NP-MRD: Showing NP-Card for ys-iv (NP0168368)

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Record Information

Version

2.0

Created at

2022-09-03 04:09:32 UTC

Updated at

2022-09-03 04:09:32 UTC

NP-MRD ID

NP0168368

Secondary Accession Numbers

None

Natural Product Identification

Common Name

ys-iv

Description

Ys-IV belongs to the class of organic compounds known as steroidal saponins. These are saponins in which the aglycone moiety is a steroid. The steroidal aglycone is usually a spirostane, furostane, spirosolane, solanidane, or curcubitacin derivative. ys-iv is found in Yucca gloriosa and Yucca guatemalensis. ys-iv was first documented in 2008 (PMID: 17675194). Based on a literature review very few articles have been published on Ys-IV.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032206092D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309032206092D          

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M  END
> <DATABASE_ID>
NP0168368

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1[C@H]2[C@H](C[C@H]3[C@@H]4CC[C@@H]5C[C@H](CC[C@]5(C)[C@H]4CC[C@]23C)O[C@@H]2O[C@H](CO)[C@H](O)[C@H](O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)O[C@]11CC[C@@H](C)CO1

> <INCHI_IDENTIFIER>
InChI=1S/C45H74O18/c1-19-7-12-45(56-18-19)20(2)30-26(63-45)14-25-23-6-5-21-13-22(8-10-43(21,3)24(23)9-11-44(25,30)4)57-42-39(62-41-37(55)35(53)32(50)28(16-47)59-41)38(33(51)29(17-48)60-42)61-40-36(54)34(52)31(49)27(15-46)58-40/h19-42,46-55H,5-18H2,1-4H3/t19-,20+,21-,22+,23-,24+,25+,26+,27-,28-,29-,30+,31-,32-,33+,34+,35+,36-,37-,38+,39-,40+,41+,42-,43+,44+,45-/m1/s1

> <INCHI_KEY>
DKEFDSJGKPNAQN-DHNDSWACSA-N

> <FORMULA>
C45H74O18

> <MOLECULAR_WEIGHT>
903.069

> <EXACT_MASS>
902.487515543

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_ATOM_COUNT>
137

> <JCHEM_AVERAGE_POLARIZABILITY>
97.01108455296726

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5S,6R)-2-{[(2R,3S,4S,5R,6R)-3-hydroxy-2-(hydroxymethyl)-6-[(1'R,2R,2'S,4'S,5R,7'S,8'R,9'S,12'S,13'S,16'S,18'R)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane]oxy]-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-4-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
0.03

> <JCHEM_LOGP>
0.020377998333338254

> <ALOGPS_LOGS>
-3.13

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
9

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.367885770384373

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.879163068508216

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981090991097746

> <JCHEM_POLAR_SURFACE_AREA>
276.14

> <JCHEM_REFRACTIVITY>
216.6558000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.70e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5S,6R)-2-{[(2R,3S,4S,5R,6R)-3-hydroxy-2-(hydroxymethyl)-6-[(1'R,2R,2'S,4'S,5R,7'S,8'R,9'S,12'S,13'S,16'S,18'R)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane]oxy]-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-4-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0      13.454  -7.989   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.686  -6.467   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      15.054  -5.760   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      14.805  -4.240   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      16.173  -3.533   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      17.268  -4.616   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      18.805  -4.526   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      19.497  -3.150   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      21.034  -3.061   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      21.880  -4.347   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      23.418  -4.258   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      24.264  -5.545   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      25.801  -5.455   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      26.647  -6.742   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      25.956  -8.118   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      26.802  -9.405   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      26.111 -10.781   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      26.957 -12.068   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      28.340  -9.315   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      29.186 -10.602   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      29.031  -7.939   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      30.568  -7.850   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      31.415  -9.136   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      30.723 -10.512   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      31.570 -11.799   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      30.878 -13.175   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      31.725 -14.462   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      33.107 -11.710   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      33.953 -12.996   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      33.798 -10.333   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      35.336 -10.244   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      32.952  -9.047   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      33.643  -7.671   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      28.185  -6.652   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      28.876  -5.276   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      28.030  -3.990   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      26.492  -4.079   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      25.646  -2.792   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      24.109  -2.882   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0      23.263  -1.595   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0      26.337  -1.416   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0      25.491  -0.129   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0      27.875  -1.327   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0      28.566   0.050   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0      28.721  -2.613   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0      30.258  -2.524   0.000  0.00  0.00           O+0
HETATM   47  C   UNK     0      23.573  -6.921   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      22.035  -7.010   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      21.189  -5.724   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      20.498  -7.100   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      19.652  -5.813   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      18.960  -7.189   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      17.423  -7.279   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      16.577  -5.992   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      15.746  -7.289   0.000  0.00  0.00           C+0
HETATM   56  O   UNK     0      13.282  -4.008   0.000  0.00  0.00           O+0
HETATM   57  C   UNK     0      12.591  -5.384   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      12.048  -6.825   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      10.528  -7.075   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0       9.552  -5.884   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0       8.032  -6.134   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      10.095  -4.443   0.000  0.00  0.00           C+0
HETATM   63  O   UNK     0      11.615  -4.193   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   57                                                  
CONECT    3    2    4   54                                                  
CONECT    4    3    5   56                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   54                                                  
CONECT    7    6    8   51                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   49                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   47                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   34                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   19                                                  
CONECT   17   16   18                                                       
CONECT   18   17                                                            
CONECT   19   16   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   34                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   32                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   28                                                  
CONECT   26   25   27                                                       
CONECT   27   26                                                            
CONECT   28   25   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   23   33                                                  
CONECT   33   32                                                            
CONECT   34   21   14   35                                                  
CONECT   35   34   36                                                       
CONECT   36   35   37   45                                                  
CONECT   37   36   38                                                       
CONECT   38   37   39   41                                                  
CONECT   39   38   40                                                       
CONECT   40   39                                                            
CONECT   41   38   42   43                                                  
CONECT   42   41                                                            
CONECT   43   41   44   45                                                  
CONECT   44   43                                                            
CONECT   45   43   36   46                                                  
CONECT   46   45                                                            
CONECT   47   12   48                                                       
CONECT   48   47   49                                                       
CONECT   49   48   10   50   51                                             
CONECT   50   49                                                            
CONECT   51   49    7   52                                                  
CONECT   52   51   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53    6    3   55                                             
CONECT   55   54                                                            
CONECT   56    4   57                                                       
CONECT   57   56    2   58   63                                             
CONECT   58   57   59                                                       
CONECT   59   58   60                                                       
CONECT   60   59   61   62                                                  
CONECT   61   60                                                            
CONECT   62   60   63                                                       
CONECT   63   62   57                                                       
MASTER        0    0    0    0    0    0    0    0   63    0  142    0
END

