NP-MRD: Showing NP-Card for Damulin B (NP0139867)

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Record Information

Version

2.0

Created at

2022-06-29 20:14:21 UTC

Updated at

2022-06-29 20:14:21 UTC

NP-MRD ID

NP0139867

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Damulin B

Description

Damulin B belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Damulin B was first documented in 2014 (PMID: 25036687). Based on a literature review a small amount of articles have been published on damulin B (PMID: 35513215) (PMID: 34738435) (PMID: 32037885) (PMID: 30562828).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652306292222142D          

 55 60  0  0  1  0            999 V2000
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  1  2  1  0  0  0  0
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  8 12  1  0  0  0  0
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M  END

     RDKit          3D

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  7  6  1  0
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  6  5  2  3
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 55125  1  0
M  END


  Mrv1652306292222142D          

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   -3.8779    0.5079    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    7.6302   -2.6340    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
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  4  5  1  0  0  0  0
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  6  7  2  0  0  0  0
  8  6  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 12 11  1  1  0  0  0
  8 12  1  0  0  0  0
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 13 14  1  0  0  0  0
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 16 17  1  0  0  0  0
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 19 18  1  6  0  0  0
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 15 20  1  0  0  0  0
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 23 24  1  0  0  0  0
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 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 23 27  1  6  0  0  0
 28 27  1  6  0  0  0
 28 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
 32 33  1  0  0  0  0
 28 33  1  0  0  0  0
 32 34  1  6  0  0  0
 34 35  1  0  0  0  0
 31 36  1  1  0  0  0
 30 37  1  6  0  0  0
 29 38  1  1  0  0  0
 39 38  1  6  0  0  0
 39 40  1  0  0  0  0
 40 41  1  0  0  0  0
 41 42  1  0  0  0  0
 42 43  1  0  0  0  0
 43 44  1  0  0  0  0
 39 44  1  0  0  0  0
 43 45  1  6  0  0  0
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 42 47  1  1  0  0  0
 41 48  1  6  0  0  0
 40 49  1  1  0  0  0
 22 50  1  1  0  0  0
 20 51  1  6  0  0  0
 16 52  1  6  0  0  0
 13 53  1  6  0  0  0
 11 54  1  1  0  0  0
  2 55  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0139867

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCCC(=C)[C@H]1CC[C@]2(C)[C@@H]1[C@H](O)C[C@@H]1[C@@]3(C)C[C@@H](O)[C@H](O[C@@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4O[C@@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4O)C(C)(C)[C@@H]3CC[C@@]21C

> <INCHI_IDENTIFIER>
InChI=1S/C42H70O13/c1-20(2)10-9-11-21(3)22-12-14-42(8)29(22)23(45)16-28-40(6)17-24(46)36(39(4,5)27(40)13-15-41(28,42)7)55-38-35(33(50)31(48)26(19-44)53-38)54-37-34(51)32(49)30(47)25(18-43)52-37/h10,22-38,43-51H,3,9,11-19H2,1-2,4-8H3/t22-,23-,24-,25-,26-,27+,28-,29+,30-,31-,32+,33+,34-,35-,36+,37+,38+,40+,41-,42-/m1/s1

> <INCHI_KEY>
YHVZKDRAJHNHJX-UDBICBSZSA-N

> <FORMULA>
C42H70O13

> <MOLECULAR_WEIGHT>
783.009

> <EXACT_MASS>
782.481642314

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
125

> <JCHEM_AVERAGE_POLARIZABILITY>
88.66566830009852

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5S,6R)-2-{[(2R,3R,4S,5S,6R)-2-{[(1R,2R,4R,5R,7R,10R,11R,14S,15R,16R)-4,16-dihydroxy-2,6,6,10,11-pentamethyl-14-(6-methylhepta-1,5-dien-2-yl)tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-5-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
1.65

