Np mrd loader

Showing NP-Card for Vinaginsenoside R13 (NP0336318)

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Record Information
Version2.0
Created at2024-09-11 05:41:11 UTC
Updated at2024-09-11 05:41:12 UTC
NP-MRD IDNP0336318
Secondary Accession NumbersNone
Natural Product Identification
Common NameVinaginsenoside R13
DescriptionVinaginsenoside R13 belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Vinaginsenoside R13 was first documented in 2013 (PMID: 24243611). Based on a literature review a small amount of articles have been published on Vinaginsenoside R13.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0336318 (Vinaginsenoside R13)


  Mrv2104 05262308132D          

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M  END
Download

3D MOL for NP0336318 (Vinaginsenoside R13)

Download
3D SDF for NP0336318 (Vinaginsenoside R13)

  Mrv2104 05262308132D          

 68 74  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
NP0336318

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)(O)C(O)CCC(C)(OC1OC(CO)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4O)C(C)(C)C3CCC21C

> <INCHI_IDENTIFIER>
InChI=1/C48H84O20/c1-43(2)26-10-15-46(6)27(45(26,5)13-12-29(43)66-42-39(36(59)33(56)25(20-51)65-42)67-40-37(60)34(57)31(54)23(18-49)63-40)17-22(52)30-21(9-14-47(30,46)7)48(8,16-11-28(53)44(3,4)62)68-41-38(61)35(58)32(55)24(19-50)64-41/h21-42,49-62H,9-20H2,1-8H3

> <INCHI_KEY>
IXHBKLVSPJTPAA-UHFFFAOYNA-N

> <FORMULA>
C48H84O20

> <MOLECULAR_WEIGHT>
981.18

> <EXACT_MASS>
980.555595105

> <JCHEM_ACCEPTOR_COUNT>
20

> <JCHEM_ATOM_COUNT>
152

> <JCHEM_AVERAGE_POLARIZABILITY>
105.84842521420683

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
14

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(2-{[1-(5,6-dihydroxy-6-methyl-2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}heptan-2-yl)-11-hydroxy-3a,3b,6,6,9a-pentamethyl-hexadecahydro-1H-cyclopenta[a]phenanthren-7-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl)oxy]-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_LOGP>
-1.9210079426666686

