Np mrd loader

Showing NP-Card for Tuberoside D (NP0047933)

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Record Information
Version2.0
Created at2022-03-17 20:48:19 UTC
Updated at2022-03-17 20:48:19 UTC
NP-MRD IDNP0047933
Secondary Accession NumbersNone
Natural Product Identification
Common NameTuberoside D
DescriptionTuberoside D 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. Tuberoside D is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, tuberoside D has been detected, but not quantified in, onion-family vegetables and potato. Tuberoside D is found in Allium tuberosum. This could make tuberoside D a potential biomarker for the consumption of these foods.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0047933 (Tuberoside D)


  Mrv0541 02241217442D          

 62 70  0  0  0  0            999 V2000
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M  END
Download

3D MOL for NP0047933 (Tuberoside D)

Download
3D SDF for NP0047933 (Tuberoside D)

  Mrv0541 02241217442D          

 62 70  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
NP0047933

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1C2C(CC3C4CCC5CC(OC6OC(CO)C(OC7OC(C)C(O)C(O)C7O)C(O)C6OC6OC(C)C(O)C(O)C6O)C(O)CC5(C)C4CCC23C)OC11CCC(C)CO1

> <INCHI_IDENTIFIER>
InChI=1S/C45H74O17/c1-18-9-12-45(55-17-18)19(2)30-28(62-45)14-25-23-8-7-22-13-27(26(47)15-44(22,6)24(23)10-11-43(25,30)5)58-42-39(61-41-36(53)34(51)32(49)21(4)57-41)37(54)38(29(16-46)59-42)60-40-35(52)33(50)31(48)20(3)56-40/h18-42,46-54H,7-17H2,1-6H3

> <INCHI_KEY>
PTMUTMGEBGQTEJ-UHFFFAOYSA-N

> <FORMULA>
C45H74O17

> <MOLECULAR_WEIGHT>
887.0589

> <EXACT_MASS>
886.492600942

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
95.61340033610782

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{[4-hydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-15'-oloxy}-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-3-yl]oxy}-6-methyloxane-3,4,5-triol

> <ALOGPS_LOGP>
0.23

> <JCHEM_LOGP>
1.0392943246666673

> <ALOGPS_LOGS>
-3.34

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
9

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.368966712896913

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.882395748061915

> <JCHEM_PKA_STRONGEST_BASIC>
-3.159232120574881

> <JCHEM_POLAR_SURFACE_AREA>
255.90999999999994

> <JCHEM_REFRACTIVITY>
214.9299000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.03e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-{[4-hydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-15'-oloxy}-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-3-yl]oxy}-6-methyloxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0047933 (Tuberoside D)
Download
PDB for NP0047933 (Tuberoside D)
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      10.703   7.245   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       9.458   6.338   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       8.052   6.965   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.890   8.497   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.135   9.403   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.544   8.777   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      11.789   9.680   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       8.052   5.425   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       6.586   4.950   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.680   3.705   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.217   4.180   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.882   3.410   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.882   1.870   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.550   1.100   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.216   1.870   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.119   1.100   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.451   1.870   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.451   3.410   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.119   4.180   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -3.786   1.100   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -3.786  -0.440   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -5.120  -1.210   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -6.453  -0.440   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -2.451  -1.210   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -2.451  -2.750   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -1.119  -3.520   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       0.216  -2.750   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      -3.786   4.180   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      -6.453  -3.520   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -5.120  -2.750   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -3.786  -3.520   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -3.786  -5.060   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -2.451  -5.830   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -2.451  -7.370   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -3.786  -8.140   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      -1.119  -5.060   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       0.216  -5.830   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       1.550  -5.060   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      -9.119   1.100   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      -9.119  -0.440   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      -7.787  -1.210   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0      -7.787  -2.750   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0      -9.119  -3.520   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      -9.119  -5.060   0.000  0.00  0.00           C+0
HETATM   45  O   UNK     0     -11.789  -0.440   0.000  0.00  0.00           O+0
HETATM   46  C   UNK     0     -10.454  -1.210   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0     -10.454  -2.750   0.000  0.00  0.00           C+0
HETATM   48  O   UNK     0     -11.789  -3.520   0.000  0.00  0.00           O+0
HETATM   49  C   UNK     0       4.376   7.252   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0       4.217   5.720   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0       5.680   6.195   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0       6.586   7.442   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0       6.111   8.905   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0       2.882   6.490   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0       1.550   5.720   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0       1.550   4.180   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0       0.216   3.410   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0       0.216   4.950   0.000  0.00  0.00           C+0
HETATM   59  O   UNK     0       1.550  -8.140   0.000  0.00  0.00           O+0
HETATM   60  C   UNK     0       0.216  -7.370   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0      -1.119  -8.140   0.000  0.00  0.00           C+0
HETATM   62  O   UNK     0      -1.119  -9.680   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    8   52                                             
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    1    5    7                                                  
CONECT    7    6                                                            
CONECT    8    3    9                                                       
CONECT    9    8   10   51                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   50                                                  
CONECT   12   11   13   56                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   57                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   20                                                  
CONECT   18   17   19   28                                                  
CONECT   19   18   57                                                       
CONECT   20   17   21                                                       
CONECT   21   20   22   24                                                  
CONECT   22   21   23   30                                                  
CONECT   23   22   41                                                       
CONECT   24   21   25                                                       
CONECT   25   24   26   31                                                  
CONECT   26   25   27                                                       
CONECT   27   26                                                            
CONECT   28   18                                                            
CONECT   29   30                                                            
CONECT   30   22   29   31                                                  
CONECT   31   25   30   32                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34   36                                                  
CONECT   34   33   35   61                                                  
CONECT   35   34                                                            
CONECT   36   33   37                                                       
CONECT   37   36   38   60                                                  
CONECT   38   37                                                            
CONECT   39   40                                                            
CONECT   40   39   41   46                                                  
CONECT   41   23   40   42                                                  
CONECT   42   41   43                                                       
CONECT   43   42   44   47                                                  
CONECT   44   43                                                            
CONECT   45   46                                                            
CONECT   46   40   45   47                                                  
CONECT   47   43   46   48                                                  
CONECT   48   47                                                            
CONECT   49   50                                                            
CONECT   50   11   49   51   54                                             
CONECT   51    9   50   52                                                  
CONECT   52    3   51   53                                                  
CONECT   53   52                                                            
CONECT   54   50   55                                                       
CONECT   55   54   56                                                       
CONECT   56   12   55   57                                                  
CONECT   57   15   19   56   58                                             
CONECT   58   57                                                            
CONECT   59   60                                                            
CONECT   60   37   59   61                                                  
CONECT   61   34   60   62                                                  
CONECT   62   61                                                            
MASTER        0    0    0    0    0    0    0    0   62    0  140    0
END