> <JCHEM_LOGP>
1.882924320666664

> <ALOGPS_LOGS>
-4.06

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.68944257679362

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.086162927992033

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810835766873476

> <JCHEM_POLAR_SURFACE_AREA>
218.98999999999998

> <JCHEM_REFRACTIVITY>
201.5194000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.80e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5S,6R)-2-{[(2R,3R,4S,5S,6R)-2-{[(1R,2R,4R,5R,7R,10R,11R,14S,15R,16R)-4,16-dihydroxy-2,6,6,10,11-pentamethyl-14-(6-methylhepta-1,5-dien-2-yl)tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-5-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-JUN-22         0                                  
HETATM    1  C   UNK     0      16.349  -3.280   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      14.823  -3.490   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      13.878  -2.275   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.353  -2.485   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      11.407  -1.269   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.882  -1.480   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.302  -2.907   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.937  -0.264   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.365   1.215   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.090   2.079   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.874   1.134   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.398  -0.314   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.405  -1.492   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.889  -1.221   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.366   0.228   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.358   1.405   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.835   2.854   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.319   3.125   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.326   1.947   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.850   0.499   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.857  -0.678   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.341  -0.407   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.182   1.041   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.810   2.218   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.332   3.252   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.028   3.743   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -1.698   1.312   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -2.691   0.135   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -4.207   0.406   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -5.200  -0.771   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -4.676  -2.220   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -3.160  -2.491   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -2.168  -1.314   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      -2.637  -3.939   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -1.121  -4.210   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      -5.669  -3.397   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      -6.716  -0.500   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      -4.730   1.854   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0      -6.246   2.125   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -6.769   3.574   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      -8.285   3.845   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      -9.278   2.667   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      -8.755   1.219   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0      -7.239   0.948   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0      -9.748   0.042   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0      -9.224  -1.407   0.000  0.00  0.00           O+0
HETATM   47  O   UNK     0     -10.794   2.939   0.000  0.00  0.00           O+0
HETATM   48  O   UNK     0      -8.809   5.293   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0      -5.777   4.751   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      -0.652  -1.585   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0       3.373  -0.949   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0       6.351   2.583   0.000  0.00  0.00           C+0
HETATM   53  O   UNK     0       6.928  -2.940   0.000  0.00  0.00           O+0
HETATM   54  C   UNK     0       6.985   2.670   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      14.243  -4.917   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   55                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   12                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   16   54                                             
CONECT   12   11    8   13                                                  
CONECT   13   12   14   53                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   20                                                  
CONECT   16   15   11   17   52                                             
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   24                                                  
CONECT   20   19   15   21   51                                             
CONECT   21   20   22                                                       
CONECT   22   21   23   50                                                  
CONECT   23   22   24   27                                                  
CONECT   24   23   19   25   26                                             
CONECT   25   24                                                            
CONECT   26   24                                                            
CONECT   27   23   28                                                       
CONECT   28   27   29   33                                                  
CONECT   29   28   30   38                                                  
CONECT   30   29   31   37                                                  
CONECT   31   30   32   36                                                  
CONECT   32   31   33   34                                                  
CONECT   33   32   28                                                       
CONECT   34   32   35                                                       
CONECT   35   34                                                            
CONECT   36   31                                                            
CONECT   37   30                                                            
CONECT   38   29   39                                                       
CONECT   39   38   40   44                                                  
CONECT   40   39   41   49                                                  
CONECT   41   40   42   48                                                  
CONECT   42   41   43   47                                                  
CONECT   43   42   44   45                                                  
CONECT   44   43   39                                                       
CONECT   45   43   46                                                       
CONECT   46   45                                                            
CONECT   47   42                                                            
CONECT   48   41                                                            
CONECT   49   40                                                            
CONECT   50   22                                                            
CONECT   51   20                                                            
CONECT   52   16                                                            
CONECT   53   13                                                            
CONECT   54   11                                                            
CONECT   55    2                                                            
MASTER        0    0    0    0    0    0    0    0   55    0  120    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₄₂H₇₀O₁₃

