NP-MRD: Showing NP-Card for Amarogentin (NP0051761)

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Record Information

Version

2.0

Created at

2022-04-27 23:00:16 UTC

Updated at

2022-04-27 23:00:16 UTC

NP-MRD ID

NP0051761

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Amarogentin

Description

(2S,3R,4S,5S,6R)-2-{[(3S,4S,4aS)-4-ethenyl-8-oxo-3H,4H,4aH,5H,6H,8H-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,3',5-trihydroxy-[1,1'-biphenyl]-2-carboxylate belongs to the class of organic compounds known as biphenyls and derivatives. These are organic compounds containing to benzene rings linked together by a C-C bond. Amarogentin is found in Gentiana lutea , Gentiana purpurea, Gentiana sp., Swertia chirayita, Swertia japonica , Swertia leducii and Swertia spp.. Based on a literature review very few articles have been published on (2S,3R,4S,5S,6R)-2-{[(3S,4S,4aS)-4-ethenyl-8-oxo-3H,4H,4aH,5H,6H,8H-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,3',5-trihydroxy-[1,1'-biphenyl]-2-carboxylate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282201002D          

 42 46  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652304282201002D          

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   -2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  6  0  0  0
  7  8  1  0  0  0  0
  4  9  1  6  0  0  0
 10  9  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 14 13  1  6  0  0  0
 14 15  1  0  0  0  0
 10 15  1  0  0  0  0
 15 16  1  1  0  0  0
 16 17  2  0  0  0  0
 14 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 13 21  1  0  0  0  0
 21 22  2  0  0  0  0
  3 23  1  1  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 24 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 26 31  1  0  0  0  0
 31 32  1  0  0  0  0
 29 33  1  0  0  0  0
 27 34  1  0  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
 38 40  1  0  0  0  0
  2 41  1  6  0  0  0
  1 42  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0051761

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](O[C@@H]2OC=C3[C@@H](CCOC3=O)[C@@H]2C=C)[C@H](OC(=O)C2=C(C=C(O)C=C2O)C2=CC=CC(O)=C2)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C29H30O13/c1-2-16-17-6-7-38-26(36)19(17)12-39-28(16)42-29-25(24(35)23(34)21(11-30)40-29)41-27(37)22-18(9-15(32)10-20(22)33)13-4-3-5-14(31)8-13/h2-5,8-10,12,16-17,21,23-25,28-35H,1,6-7,11H2/t16-,17-,21+,23+,24-,25+,28-,29-/m0/s1

> <INCHI_KEY>
DBOVHQOUSDWAPQ-KUGCKIRFSA-N

> <FORMULA>
C29H30O13

> <MOLECULAR_WEIGHT>
586.546

> <EXACT_MASS>
586.168641026

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
55.28339938624811

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5S,6R)-2-{[(3S,4S,4aS)-4-ethenyl-8-oxo-3H,4H,4aH,5H,6H,8H-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,3',5-trihydroxy-[1,1'-biphenyl]-2-carboxylate

> <ALOGPS_LOGP>
1.89

> <JCHEM_LOGP>
2.752634515333334

> <ALOGPS_LOGS>
-3.17

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.676622255255449

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.439058411570242

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981085408876641

> <JCHEM_POLAR_SURFACE_AREA>
201.67

> <JCHEM_REFRACTIVITY>
142.3489

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.94e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5S,6R)-2-{[(3S,4S,4aS)-4-ethenyl-8-oxo-3H,4H,4aH,5H,6H-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,3',5-trihydroxy-[1,1'-biphenyl]-2-carboxylate

> <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      -6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -6.668  -5.390   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -5.335   1.540   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -8.002   1.540   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -6.668   3.850   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -8.002   4.620   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -8.002   6.160   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -6.668   6.930   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -5.335   6.160   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -5.335   4.620   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -4.001   3.850   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -6.668   8.470   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      -9.336   3.850   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -9.336   2.310   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0     -10.669   1.540   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0     -12.003   2.310   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0     -12.003   3.850   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0     -10.669   4.620   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0     -13.337   4.620   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0      -8.002   0.000   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0      -8.002  -3.080   0.000  0.00  0.00           O+0
CONECT    1    2    6   42                                                  
CONECT    2    1    3   41                                                  
CONECT    3    2    4   23                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7                                                            
CONECT    9    4   10                                                       
CONECT   10    9   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   21                                                  
CONECT   14   13   15   18                                                  
CONECT   15   14   10   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16                                                            
CONECT   18   14   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   13   22                                                  
CONECT   22   21                                                            
CONECT   23    3   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27   31                                                  
CONECT   27   26   28   34                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   33                                                  
CONECT   30   29   31                                                       
CONECT   31   30   26   32                                                  
CONECT   32   31                                                            
CONECT   33   29                                                            
CONECT   34   27   35   39                                                  
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   39   40                                                  
CONECT   39   38   34                                                       
CONECT   40   38                                                            
CONECT   41    2                                                            
CONECT   42    1                                                            
MASTER        0    0    0    0    0    0    0    0   42    0   92    0
END