Download
3D PDB for NP0047933 (Tuberoside D)
Download
SMILES for NP0047933 (Tuberoside D)
CC1C2C(CC3C4CCC5CC(OC6OC(CO)C(OC7OC(C)C(O)C(O)C7O)C(O)C6OC6OC(C)C(O)C(O)C6O)C(O)CC5(C)C4CCC23C)OC11CCC(C)CO1
Download
INCHI for NP0047933 (Tuberoside D)
InChI=1S/C45H74O17/c1-18-9-12-45(55-17-18)19(2)30-28(62-45)14-25-23-8-7-22-13-27(26(47)15-44(22,6)24(23)10-11-43(25,30)5)58-42-39(61-41-36(53)34(51)32(49)21(4)57-41)37(54)38(29(16-46)59-42)60-40-35(52)33(50)31(48)20(3)56-40/h18-42,46-54H,7-17H2,1-6H3
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View in JSmol
Synonyms
ValueSource
Tuberoside DMeSH
Tuberoside-DMeSH
Chemical FormulaC45H74O17
Average Mass887.0589 Da
Monoisotopic Mass886.49260 Da
IUPAC Name2-{[4-hydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-15'-oloxy}-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-3-yl]oxy}-6-methyloxane-3,4,5-triol
Traditional Name2-{[4-hydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-15'-oloxy}-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-3-yl]oxy}-6-methyloxane-3,4,5-triol
CAS Registry Number234771-06-3
SMILES
CC1C2C(CC3C4CCC5CC(OC6OC(CO)C(OC7OC(C)C(O)C(O)C7O)C(O)C6OC6OC(C)C(O)C(O)C6O)C(O)CC5(C)C4CCC23C)OC11CCC(C)CO1
InChI Identifier
InChI=1S/C45H74O17/c1-18-9-12-45(55-17-18)19(2)30-28(62-45)14-25-23-8-7-22-13-27(26(47)15-44(22,6)24(23)10-11-43(25,30)5)58-42-39(61-41-36(53)34(51)32(49)21(4)57-41)37(54)38(29(16-46)59-42)60-40-35(52)33(50)31(48)20(3)56-40/h18-42,46-54H,7-17H2,1-6H3
InChI KeyPTMUTMGEBGQTEJ-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Allium cepaFooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Allium fistulosumFooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Allium tuberosumLOTUS Database
Solanum tuberosumFooDB
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.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassSteroids and steroid derivatives  
Sub ClassSteroidal glycosides  
Direct ParentSteroidal saponins  
Alternative Parents
Substituents
  • Steroidal saponin
    • 

  • Triterpenoid
    • 

  • Spirostane skeleton
    • 

  • Oligosaccharide
    • 

  • 2-hydroxysteroid
    • 

  • Hydroxysteroid
    • 

  • Glycosyl compound
    • 

  • O-glycosyl compound
    • 

  • Ketal
    • 

  • Oxane
    • 

  • Cyclic alcohol
    • 

  • Tetrahydrofuran
    • 

  • Secondary alcohol
    • 

  • Organoheterocyclic compound
    • 

  • Oxacycle
    • 

  • Acetal
    • 

  • Polyol
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxygen compound
    • 

  • Primary alcohol
    • 

  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP0.23ALOGPS
logP1.04ChemAxon
logS-3.3ALOGPS
pKa (Strongest Acidic)11.88ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count17ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area255.91 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity214.93 m³·mol⁻¹ChemAxon
Polarizability95.61 ųChemAxon
Number of Rings9ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
HMDB IDHMDB0034304  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012652  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound73020465  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References