NP-MRD: Showing NP-Card for 16'-{[5-hydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl]oxy}-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-10'-one (NP0320085)

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Record Information

Version

2.0

Created at

2022-09-11 21:29:51 UTC

Updated at

2022-09-11 21:29:51 UTC

NP-MRD ID

NP0320085

Secondary Accession Numbers

None

Natural Product Identification

Common Name

16'-{[5-hydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl]oxy}-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-10'-one

Description

Schidigerasaponin E1 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. 16'-{[5-hydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl]oxy}-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-10'-one is found in Yucca schidigera. Schidigerasaponin E1 is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241209442D          

 62 70  0  0  0  0            999 V2000
   -1.3783   -1.2313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3783   -2.0586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.6637   -0.8190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv0541 02241209442D          

 62 70  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
NP0320085

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1C2C(CC3C4CCC5CC(CCC5(C)C4CC(=O)C23C)OC2OC(CO)C(O)C(OC3OCC(O)C(O)C3O)C2OC2OC(CO)C(O)C(O)C2O)OC11CCC(C)CO1

> <INCHI_IDENTIFIER>
InChI=1S/C44H70O18/c1-18-7-10-44(56-16-18)19(2)30-26(62-44)12-24-22-6-5-20-11-21(8-9-42(20,3)23(22)13-29(48)43(24,30)4)57-41-38(61-40-36(54)34(52)32(50)27(14-45)58-40)37(33(51)28(15-46)59-41)60-39-35(53)31(49)25(47)17-55-39/h18-28,30-41,45-47,49-54H,5-17H2,1-4H3

> <INCHI_KEY>
AADIIQJBIMAADJ-UHFFFAOYSA-N

> <FORMULA>
C44H70O18

> <MOLECULAR_WEIGHT>
887.0158

> <EXACT_MASS>
886.456215436

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
94.59142335231442

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
16'-{[5-hydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl]oxy}-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-10'-one

> <ALOGPS_LOGP>
-0.05

> <JCHEM_LOGP>
-0.016570420999996616

> <ALOGPS_LOGS>
-3.10

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
9

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.390489920643184

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.894560954180845

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810909910944696

> <JCHEM_POLAR_SURFACE_AREA>
272.97999999999996

> <JCHEM_REFRACTIVITY>
211.38650000000007

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.04e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
16'-{[5-hydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl]oxy}-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-10'-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -2.573  -2.298   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.573  -3.843   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.239  -4.617   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.095  -3.843   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.095  -2.298   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.239  -1.529   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.431  -4.617   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.765  -3.843   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.765  -2.298   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.431  -1.529   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.097  -1.529   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.097   0.007   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.765   0.777   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.431   0.007   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.556  -2.001   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.454  -0.759   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.556   0.480   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       7.909  -0.287   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       7.909   1.239   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.454   1.708   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       9.248   0.480   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      10.584   1.239   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      10.584   2.781   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       9.248   3.550   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       7.909   2.781   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       6.057   3.201   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.097   1.552   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       2.765   2.321   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       0.095  -0.759   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -3.912  -4.617   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -5.246  -3.843   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -5.246  -2.298   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -6.580  -1.529   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -7.914  -2.298   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -7.914  -3.843   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -6.580  -4.617   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      -9.248  -4.617   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0     -10.582  -3.843   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      -9.248  -1.529   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0      -6.580   0.007   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0      -3.912  -1.529   0.000  0.00  0.00           O+0
HETATM   42  C   UNK     0      -3.142  -0.205   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0      -1.603  -0.205   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0      -0.834   1.126   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      -1.603   2.457   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      -3.142   2.457   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      -3.912   1.126   0.000  0.00  0.00           C+0
HETATM   48  O   UNK     0      -0.834   3.791   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0      -3.912   3.791   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      -5.451   1.126   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0      -7.914   0.777   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      -7.914   2.321   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      -9.248   3.078   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0     -10.582   2.321   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0     -10.582   0.777   0.000  0.00  0.00           C+0
HETATM   56  O   UNK     0      -9.248   0.007   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0     -11.915   3.078   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      -9.248   4.617   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0      -6.580   3.078   0.000  0.00  0.00           O+0
HETATM   60  C   UNK     0       0.705   1.126   0.000  0.00  0.00           C+0
HETATM   61  O   UNK     0       1.103   2.614   0.000  0.00  0.00           O+0
HETATM   62  C   UNK     0      11.915   3.550   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3   30                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    7                                                  
CONECT    5    4    6   10   29                                             
CONECT    6    1    5                                                       
CONECT    7    4    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    5    9   14                                                  
CONECT   11    9   12   15                                                  
CONECT   12   11   13   17   27                                             
CONECT   13   12   14   28                                                  
CONECT   14   10   13                                                       
CONECT   15   11   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   12   16   20                                                  
CONECT   18   16   19                                                       
CONECT   19   18   20   21   25                                             
CONECT   20   17   19   26                                                  
CONECT   21   19   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   62                                                  
CONECT   24   23   25                                                       
CONECT   25   19   24                                                       
CONECT   26   20                                                            
CONECT   27   12                                                            
CONECT   28   13                                                            
CONECT   29    5                                                            
CONECT   30    2   31                                                       
CONECT   31   30   32   36                                                  
CONECT   32   31   33   41                                                  
CONECT   33   32   34   40                                                  
CONECT   34   33   35   39                                                  
CONECT   35   34   36   37                                                  
CONECT   36   31   35                                                       
CONECT   37   35   38                                                       
CONECT   38   37                                                            
CONECT   39   34                                                            
CONECT   40   33   51                                                       
CONECT   41   32   42                                                       
CONECT   42   41   43   47                                                  
CONECT   43   42   44                                                       
CONECT   44   43   45   60                                                  
CONECT   45   44   46   48                                                  
CONECT   46   45   47   49                                                  
CONECT   47   42   46   50                                                  
CONECT   48   45                                                            
CONECT   49   46                                                            
CONECT   50   47                                                            
CONECT   51   40   52   56                                                  
CONECT   52   51   53   59                                                  
CONECT   53   52   54   58                                                  
CONECT   54   53   55   57                                                  
CONECT   55   54   56                                                       
CONECT   56   51   55                                                       
CONECT   57   54                                                            
CONECT   58   53                                                            
CONECT   59   52                                                            
CONECT   60   44   61                                                       
CONECT   61   60                                                            
CONECT   62   23                                                            
MASTER        0    0    0    0    0    0    0    0   62    0  140    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₄₄H₇₀O₁₈