Average Mass

783.0090 Da

Monoisotopic Mass

782.48164 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CC(C)=CCCC(=C)[C@H]1CC[C@]2(C)[C@@H]1[C@H](O)C[C@@H]1[C@@]3(C)C[C@@H](O)[C@H](O[C@@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4O[C@@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4O)C(C)(C)[C@@H]3CC[C@@]21C

InChI Identifier

InChI=1S/C42H70O13/c1-20(2)10-9-11-21(3)22-12-14-42(8)29(22)23(45)16-28-40(6)17-24(46)36(39(4,5)27(40)13-15-41(28,42)7)55-38-35(33(50)31(48)26(19-44)53-38)54-37-34(51)32(49)30(47)25(18-43)52-37/h10,22-38,43-51H,3,9,11-19H2,1-2,4-8H3/t22-,23-,24-,25-,26-,27+,28-,29+,30-,31-,32+,33+,34-,35-,36+,37+,38+,40+,41-,42-/m1/s1

InChI Key

YHVZKDRAJHNHJX-UDBICBSZSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Triterpenoids

Direct Parent

Triterpenoids

Alternative Parents

Substituents

Triterpenoid
Steroidal glycoside
12-hydroxysteroid
14-alpha-methylsteroid
2-hydroxysteroid
Hydroxysteroid
Steroid
Disaccharide
Glycosyl compound
O-glycosyl compound
Oxane
Cyclic alcohol
Secondary alcohol
Polyol
Oxacycle
Acetal
Organoheterocyclic compound
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
Alcohol
Primary alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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

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

28479235

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

57390324

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Xie P, Guo M, Xie JB, Xiao MY, Qi YS, Duan Y, Li FF, Piao XL: Effects of heat-processed Gynostemma pentaphyllum on high-fat diet-fed mice of obesity and functional analysis on network pharmacology and molecular docking strategy. J Ethnopharmacol. 2022 Aug 10;294:115335. doi: 10.1016/j.jep.2022.115335. Epub 2022 May 2. [PubMed:35513215 ]
Duan Y, Yang J, Xie JB, Xie P, Qi YS, Zhao MT, Piao XL: [Simultaneous quantitative analysis of nine saponins in Gynostemma pentaphyllum before and after heat processing based on UPLC-Q-Trap-MS]. Zhongguo Zhong Yao Za Zhi. 2021 Oct;46(20):5314-5319. doi: 10.19540/j.cnki.cjcmm.20210702.201. [PubMed:34738435 ]
Wu Q, Jang M, Piao XL: Determination by UPLC-MS of four dammarane-type saponins from heat-processed Gynostemma pentaphyllum. Biosci Biotechnol Biochem. 2014;78(2):311-6. doi: 10.1080/09168451.2014.882751. Epub 2014 Apr 14. [PubMed:25036687 ]
Cui WY, Jin Y, Liu H, Zu ML, Zhai XF, Yang C, Gu YL, Cheng Y, Piao XL: Dammarane-type saponins from Gynostemma pentaphyllum and their cytotoxicities. Nat Prod Res. 2021 Nov;35(22):4433-4441. doi: 10.1080/14786419.2020.1723093. Epub 2020 Feb 10. [PubMed:32037885 ]
Xing SF, Liu LH, Zu ML, Lin M, Zhai XF, Piao XL: Inhibitory Effect of Damulin B from Gynostemma pentaphyllum on Human Lung Cancer Cells. Planta Med. 2019 Mar;85(5):394-405. doi: 10.1055/a-0810-7738. Epub 2018 Dec 18. [PubMed:30562828 ]

Showing NP-Card for Damulin B (NP0139867)

MOL for NP0139867 (Damulin B)

3D MOL for NP0139867 (Damulin B)

3D SDF for NP0139867 (Damulin B)

3D-SDF for NP0139867 (Damulin B)

PDB for NP0139867 (Damulin B)

3D PDB for NP0139867 (Damulin B)

SMILES for NP0139867 (Damulin B)

INCHI for NP0139867 (Damulin B)

Structure for NP0139867 (Damulin B)

3D Structure for NP0139867 (Damulin B)