View in JSmol

Synonyms

Value	Source
(2S,3R,4S,5S,6R)-2-{[(3S,4S,4as)-4-ethenyl-8-oxo-3H,4H,4ah,5H,6H,8H-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,3',5-trihydroxy-[1,1'-biphenyl]-2-carboxylic acid	Generator

Chemical Formula

C₂₉H₃₀O₁₃

Average Mass

586.5460 Da

Monoisotopic Mass

586.16864 Da

IUPAC Name

(2S,3R,4S,5S,6R)-2-{[(3S,4S,4aS)-4-ethenyl-8-oxo-3H,4H,4aH,5H,6H,8H-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,3',5-trihydroxy-[1,1'-biphenyl]-2-carboxylate

Traditional Name

(2S,3R,4S,5S,6R)-2-{[(3S,4S,4aS)-4-ethenyl-8-oxo-3H,4H,4aH,5H,6H-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl 3,3',5-trihydroxy-[1,1'-biphenyl]-2-carboxylate

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](O[C@@H]2OC=C3[C@@H](CCOC3=O)[C@@H]2C=C)[C@H](OC(=O)C2=C(C=C(O)C=C2O)C2=CC=CC(O)=C2)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C29H30O13/c1-2-16-17-6-7-38-26(36)19(17)12-39-28(16)42-29-25(24(35)23(34)21(11-30)40-29)41-27(37)22-18(9-15(32)10-20(22)33)13-4-3-5-14(31)8-13/h2-5,8-10,12,16-17,21,23-25,28-35H,1,6-7,11H2/t16-,17-,21+,23+,24-,25+,28-,29-/m0/s1

InChI Key

DBOVHQOUSDWAPQ-KUGCKIRFSA-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
Gentiana lutea	Plant	KNApSAcK
Gentiana purpurea	LOTUS Database	35616633
Gentiana sp.	Plant	KNApSAcK
Swertia chirata	LOTUS Database	35616633
Swertia japonica	Plant	KNApSAcK
Swertia leducii	LOTUS Database	35616633
Swertia spp.	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as biphenyls and derivatives. These are organic compounds containing to benzene rings linked together by a C-C bond.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Biphenyls and derivatives

Direct Parent

Biphenyls and derivatives

Alternative Parents

Substituents

Hexose monosaccharide
Biphenyl
P-hydroxybenzoic acid alkyl ester
P-hydroxybenzoic acid ester
O-hydroxybenzoic acid ester
O-glycosyl compound
Dihydroxybenzoic acid
Glycosyl compound
Salicylic acid or derivatives
Benzoate ester
Benzoic acid or derivatives
Resorcinol
Benzoyl
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Delta_valerolactone
Delta valerolactone
Oxane
Monosaccharide
Dicarboxylic acid or derivatives
Vinylogous ester
Vinylogous acid
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Carboxylic acid derivative
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
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	1.89	ALOGPS
logP	2.75	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	8.44	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	201.67 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	142.35 m³·mol⁻¹	ChemAxon
Polarizability	55.28 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

154496142

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Amarogentin (NP0051761)

MOL for NP0051761 (Amarogentin)

3D MOL for NP0051761 (Amarogentin)

3D SDF for NP0051761 (Amarogentin)

3D-SDF for NP0051761 (Amarogentin)

PDB for NP0051761 (Amarogentin)

3D PDB for NP0051761 (Amarogentin)

SMILES for NP0051761 (Amarogentin)

INCHI for NP0051761 (Amarogentin)

Structure for NP0051761 (Amarogentin)

3D Structure for NP0051761 (Amarogentin)