NP-MRD: Showing NP-Card for 3β,16β-dihydroxy-5α-pregnane-20-carboxylic acid 16,22-lactone-3-O-β-D-glucopyranosyl-(1→3)-β-D-glucopyranosyl-(1→4)-galactopyranoside (NP0332125)

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Record Information

Version

1.0

Created at

2023-11-21 12:01:15 UTC

Updated at

2024-05-05 00:33:37 UTC

NP-MRD ID

NP0332125

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3β,16β-dihydroxy-5α-pregnane-20-carboxylic acid 16,22-lactone-3-O-β-D-glucopyranosyl-(1→3)-β-D-glucopyranosyl-(1→4)-galactopyranoside

Description

Not Available

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 11212312012D          

 64 71  0  0  1  0            999 V2000
    6.5077    0.2335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8390    0.9891    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.1703    1.7446    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.6816    2.4093    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8616    2.3185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5303    1.5629    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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    6.0190    0.8982    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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    5.6877    0.1427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.7103    1.4721    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.9608    2.2581    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0941    2.0206    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3820    1.6041    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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    4.1066    1.4143    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
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    9.7710   -2.9991    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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M  END


  Mrv2104 11212312012D          

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    6.8390    0.9891    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0332125

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12C[C@@]3([H])[C@]4([H])CC[C@@]5([H])C[C@H](CC[C@]5(C)[C@@]4([H])CC[C@]3(C)[C@@]1([H])[C@H](C)C(=O)O2)O[C@@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O[C@@H]3O[C@H](CO)[C@@H](O)C(O)[C@H]3O)[C@H]2O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C40H64O18/c1-15-25-21(53-35(15)51)11-20-18-5-4-16-10-17(6-8-39(16,2)19(18)7-9-40(20,25)3)52-36-31(49)29(47)33(24(14-43)56-36)57-38-32(50)34(27(45)23(13-42)55-38)58-37-30(48)28(46)26(44)22(12-41)54-37/h15-34,36-38,41-50H,4-14H2,1-3H3/t15-,16-,17-,18+,19-,20-,21-,22+,23+,24+,25-,26+,27+,28?,29+,30+,31+,32+,33-,34-,36+,37-,38-,39-,40-/m0/s1

> <INCHI_KEY>
ASSSLAPJYILCPJ-ICJYXLMTSA-N

> <FORMULA>
C40H64O18

> <MOLECULAR_WEIGHT>
832.934

> <EXACT_MASS>
832.409265221

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_ATOM_COUNT>
122

> <JCHEM_AVERAGE_POLARIZABILITY>
88.71673411659823

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2S,4S,7S,8R,9S,12S,13S,16S,18S)-16-{[(2R,3R,4R,5R,6R)-5-{[(2S,3R,4S,5R,6R)-3,5-dihydroxy-6-(hydroxymethyl)-4-{[(2S,3R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-7,9,13-trimethyl-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan-6-one

