NP-MRD: Showing NP-Card for Epimedin C (NP0140710)

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Record Information

Version

2.0

Created at

2022-06-29 21:48:05 UTC

Updated at

2022-06-29 21:48:05 UTC

NP-MRD ID

NP0140710

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Epimedin C

Description

Epimedin c belongs to the class of organic compounds known as flavonoid-7-o-glycosides. These are phenolic compounds containing a flavonoid moiety which is O-glycosidically linked to carbohydrate moiety at the C7-position. Thus, epimedin c is considered to be a flavonoid. Epimedin C is found in Epimedium sagittatum. Epimedin C was first documented in 2022 (PMID: 35860032). Based on a literature review a small amount of articles have been published on Epimedin c (PMID: 35813313) (PMID: 35736128) (PMID: 35472682) (PMID: 35462273).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652306292223482D          

 58 63  0  0  1  0            999 V2000
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  3 58  1  1  0  0  0
M  END

     RDKit          3D

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M  END


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  2  7  1  0  0  0  0
  6  8  1  1  0  0  0
  9  8  1  6  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
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 25 32  1  0  0  0  0
 33 32  1  1  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
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 37 39  1  1  0  0  0
 39 40  1  0  0  0  0
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 35 42  1  1  0  0  0
 34 43  1  6  0  0  0
 23 44  1  0  0  0  0
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 45 46  2  0  0  0  0
 46 47  1  0  0  0  0
 47 48  2  0  0  0  0
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 49 50  2  0  0  0  0
 45 50  1  0  0  0  0
 48 51  1  0  0  0  0
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  5 56  1  6  0  0  0
  4 57  1  6  0  0  0
  3 58  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0140710

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC=C(C=C1)C1=C(O[C@@H]2O[C@@H](C)[C@H](O)[C@@H](O)[C@H]2O[C@@H]2O[C@@H](C)[C@H](O)[C@@H](O)[C@H]2O)C(=O)C2=C(O1)C(CC=C(C)C)=C(O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)C=C2O

> <INCHI_IDENTIFIER>
InChI=1S/C39H50O19/c1-14(2)6-11-19-21(54-38-32(50)29(47)26(44)22(13-40)55-38)12-20(41)23-27(45)35(33(56-34(19)23)17-7-9-18(51-5)10-8-17)57-39-36(30(48)25(43)16(4)53-39)58-37-31(49)28(46)24(42)15(3)52-37/h6-10,12,15-16,22,24-26,28-32,36-44,46-50H,11,13H2,1-5H3/t15-,16-,22+,24-,25-,26+,28+,29-,30+,31+,32+,36+,37-,38+,39-/m0/s1

> <INCHI_KEY>
ULZLIYVOYYQJRO-JIYCBSMMSA-N

> <FORMULA>
C39H50O19

> <MOLECULAR_WEIGHT>
822.81

> <EXACT_MASS>
822.29462939

> <JCHEM_ACCEPTOR_COUNT>
19

> <JCHEM_ATOM_COUNT>
108

> <JCHEM_AVERAGE_POLARIZABILITY>
81.40826774548418

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-{[(2S,3R,4R,5R,6S)-4,5-dihydroxy-6-methyl-3-{[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-2-yl]oxy}-5-hydroxy-2-(4-methoxyphenyl)-8-(3-methylbut-2-en-1-yl)-7-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4H-chromen-4-one

> <ALOGPS_LOGP>
0.73

> <JCHEM_LOGP>
0.08810727533333329

> <ALOGPS_LOGS>
-2.78

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.875886232196436

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.068545140253953

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6124972640574935

> <JCHEM_POLAR_SURFACE_AREA>
293.21

> <JCHEM_REFRACTIVITY>
197.49000000000007

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.38e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-{[(2S,3R,4R,5R,6S)-4,5-dihydroxy-6-methyl-3-{[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-2-yl]oxy}-5-hydroxy-2-(4-methoxyphenyl)-8-(3-methylbut-2-en-1-yl)-7-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}chromen-4-one

> <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      -8.002   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -8.002   4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -9.336   3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -9.336   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -8.002   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -6.668   3.850   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -5.335   1.540   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.001   3.850   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -1.334  -0.770   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  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.668  -0.770   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       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0      12.003  -2.310   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0      10.669  -0.000   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0       8.002   1.540   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   51  O   UNK     0      -6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   52  C   UNK     0      -6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM   54  O   UNK     0      -2.667   6.160   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0      -5.335   4.620   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      -8.002   0.000   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0     -10.669   1.540   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0     -10.669   4.620   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4   58                                                  
CONECT    4    3    5   57                                                  
CONECT    5    4    6   56                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6    2                                                       
CONECT    8    6    9                                                       
CONECT    9    8   10   14                                                  
CONECT   10    9   11   55                                                  
CONECT   11   10   12   54                                                  
CONECT   12   11   13   53                                                  
CONECT   13   12   14                                                       
CONECT   14   13    9   15                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   21                                                  
CONECT   17   16   18   45                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   26                                                  
CONECT   20   19   21   23                                                  
CONECT   21   20   16   22                                                  
CONECT   22   21                                                            
CONECT   23   20   24   44                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   32                                                  
CONECT   26   25   19   27                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29                                                            
CONECT   32   25   33                                                       
CONECT   33   32   34   38                                                  
CONECT   34   33   35   43                                                  
CONECT   35   34   36   42                                                  
CONECT   36   35   37   41                                                  
CONECT   37   36   38   39                                                  
CONECT   38   37   33                                                       
CONECT   39   37   40                                                       
CONECT   40   39                                                            
CONECT   41   36                                                            
CONECT   42   35                                                            
CONECT   43   34                                                            
CONECT   44   23                                                            
CONECT   45   17   46   50                                                  
CONECT   46   45   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47   49   51                                                  
CONECT   49   48   50                                                       
CONECT   50   49   45                                                       
CONECT   51   48   52                                                       
CONECT   52   51                                                            
CONECT   53   12                                                            
CONECT   54   11                                                            
CONECT   55   10                                                            
CONECT   56    5                                                            
CONECT   57    4                                                            
CONECT   58    3                                                            
MASTER        0    0    0    0    0    0    0    0   58    0  126    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₉H₅₀O₁₉

