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Showing NP-Card for Icariside D1 (NP0049739)

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Record Information
Version2.0
Created at2022-03-17 21:17:20 UTC
Updated at2022-03-17 21:17:20 UTC
NP-MRD IDNP0049739
Secondary Accession NumbersNone
Natural Product Identification
Common NameIcariside D1
Description Icariside D1 is found in Atractylodes lancea, Bupleurum falcatum L. , Epimedium grandiflorum, Glochidion rubrum, Helichrysum arenarium and Tinospora sinensis .
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0049739 (Icariside D1)


  Mrv0541 02241209482D          

 29 31  0  0  0  0            999 V2000
   -1.2891   -3.8951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0039   -4.3076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.0039   -2.6577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891   -3.0701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5754   -2.6577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5754   -1.8327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891   -1.4203    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891   -0.5953    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0039   -0.1829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.5754   -0.1829    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5754    0.6421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1395    1.0545    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1395    1.8795    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8751    2.2534    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0030    3.0687    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4199    3.6517    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891    1.8795    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.0039    0.6421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7175    1.0545    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6093    1.8795    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1923    2.4624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8183    3.1980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5882    3.4936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7175    4.3076    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6051    3.9941    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
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  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 13  1  0  0  0  0
 11 12  1  0  0  0  0
 11 22  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 21  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 24  1  0  0  0  0
 18 19  1  0  0  0  0
 18 26  1  0  0  0  0
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 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 29  1  0  0  0  0
 27 28  1  0  0  0  0
M  END
Download

3D MOL for NP0049739 (Icariside D1)

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3D SDF for NP0049739 (Icariside D1)

  Mrv0541 02241209482D          

 29 31  0  0  0  0            999 V2000
   -1.2891   -3.8951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0039   -4.3076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7175   -3.8951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7175   -3.0701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0039   -2.6577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891   -3.0701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5754   -2.6577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5754   -1.8327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891   -1.4203    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891   -0.5953    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0039   -0.1829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7175   -0.5953    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5754   -0.1829    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5754    0.6421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1395    1.0545    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1395    1.8795    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8751    2.2534    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0030    3.0687    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4199    3.6517    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891    1.8795    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891    1.0545    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0039    0.6421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7175    1.0545    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6093    1.8795    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1923    2.4624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8183    3.1980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5882    3.4936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7175    4.3076    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6051    3.9941    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 13  1  0  0  0  0
 11 12  1  0  0  0  0
 11 22  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
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 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 24  1  0  0  0  0
 18 19  1  0  0  0  0
 18 26  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 24 25  1  0  0  0  0
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 26 27  1  0  0  0  0
 26 29  1  0  0  0  0
 27 28  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0049739

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1(O)COC(OCC2OC(OCCC3=CC=CC=C3)C(O)C(O)C2O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C19H28O10/c20-9-19(25)10-28-18(16(19)24)27-8-12-13(21)14(22)15(23)17(29-12)26-7-6-11-4-2-1-3-5-11/h1-5,12-18,20-25H,6-10H2

> <INCHI_KEY>
GZSQKOFXMZDKPV-UHFFFAOYSA-N

> <FORMULA>
C19H28O10

> <MOLECULAR_WEIGHT>
416.4196

> <EXACT_MASS>
416.168247116

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
42.005174282739894

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-6-(2-phenylethoxy)oxane-3,4,5-triol

> <ALOGPS_LOGP>
-1.19

> <JCHEM_LOGP>
-1.5527774520000004

> <ALOGPS_LOGS>
-1.61

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.318486073980544

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.705149140598072

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1423790163389214

> <JCHEM_POLAR_SURFACE_AREA>
158.3

> <JCHEM_REFRACTIVITY>
96.71239999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.02e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-6-(2-phenylethoxy)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0049739 (Icariside D1)
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PDB for NP0049739 (Icariside D1)
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      -2.406  -7.271   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.741  -8.041   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.073  -7.271   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.073  -5.731   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.741  -4.961   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.406  -5.731   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.074  -4.961   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.074  -3.421   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.406  -2.651   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -2.406  -1.111   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.741  -0.341   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -5.073  -1.111   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -1.074  -0.341   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -1.074   1.199   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.260   1.968   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.260   3.508   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       1.634   4.206   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.872   5.728   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       0.784   6.817   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -2.406   3.508   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -2.406   1.968   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -3.741   1.199   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -5.073   1.968   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       3.004   3.508   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       4.092   4.596   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.394   5.970   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.831   6.521   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       5.073   8.041   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       2.996   7.456   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    1    5    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   13                                                  
CONECT   11   10   12   22                                                  
CONECT   12   11                                                            
CONECT   13   10   14                                                       
CONECT   14   13   15   21                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   24                                                  
CONECT   18   17   19   26                                                  
CONECT   19   18                                                            
CONECT   20   21                                                            
CONECT   21   14   20   22                                                  
CONECT   22   11   21   23                                                  
CONECT   23   22                                                            
CONECT   24   17   25                                                       
CONECT   25   24   26                                                       
CONECT   26   18   25   27   29                                             
CONECT   27   26   28                                                       
CONECT   28   27                                                            
CONECT   29   26                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   62    0
END

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3D PDB for NP0049739 (Icariside D1)
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SMILES for NP0049739 (Icariside D1)
OCC1(O)COC(OCC2OC(OCCC3=CC=CC=C3)C(O)C(O)C2O)C1O
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INCHI for NP0049739 (Icariside D1)
InChI=1S/C19H28O10/c20-9-19(25)10-28-18(16(19)24)27-8-12-13(21)14(22)15(23)17(29-12)26-7-6-11-4-2-1-3-5-11/h1-5,12-18,20-25H,6-10H2
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View in JSmol
SynonymsNot Available
Chemical FormulaC19H28O10
Average Mass416.4196 Da
Monoisotopic Mass416.16825 Da
IUPAC Name2-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-6-(2-phenylethoxy)oxane-3,4,5-triol
Traditional Name2-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-6-(2-phenylethoxy)oxane-3,4,5-triol
CAS Registry Number112267-85-3
SMILES
OCC1(O)COC(OCC2OC(OCCC3=CC=CC=C3)C(O)C(O)C2O)C1O
InChI Identifier
InChI=1S/C19H28O10/c20-9-19(25)10-28-18(16(19)24)27-8-12-13(21)14(22)15(23)17(29-12)26-7-6-11-4-2-1-3-5-11/h1-5,12-18,20-25H,6-10H2
InChI KeyGZSQKOFXMZDKPV-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Atractylodes lanceaLOTUS Database
Bupleurum falcatumPlant
Epimedium grandiflorumLOTUS Database
Glochidion rubrumPlant
Helichrysum arenariumLOTUS Database
Pimpinella anisumFooDB
Punica granatumFooDB
Tinospora sinensisPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbohydrates and carbohydrate conjugates  
Direct ParentO-glycosyl compounds  
Alternative Parents
Substituents
  • Disaccharide
    • 

  • O-glycosyl compound
    • 

  • Monocyclic benzene moiety
    • 

  • Oxane
    • 

  • Benzenoid
    • 

  • Tertiary alcohol
    • 

  • Tetrahydrofuran
    • 

  • Secondary alcohol
    • 

  • Polyol
    • 

  • Oxacycle
    • 

  • Acetal
    • 

  • Organoheterocyclic compound
    • 

  • Primary alcohol
    • 

  • Alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic 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-1.2ALOGPS
logP-1.6ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)11.71ChemAxon
pKa (Strongest Basic)-3.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area158.3 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity96.71 m³·mol⁻¹ChemAxon
Polarizability42.01 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB020703  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound13893574  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available