> <JCHEM_LOGP>
-1.5679004366666662

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.21954389267106

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.77576345591746

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9813780576086115

> <JCHEM_POLAR_SURFACE_AREA>
283.97999999999996

> <JCHEM_REFRACTIVITY>
193.84540000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S,4S,7S,8R,9S,12S,13S,16S,18S)-16-{[(2R,3R,4R,5R,6R)-5-{[(2S,3R,4S,5R,6R)-3,5-dihydroxy-6-(hydroxymethyl)-4-{[(2S,3R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-7,9,13-trimethyl-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan-6-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 21-NOV-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-NOV-23         0                                  
HETATM    1  C   UNK     0      12.148   0.436   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.766   1.846   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      13.384   3.257   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.472   4.497   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.942   4.328   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.323   2.917   0.000  0.00  0.00           C+0
HETATM    7  H   UNK     0       9.705   1.507   0.000  0.00  0.00           H+0
HETATM    8  C   UNK     0      11.235   1.677   0.000  0.00  0.00           C+0
HETATM    9  H   UNK     0      11.854   3.087   0.000  0.00  0.00           H+0
HETATM   10  C   UNK     0      10.617   0.266   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.086   0.097   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.174   1.337   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.412  -0.001   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.793   2.748   0.000  0.00  0.00           C+0
HETATM   15  H   UNK     0       9.260   4.215   0.000  0.00  0.00           H+0
HETATM   16  C   UNK     0       7.642   3.772   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.313   2.994   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.781   3.147   0.000  0.00  0.00           O+0
HETATM   19  H   UNK     0       5.984   4.499   0.000  0.00  0.00           H+0
HETATM   20  C   UNK     0       6.642   1.490   0.000  0.00  0.00           C+0
HETATM   21  H   UNK     0       7.666   2.640   0.000  0.00  0.00           H+0
HETATM   22  C   UNK     0       5.312   0.712   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.160  -0.820   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.162   1.736   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       2.658   1.408   0.000  0.00  0.00           O+0
HETATM   26  H   UNK     0      14.297   2.016   0.000  0.00  0.00           H+0
HETATM   27  C   UNK     0      14.915   3.426   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      15.827   2.185   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      17.358   2.355   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      18.270   1.114   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      19.801   1.284   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      20.713   0.043   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      22.244   0.213   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      23.156  -1.028   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      20.095  -1.367   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      21.007  -2.608   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      20.388  -4.018   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      21.301  -5.259   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      20.682  -6.669   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      19.151  -6.839   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      18.533  -8.249   0.000  0.00  0.00           O+0
HETATM   42  C   UNK     0      18.239  -5.598   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      16.709  -5.768   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0      15.796  -4.527   0.000  0.00  0.00           O+0
HETATM   45  O   UNK     0      18.858  -4.188   0.000  0.00  0.00           O+0
HETATM   46  O   UNK     0      21.594  -7.910   0.000  0.00  0.00           O+0
HETATM   47  C   UNK     0      20.976  -9.321   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      21.888 -10.561   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      21.270 -11.972   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      19.739 -12.141   0.000  0.00  0.00           C+0
HETATM   51  O   UNK     0      19.121 -13.552   0.000  0.00  0.00           O+0
HETATM   52  C   UNK     0      18.827 -10.901   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      17.296 -11.070   0.000  0.00  0.00           C+0
HETATM   54  O   UNK     0      16.384  -9.829   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0      19.445  -9.490   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      22.182 -13.212   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0      23.419 -10.392   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      22.831  -5.089   0.000  0.00  0.00           O+0
HETATM   59  C   UNK     0      18.564  -1.537   0.000  0.00  0.00           C+0
HETATM   60  O   UNK     0      17.945  -2.947   0.000  0.00  0.00           O+0
HETATM   61  C   UNK     0      17.652  -0.296   0.000  0.00  0.00           C+0
HETATM   62  O   UNK     0      16.121  -0.466   0.000  0.00  0.00           O+0
HETATM   63  C   UNK     0      15.209   0.775   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      13.678   0.606   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    8   64                                             
CONECT    3    2    4   26   27                                             
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8   14                                             
CONECT    7    6                                                            
CONECT    8    6    2    9   10                                             
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14   20                                             
CONECT   13   12                                                            
CONECT   14   12    6   15   16                                             
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18   19   20                                             
CONECT   18   17   24                                                       
CONECT   19   17                                                            
CONECT   20   17   12   21   22                                             
CONECT   21   20                                                            
CONECT   22   20   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   18   25                                                  
CONECT   25   24                                                            
CONECT   26    3                                                            
CONECT   27    3   28                                                       
CONECT   28   27   29   63                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31   61                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33   35                                                  
CONECT   33   32   34                                                       
CONECT   34   33                                                            
CONECT   35   32   36   59                                                  
CONECT   36   35   37                                                       
CONECT   37   36   38   45                                                  
CONECT   38   37   39   58                                                  
CONECT   39   38   40   46                                                  
CONECT   40   39   41   42                                                  
CONECT   41   40                                                            
CONECT   42   40   43   45                                                  
CONECT   43   42   44                                                       
CONECT   44   43                                                            
CONECT   45   42   37                                                       
CONECT   46   39   47                                                       
CONECT   47   46   48   55                                                  
CONECT   48   47   49   57                                                  
CONECT   49   48   50   56                                                  
CONECT   50   49   51   52                                                  
CONECT   51   50                                                            
CONECT   52   50   53   55                                                  
CONECT   53   52   54                                                       
CONECT   54   53                                                            
CONECT   55   52   47                                                       
CONECT   56   49                                                            
CONECT   57   48                                                            
CONECT   58   38                                                            
CONECT   59   35   60   61                                                  
CONECT   60   59                                                            
CONECT   61   59   30   62                                                  
CONECT   62   61                                                            
CONECT   63   28   64                                                       
CONECT   64   63    2                                                       
MASTER        0    0    0    0    0    0    0    0   64    0  142    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₄₀H₆₄O₁₈