Average Mass

822.8100 Da

Monoisotopic Mass

822.29463 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

COC1=CC=C(C=C1)C1=C(O[C@@H]2O[C@@H](C)[C@H](O)[C@@H](O)[C@H]2O[C@@H]2O[C@@H](C)[C@H](O)[C@@H](O)[C@H]2O)C(=O)C2=C(O1)C(CC=C(C)C)=C(O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)C=C2O

InChI Identifier

InChI=1S/C39H50O19/c1-14(2)6-11-19-21(54-38-32(50)29(47)26(44)22(13-40)55-38)12-20(41)23-27(45)35(33(56-34(19)23)17-7-9-18(51-5)10-8-17)57-39-36(30(48)25(43)16(4)53-39)58-37-31(49)28(46)24(42)15(3)52-37/h6-10,12,15-16,22,24-26,28-32,36-44,46-50H,11,13H2,1-5H3/t15-,16-,22+,24-,25-,26+,28+,29-,30+,31+,32+,36+,37-,38+,39-/m0/s1

InChI Key

ULZLIYVOYYQJRO-JIYCBSMMSA-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

Species Name	Source	Reference
Epimedium sagittatum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavonoid-7-o-glycosides. These are phenolic compounds containing a flavonoid moiety which is O-glycosidically linked to carbohydrate moiety at the C7-position.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Flavonoid-7-O-glycosides

Alternative Parents

Substituents

8-prenylated flavone
Flavonoid-3-o-glycoside
Flavonoid-7-o-glycoside
4p-methoxyflavonoid-skeleton
Flavone
Hydroxyflavonoid
5-hydroxyflavonoid
Phenolic glycoside
Glycosyl compound
O-glycosyl compound
Disaccharide
Chromone
1-benzopyran
Benzopyran
Anisole
Phenoxy compound
Phenol ether
Methoxybenzene
Alkyl aryl ether
Pyranone
1-hydroxy-2-unsubstituted benzenoid
Pyran
Oxane
Benzenoid
Monocyclic benzene moiety
Heteroaromatic compound
Vinylogous acid
Secondary alcohol
Acetal
Oxacycle
Organoheterocyclic compound
Polyol
Ether
Organic oxide
Organic oxygen compound
Primary alcohol
Alcohol
Organooxygen compound
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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00005830

Chemspider ID

4677925

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5748394

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Xu Y, Chen S, Huang L, Han W, Shao Y, Chen M, Zhang Y, He R, Xie B: Epimedin C Alleviates Glucocorticoid-Induced Suppression of Osteogenic Differentiation by Modulating PI3K/AKT/RUNX2 Signaling Pathway. Front Pharmacol. 2022 Jul 4;13:894832. doi: 10.3389/fphar.2022.894832. eCollection 2022. [PubMed:35860032 ]
Liang R, Yang XN, Lin S, Yi WQ, Chen XG, Dong X, Guo LG, Li YK, Zhao YR, Xu H: New indication of Chuankezhi injection for steroid-resistant focal segmental glomerulosclerosis and its mechanism of action. Ann Transl Med. 2022 Jun;10(11):639. doi: 10.21037/atm-22-1962. [PubMed:35813313 ]
Lou H, Liu X, Liu S, Chen Q: Purification and Characterization of a Novel alpha-L-Rhamnosidase from Papiliotrema laurentii ZJU-L07 and Its Application in Production of Icariin from Epimedin C. J Fungi (Basel). 2022 Jun 20;8(6). pii: jof8060644. doi: 10.3390/jof8060644. [PubMed:35736128 ]
Xie J, Zhao J, Zhang N, Xu H, Yang J, Ye J, Jiang J: Efficient production of isoquercitin, icariin and icariside II by a novel thermostable alpha-l-rhamnosidase PodoRha from Paenibacillus odorifer with high alpha-1, 6-/alpha-1, 2- glycoside specificity. Enzyme Microb Technol. 2022 Aug;158:110039. doi: 10.1016/j.enzmictec.2022.110039. Epub 2022 Apr 7. [PubMed:35472682 ]
Lu C, Dong Y, Ke K, Zou K, Wang Z, Xiao W, Pei J, Zhao L: Modification to increase the thermostability and catalytic efficiency of alpha-L-rhamnosidase from Bacteroides thetaiotaomicron and high-level expression. Enzyme Microb Technol. 2022 Aug;158:110040. doi: 10.1016/j.enzmictec.2022.110040. Epub 2022 Apr 6. [PubMed:35462273 ]

Showing NP-Card for Epimedin C (NP0140710)

MOL for NP0140710 (Epimedin C)

3D MOL for NP0140710 (Epimedin C)

3D SDF for NP0140710 (Epimedin C)

3D-SDF for NP0140710 (Epimedin C)

PDB for NP0140710 (Epimedin C)

3D PDB for NP0140710 (Epimedin C)

SMILES for NP0140710 (Epimedin C)

INCHI for NP0140710 (Epimedin C)

Structure for NP0140710 (Epimedin C)

3D Structure for NP0140710 (Epimedin C)