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.313264759871124

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.847210195899308

> <JCHEM_PKA_STRONGEST_BASIC>
-3.648377595753652

> <JCHEM_POLAR_SURFACE_AREA>
338.6000000000001

> <JCHEM_REFRACTIVITY>
236.82340000000008

> <JCHEM_ROTATABLE_BOND_COUNT>
14

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
2-[(2-{[1-(5,6-dihydroxy-6-methyl-2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}heptan-2-yl)-11-hydroxy-3a,3b,6,6,9a-pentamethyl-dodecahydro-1H-cyclopenta[a]phenanthren-7-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl)oxy]-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0336318 (Vinaginsenoside R13)
Download
PDB for NP0336318 (Vinaginsenoside R13)
HEADER    PROTEIN                                 26-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-23         0                                  
HETATM    1  C   UNK     0       6.437  -2.827   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.457  -2.816   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.978   7.321   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      17.601   4.305   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.808   2.200   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.443   2.226   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.958  -0.124   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      13.724   3.733   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      13.179   2.165   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.121  -1.657   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      14.757   6.652   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.133   0.675   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.470   1.438   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      12.267   0.924   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.458  -0.895   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      13.249   6.340   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.146   2.963   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.161   6.087   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.755   9.346   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -2.549  -1.597   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      12.281   3.416   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.484   3.725   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.491   5.310   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       9.217   8.862   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.211  -0.835   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       6.791  -0.880   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       8.138   1.423   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      15.781   5.501   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.124  -0.865   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      10.814   2.948   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       2.829   6.073   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      10.367   9.886   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -1.202   0.705   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       4.158   5.295   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      11.829   9.402   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       0.136   1.467   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       4.150   3.755   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      12.141   7.894   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       1.465   0.690   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       2.812   2.993   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      10.991   6.870   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       1.457  -0.850   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       5.453  -1.642   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      17.289   5.813   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       6.800   0.660   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       9.467   0.645   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      10.805   1.408   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      12.765   4.878   0.000  0.00  0.00           C+0
HETATM   49  O   UNK     0       0.170   7.627   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0       7.444  10.854   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      -2.557  -3.138   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0       9.493   5.265   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0      15.297   4.039   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0       2.837   7.612   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0      10.056  11.394   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      -2.532   1.482   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0       5.496   6.058   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      12.980  10.426   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0       0.144   3.007   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0       5.479   2.978   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0      13.603   7.410   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0      18.797   6.125   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0       1.482   3.770   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0       9.529   7.354   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0       0.119  -1.612   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0       2.786  -1.627   0.000  0.00  0.00           O+0
HETATM   67  O   UNK     0       2.803   1.453   0.000  0.00  0.00           O+0
HETATM   68  O   UNK     0      11.303   5.362   0.000  0.00  0.00           O+0
CONECT    1   43                                                            
CONECT    2   43                                                            
CONECT    3   44                                                            
CONECT    4   44                                                            
CONECT    5   45                                                            
CONECT    6   46                                                            
CONECT    7   47                                                            
CONECT    8   48                                                            
CONECT    9   14   21                                                       
CONECT   10   15   26                                                       
CONECT   11   16   28                                                       
CONECT   12   13   29                                                       
CONECT   13   12   45                                                       
CONECT   14    9   47                                                       
CONECT   15   10   46                                                       
CONECT   16   11   48                                                       
CONECT   17   22   27                                                       
CONECT   18   23   49                                                       
CONECT   19   24   50                                                       
CONECT   20   25   51                                                       
CONECT   21    9   30   48                                                  
CONECT   22   17   30   52                                                  
CONECT   23   18   31   63                                                  
CONECT   24   19   32   64                                                  
CONECT   25   20   33   65                                                  
CONECT   26   10   43   45                                                  
CONECT   27   17   45   46                                                  
CONECT   28   11   44   53                                                  
CONECT   29   12   43   66                                                  
CONECT   30   21   22   47                                                  
CONECT   31   23   34   54                                                  
CONECT   32   24   35   55                                                  
CONECT   33   25   36   56                                                  
CONECT   34   31   37   57                                                  
CONECT   35   32   38   58                                                  
CONECT   36   33   39   59                                                  
CONECT   37   34   40   60                                                  
CONECT   38   35   41   61                                                  
CONECT   39   36   42   67                                                  
CONECT   40   37   63   67                                                  
CONECT   41   38   64   68                                                  
CONECT   42   39   65   66                                                  
CONECT   43    1    2   26   29                                             
CONECT   44    3    4   28   62                                             
CONECT   45    5   13   26   27                                             
CONECT   46    6   15   27   47                                             
CONECT   47    7   14   30   46                                             
CONECT   48    8   16   21   68                                             
CONECT   49   18                                                            
CONECT   50   19                                                            
CONECT   51   20                                                            
CONECT   52   22                                                            
CONECT   53   28                                                            
CONECT   54   31                                                            
CONECT   55   32                                                            
CONECT   56   33                                                            
CONECT   57   34                                                            
CONECT   58   35                                                            
CONECT   59   36                                                            
CONECT   60   37                                                            
CONECT   61   38                                                            
CONECT   62   44                                                            
CONECT   63   23   40                                                       
CONECT   64   24   41                                                       
CONECT   65   25   42                                                       
CONECT   66   29   42                                                       
CONECT   67   39   40                                                       
CONECT   68   41   48                                                       
MASTER        0    0    0    0    0    0    0    0   68    0  148    0
END