Average Mass

887.0158 Da

Monoisotopic Mass

886.45622 Da

IUPAC Name

Traditional Name

CAS Registry Number

Not Available

SMILES

CC1C2C(CC3C4CCC5CC(CCC5(C)C4CC(=O)C23C)OC2OC(CO)C(O)C(OC3OCC(O)C(O)C3O)C2OC2OC(CO)C(O)C(O)C2O)OC11CCC(C)CO1

InChI Identifier

InChI=1S/C44H70O18/c1-18-7-10-44(56-16-18)19(2)30-26(62-44)12-24-22-6-5-20-11-21(8-9-42(20,3)23(22)13-29(48)43(24,30)4)57-41-38(61-40-36(54)34(52)32(50)27(14-45)58-40)37(33(51)28(15-46)59-41)60-39-35(53)31(49)25(47)17-55-39/h18-28,30-41,45-47,49-54H,5-17H2,1-4H3

InChI Key

AADIIQJBIMAADJ-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Yucca schidigera	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

Not Available

Substituents

Not Available

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
logP	-0.05	ALOGPS
logP	-0.017	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	11.89	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	18	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	272.98 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	211.39 m³·mol⁻¹	ChemAxon
Polarizability	94.59 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

HMDB0036297

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB015164

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

73798945

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 16'-{[5-hydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl]oxy}-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-10'-one (NP0320085)

MOL for NP0320085 (16'-{[5-hydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl]oxy}-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-10'-one)

3D MOL for NP0320085 (16'-{[5-hydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl]oxy}-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-10'-one)

3D SDF for NP0320085 (16'-{[5-hydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl]oxy}-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-10'-one)

3D-SDF for NP0320085 (16'-{[5-hydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl]oxy}-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-10'-one)

PDB for NP0320085 (16'-{[5-hydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl]oxy}-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-10'-one)

3D PDB for NP0320085 (16'-{[5-hydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl]oxy}-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-10'-one)

SMILES for NP0320085 (16'-{[5-hydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl]oxy}-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-10'-one)

INCHI for NP0320085 (16'-{[5-hydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl]oxy}-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-10'-one)

Structure for NP0320085 (16'-{[5-hydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl]oxy}-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-10'-one)

3D Structure for NP0320085 (16'-{[5-hydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl]oxy}-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-10'-one)