View in JSmol

Synonyms

Value	Source
Smilagenin 3-O-beta-D-glucopyranosyl-(1->2)-[beta-D-glucopyranosyl-(1->3)]-beta-D-galactopyranoside	ChEBI
Smilagenin 3-O-b-D-glucopyranosyl-(1->2)-[b-D-glucopyranosyl-(1->3)]-b-D-galactopyranoside	Generator
Smilagenin 3-O-β-D-glucopyranosyl-(1->2)-[β-D-glucopyranosyl-(1->3)]-β-D-galactopyranoside	Generator

Chemical Formula

C₄₅H₇₄O₁₈

Average Mass

903.0690 Da

Monoisotopic Mass

902.48752 Da

IUPAC Name

(2S,3R,4S,5S,6R)-2-{[(2R,3S,4S,5R,6R)-3-hydroxy-2-(hydroxymethyl)-6-[(1'R,2R,2'S,4'S,5R,7'S,8'R,9'S,12'S,13'S,16'S,18'R)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane]oxy]-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-4-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

CAS Registry Number

Not Available

SMILES

C[C@H]1[C@H]2[C@H](C[C@H]3[C@@H]4CC[C@@H]5C[C@H](CC[C@]5(C)[C@H]4CC[C@]23C)O[C@@H]2O[C@H](CO)[C@H](O)[C@H](O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)O[C@]11CC[C@@H](C)CO1

InChI Identifier

InChI=1S/C45H74O18/c1-19-7-12-45(56-18-19)20(2)30-26(63-45)14-25-23-6-5-21-13-22(8-10-43(21,3)24(23)9-11-44(25,30)4)57-42-39(62-41-37(55)35(53)32(50)28(16-47)59-41)38(33(51)29(17-48)60-42)61-40-36(54)34(52)31(49)27(15-46)58-40/h19-42,46-55H,5-18H2,1-4H3/t19-,20+,21-,22+,23-,24+,25+,26+,27-,28-,29-,30+,31-,32-,33+,34+,35+,36-,37-,38+,39-,40+,41+,42-,43+,44+,45-/m1/s1

InChI Key

DKEFDSJGKPNAQN-DHNDSWACSA-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
Yucca gloriosa	LOTUS Database	35616633
Yucca guatemalensis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as steroidal saponins. These are saponins in which the aglycone moiety is a steroid. The steroidal aglycone is usually a spirostane, furostane, spirosolane, solanidane, or curcubitacin derivative.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroidal glycosides

Direct Parent

Steroidal saponins

Alternative Parents

Substituents

Steroidal saponin
Triterpenoid
Spirostane skeleton
Oligosaccharide
Glycosyl compound
O-glycosyl compound
Ketal
Oxane
Tetrahydrofuran
Secondary alcohol
Polyol
Organoheterocyclic compound
Oxacycle
Acetal
Primary alcohol
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

organic heterohexacyclic compound (CHEBI:66498 )
trisaccharide derivative (CHEBI:66498 )
oxaspiro compound (CHEBI:66498 )
spirostanyl glycoside (CHEBI:66498 )

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	0.03	ALOGPS
logP	0.02	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	11.88	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	18	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	276.14 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	216.66 m³·mol⁻¹	ChemAxon
Polarizability	97.01 Å³	ChemAxon
Number of Rings	9	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

10235500

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21603424

PDB ID

Not Available

ChEBI ID

66498

Good Scents ID

Not Available

References

General References

Zhang Y, Zhang YJ, Jacob MR, Li XC, Yang CR: Steroidal saponins from the stem of Yucca elephantipes. Phytochemistry. 2008 Jan;69(1):264-70. doi: 10.1016/j.phytochem.2007.06.015. Epub 2007 Aug 1. [PubMed:17675194 ]
LOTUS database [Link]

Showing NP-Card for ys-iv (NP0168368)

MOL for NP0168368 (ys-iv)

3D MOL for NP0168368 (ys-iv)

3D SDF for NP0168368 (ys-iv)

3D-SDF for NP0168368 (ys-iv)

PDB for NP0168368 (ys-iv)

3D PDB for NP0168368 (ys-iv)

SMILES for NP0168368 (ys-iv)

INCHI for NP0168368 (ys-iv)

Structure for NP0168368 (ys-iv)

3D Structure for NP0168368 (ys-iv)