Average Mass

832.9340 Da

Monoisotopic Mass

832.40927 Da

IUPAC Name

(1R,2S,4S,7S,8R,9S,12S,13S,16S,18S)-16-{[(2R,3R,4R,5R,6R)-5-{[(2S,3R,4S,5R,6R)-3,5-dihydroxy-6-(hydroxymethyl)-4-{[(2S,3R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-7,9,13-trimethyl-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan-6-one

Traditional Name

CAS Registry Number

Not Available

SMILES

[H][C@]12C[C@@]3([H])[C@]4([H])CC[C@@]5([H])C[C@H](CC[C@]5(C)[C@@]4([H])CC[C@]3(C)[C@@]1([H])[C@H](C)C(=O)O2)O[C@@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O[C@@H]3O[C@H](CO)[C@@H](O)C(O)[C@H]3O)[C@H]2O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C40H64O18/c1-15-25-21(53-35(15)51)11-20-18-5-4-16-10-17(6-8-39(16,2)19(18)7-9-40(20,25)3)52-36-31(49)29(47)33(24(14-43)56-36)57-38-32(50)34(27(45)23(13-42)55-38)58-37-30(48)28(46)26(44)22(12-41)54-37/h15-34,36-38,41-50H,4-14H2,1-3H3/t15-,16-,17-,18+,19-,20-,21-,22+,23+,24+,25-,26+,27+,28?,29+,30+,31+,32+,33-,34-,36+,37-,38-,39-,40-/m0/s1

InChI Key

ASSSLAPJYILCPJ-ICJYXLMTSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, C5D5N, experimental)	wuhonghua2011@tjutcm.edu.cn	Tianjin University of Traditional Chinese Medicine	Hong-Hua Wu	2024-05-03	View Spectrum
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, C5D5N, experimental)	wuhonghua2011@tjutcm.edu.cn	Tianjin University of Traditional Chinese Medicine	Hong-Hua Wu	2024-05-03	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, C5D5N, experimental)	wuhonghua2011@tjutcm.edu.cn	Tianjin University of Traditional Chinese Medicine	Hong-Hua Wu	2024-05-03	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, C5D5N, experimental)	wuhonghua2011@tjutcm.edu.cn	Tianjin University of Traditional Chinese Medicine	Hong-Hua Wu	2024-05-03	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, C5D5N, experimental)	wuhonghua2011@tjutcm.edu.cn	Tianjin University of Traditional Chinese Medicine	Hong-Hua Wu	2024-05-03	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, C5D5N, experimental)	wuhonghua2011@tjutcm.edu.cn	Tianjin University of Traditional Chinese Medicine	Hong-Hua Wu	2024-05-03	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, C5D5N, experimental)	wuhonghua2011@tjutcm.edu.cn	Tianjin University of Traditional Chinese Medicine	Hong-Hua Wu	2024-05-03	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, C2D6OS, experimental)	wuhonghua2011@tjutcm.edu.cn	Tianjin University of Traditional Chinese Medicine	Hong-Hua Wu	2024-05-03	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600.203706235, C5D5deposition_typeN, simulated)	wuhonghua2011@tjutcm.edu.cn	Tianjin University of Traditional Chinese Medicine	Hong-Hua Wu	2024-05-03	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
lyratum		Not Available

