxyflavonoid
Hydroxyflavonoid
Cinnamylphenol
Linear 1,3-diarylpropanoid
1-benzopyran
Chromane
Benzopyran
Benzenetriol
Phloroglucinol derivative
Catechol
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Phenol
1-hydroxy-4-unsubstituted benzenoid
Monocyclic benzene moiety
Benzenoid
Secondary alcohol
Polyol
Oxacycle
Organoheterocyclic compound
Ether
Organooxygen compound
Organic oxygen compound
Alcohol
Hydrocarbon derivative
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	2.11	ALOGPS
logP	3.37	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	8.75	ChemAxon
pKa (Strongest Basic)	-5.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	231.76 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	149.08 m³·mol⁻¹	ChemAxon
Polarizability	55.16 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

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

101406540

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Gambiriin A1 (NP0056161)

MOL for NP0056161 (Gambiriin A1)

3D MOL for NP0056161 (Gambiriin A1)

3D SDF for NP0056161 (Gambiriin A1)

3D-SDF for NP0056161 (Gambiriin A1)

PDB for NP0056161 (Gambiriin A1)

3D PDB for NP0056161 (Gambiriin A1)

SMILES for NP0056161 (Gambiriin A1)

INCHI for NP0056161 (Gambiriin A1)

Structure for NP0056161 (Gambiriin A1)

3D Structure for NP0056161 (Gambiriin A1)