Download
3D PDB for NP0336318 (Vinaginsenoside R13)
Download
SMILES for NP0336318 (Vinaginsenoside R13)
CC(C)(O)C(O)CCC(C)(OC1OC(CO)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4O)C(C)(C)C3CCC21C
Download
INCHI for NP0336318 (Vinaginsenoside R13)
InChI=1/C48H84O20/c1-43(2)26-10-15-46(6)27(45(26,5)13-12-29(43)66-42-39(36(59)33(56)25(20-51)65-42)67-40-37(60)34(57)31(54)23(18-49)63-40)17-22(52)30-21(9-14-47(30,46)7)48(8,16-11-28(53)44(3,4)62)68-41-38(61)35(58)32(55)24(19-50)64-41/h21-42,49-62H,9-20H2,1-8H3
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View in JSmol
SynonymsNot Available
Chemical FormulaC48H84O20
Average Mass981.1800 Da
Monoisotopic Mass980.55560 Da
IUPAC Name2-[(2-{[1-(5,6-dihydroxy-6-methyl-2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}heptan-2-yl)-11-hydroxy-3a,3b,6,6,9a-pentamethyl-hexadecahydro-1H-cyclopenta[a]phenanthren-7-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl)oxy]-6-(hydroxymethyl)oxane-3,4,5-triol
Traditional Name2-[(2-{[1-(5,6-dihydroxy-6-methyl-2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}heptan-2-yl)-11-hydroxy-3a,3b,6,6,9a-pentamethyl-dodecahydro-1H-cyclopenta[a]phenanthren-7-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl)oxy]-6-(hydroxymethyl)oxane-3,4,5-triol
CAS Registry NumberNot Available
SMILES
CC(C)(O)C(O)CCC(C)(OC1OC(CO)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4O)C(C)(C)C3CCC21C
InChI Identifier
InChI=1/C48H84O20/c1-43(2)26-10-15-46(6)27(45(26,5)13-12-29(43)66-42-39(36(59)33(56)25(20-51)65-42)67-40-37(60)34(57)31(54)23(18-49)63-40)17-22(52)30-21(9-14-47(30,46)7)48(8,16-11-28(53)44(3,4)62)68-41-38(61)35(58)32(55)24(19-50)64-41/h21-42,49-62H,9-20H2,1-8H3
InChI KeyIXHBKLVSPJTPAA-UHFFFAOYNA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassPrenol lipids  
Sub ClassTriterpenoids  
Direct ParentTriterpenoids  
Alternative Parents
Substituents
  • Triterpenoid
    • 

  • Steroidal glycoside
    • 

  • 25-hydroxysteroid
    • 

  • 24-hydroxysteroid
    • 

  • 12-hydroxysteroid
    • 

  • Hydroxysteroid
    • 

  • Steroid
    • 

  • Fatty acyl glycoside
    • 

  • Fatty acyl glycoside of mono- or disaccharide
    • 

  • Alkyl glycoside
    • 

  • Disaccharide
    • 

  • Glycosyl compound
    • 

  • O-glycosyl compound
    • 

  • Fatty acyl
    • 

  • Oxane
    • 

  • Cyclic alcohol
    • 

  • Tertiary alcohol
    • 

  • Secondary alcohol
    • 

  • Organoheterocyclic compound
    • 

  • Oxacycle
    • 

  • Acetal
    • 

  • Polyol
    • 

  • Primary alcohol
    • 

  • Alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxygen compound
    • 

  • Organooxygen compound
    • 

  • 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
logP-1.9ChemAxon
pKa (Strongest Acidic)11.85ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count20ChemAxon
Hydrogen Donor Count14ChemAxon
Polar Surface Area338.6 ŲChemAxon
Rotatable Bond Count14ChemAxon
Refractivity236.82 m³·mol⁻¹ChemAxon
Polarizability105.85 ųChemAxon
Number of Rings7ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Luo SL, Dang LZ, Li JF, Zou CG, Zhang KQ, Li GH: Biotransformation of saponins by endophytes isolated from Panax notoginseng. Chem Biodivers. 2013 Nov;10(11):2021-31. doi: 10.1002/cbdv.201300005. [PubMed:24243611  ]