Chemical Taxonomy

Classification

Not classified

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	-1.6	ChemAxon
pKa (Strongest Acidic)	11.78	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	17	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	283.98 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	193.85 m³·mol⁻¹	ChemAxon
Polarizability	88.72 Å³	ChemAxon
Number of Rings	8	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

Not Available

References

General References

Lai JX, Zhao Y, Gao WK, Zhang LH, Yu HY, Yang WZ, Wu HH: Steroidal Saponins from Solanum lyratum Thunb. Chem Biodivers. 2023 Dec;20(12):e202301381. doi: 10.1002/cbdv.202301381. Epub 2023 Nov 23. [PubMed:37968243 ]

Showing NP-Card for 3β,16β-dihydroxy-5α-pregnane-20-carboxylic acid 16,22-lactone-3-O-β-D-glucopyranosyl-(1→3)-β-D-glucopyranosyl-(1→4)-galactopyranoside (NP0332125)

MOL for NP0332125 (3β,16β-dihydroxy-5α-pregnane-20-carboxylic acid 16,22-lactone-3-O-β-D-glucopyranosyl-(1→3)-β-D-glucopyranosyl-(1→4)-galactopyranoside)

3D MOL for NP0332125 (3β,16β-dihydroxy-5α-pregnane-20-carboxylic acid 16,22-lactone-3-O-β-D-glucopyranosyl-(1→3)-β-D-glucopyranosyl-(1→4)-galactopyranoside)

3D SDF for NP0332125 (3β,16β-dihydroxy-5α-pregnane-20-carboxylic acid 16,22-lactone-3-O-β-D-glucopyranosyl-(1→3)-β-D-glucopyranosyl-(1→4)-galactopyranoside)

3D-SDF for NP0332125 (3β,16β-dihydroxy-5α-pregnane-20-carboxylic acid 16,22-lactone-3-O-β-D-glucopyranosyl-(1→3)-β-D-glucopyranosyl-(1→4)-galactopyranoside)

PDB for NP0332125 (3β,16β-dihydroxy-5α-pregnane-20-carboxylic acid 16,22-lactone-3-O-β-D-glucopyranosyl-(1→3)-β-D-glucopyranosyl-(1→4)-galactopyranoside)

3D PDB for NP0332125 (3β,16β-dihydroxy-5α-pregnane-20-carboxylic acid 16,22-lactone-3-O-β-D-glucopyranosyl-(1→3)-β-D-glucopyranosyl-(1→4)-galactopyranoside)

SMILES for NP0332125 (3β,16β-dihydroxy-5α-pregnane-20-carboxylic acid 16,22-lactone-3-O-β-D-glucopyranosyl-(1→3)-β-D-glucopyranosyl-(1→4)-galactopyranoside)

INCHI for NP0332125 (3β,16β-dihydroxy-5α-pregnane-20-carboxylic acid 16,22-lactone-3-O-β-D-glucopyranosyl-(1→3)-β-D-glucopyranosyl-(1→4)-galactopyranoside)

Structure for NP0332125 (3β,16β-dihydroxy-5α-pregnane-20-carboxylic acid 16,22-lactone-3-O-β-D-glucopyranosyl-(1→3)-β-D-glucopyranosyl-(1→4)-galactopyranoside)

3D Structure for NP0332125 (3β,16β-dihydroxy-5α-pregnane-20-carboxylic acid 16,22-lactone-3-O-β-D-glucopyranosyl-(1→3)-β-D-glucopyranosyl-(1→4)-galactopyranoside)