NP-MRD: Showing NP-Card for Glycyphyllin (NP0050585)

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Record Information

Version

2.0

Created at

2022-04-27 21:58:05 UTC

Updated at

2022-04-27 21:58:05 UTC

NP-MRD ID

NP0050585

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Glycyphyllin

Description

1-(2,4-Dihydroxy-6-{[(2S,3R,4S,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}phenyl)-3-(4-hydroxyphenyl)propan-1-one belongs to the class of organic compounds known as flavonoid o-glycosides. Flavonoid O-glycosides are compounds containing a carbohydrate moiety which is O-glycosidically linked to the 2-phenylchromen-4-one flavonoid backbone. Glycyphyllin is found in Smilax glycyphylla and Smilax spp.. Based on a literature review very few articles have been published on 1-(2,4-dihydroxy-6-{[(2S,3R,4S,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}phenyl)-3-(4-hydroxyphenyl)propan-1-one.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304272223582D          

 30 32  0  0  1  0            999 V2000
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -6.6000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 12 17  1  0  0  0  0
 15 18  1  0  0  0  0
  3 19  1  0  0  0  0
 20 19  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 20 25  1  0  0  0  0
 24 26  1  6  0  0  0
 23 27  1  1  0  0  0
 22 28  1  1  0  0  0
 21 29  1  6  0  0  0
  1 30  1  0  0  0  0
M  END


  Mrv1652304272223582D          

 30 32  0  0  1  0            999 V2000
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -6.6000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 12 17  1  0  0  0  0
 15 18  1  0  0  0  0
  3 19  1  0  0  0  0
 20 19  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 20 25  1  0  0  0  0
 24 26  1  6  0  0  0
 23 27  1  1  0  0  0
 22 28  1  1  0  0  0
 21 29  1  6  0  0  0
  1 30  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0050585

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1O[C@@H](OC2=C(C(=O)CCC3=CC=C(O)C=C3)C(O)=CC(O)=C2)[C@H](O)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C21H24O9/c1-10-18(26)19(27)20(28)21(29-10)30-16-9-13(23)8-15(25)17(16)14(24)7-4-11-2-5-12(22)6-3-11/h2-3,5-6,8-10,18-23,25-28H,4,7H2,1H3/t10-,18-,19-,20+,21-/m0/s1

> <INCHI_KEY>
GLLUYNRFPAMGQR-YTLNPQBGSA-N

> <FORMULA>
C21H24O9

> <MOLECULAR_WEIGHT>
420.414

> <EXACT_MASS>
420.142032353

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
54

> <JCHEM_AVERAGE_POLARIZABILITY>
41.597675786687645

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-(2,4-dihydroxy-6-{[(2S,3R,4S,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}phenyl)-3-(4-hydroxyphenyl)propan-1-one

> <ALOGPS_LOGP>
1.15

> <JCHEM_LOGP>
2.024382406

> <ALOGPS_LOGS>
-2.65

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.353071695284198

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.869760947657564

> <JCHEM_PKA_STRONGEST_BASIC>
-3.612200363306619

> <JCHEM_POLAR_SURFACE_AREA>
156.91

> <JCHEM_REFRACTIVITY>
104.30799999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.49e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-(2,4-dihydroxy-6-{[(2S,3R,4S,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}phenyl)-3-(4-hydroxyphenyl)propan-1-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 27-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-APR-22         0                                  
HETATM    1  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.335  -7.700   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.334 -11.550   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000 -12.320   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.334 -11.550   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -2.667 -12.320   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      -4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
CONECT    1    2    6   30                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   19                                                  
CONECT    4    3    5    8                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5                                                            
CONECT    8    4    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   17                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   18                                                  
CONECT   16   15   17                                                       
CONECT   17   16   12                                                       
CONECT   18   15                                                            
CONECT   19    3   20                                                       
CONECT   20   19   21   25                                                  
CONECT   21   20   22   29                                                  
CONECT   22   21   23   28                                                  
CONECT   23   22   24   27                                                  
CONECT   24   23   25   26                                                  
CONECT   25   24   20                                                       
CONECT   26   24                                                            
CONECT   27   23                                                            
CONECT   28   22                                                            
CONECT   29   21                                                            
CONECT   30    1                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   64    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₁H₂₄O₉

Average Mass

420.4140 Da

Monoisotopic Mass

420.14203 Da

IUPAC Name

1-(2,4-dihydroxy-6-{[(2S,3R,4S,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}phenyl)-3-(4-hydroxyphenyl)propan-1-one

Traditional Name

1-(2,4-dihydroxy-6-{[(2S,3R,4S,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}phenyl)-3-(4-hydroxyphenyl)propan-1-one

CAS Registry Number

Not Available

SMILES

C[C@@H]1O[C@@H](OC2=C(C(=O)CCC3=CC=C(O)C=C3)C(O)=CC(O)=C2)[C@H](O)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C21H24O9/c1-10-18(26)19(27)20(28)21(29-10)30-16-9-13(23)8-15(25)17(16)14(24)7-4-11-2-5-12(22)6-3-11/h2-3,5-6,8-10,18-23,25-28H,4,7H2,1H3/t10-,18-,19-,20+,21-/m0/s1

InChI Key

GLLUYNRFPAMGQR-YTLNPQBGSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Smilax glycyphylla	Plant	KNApSAcK
Smilax spp.	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavonoid o-glycosides. Flavonoid O-glycosides are compounds containing a carbohydrate moiety which is O-glycosidically linked to the 2-phenylchromen-4-one flavonoid backbone.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Flavonoid O-glycosides

Alternative Parents

Substituents

Flavonoid o-glycoside
2'-hydroxy-dihydrochalcone
Phenolic glycoside
Cinnamylphenol
Linear 1,3-diarylpropanoid
Alkyl-phenylketone
Hexose monosaccharide
O-glycosyl compound
Glycosyl compound
Butyrophenone
Phenylketone
Phenoxy compound
Aryl alkyl ketone
Aryl ketone
Resorcinol
Phenol ether
Benzoyl
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Benzenoid
Oxane
Monosaccharide
Monocyclic benzene moiety
Vinylogous acid
Secondary alcohol
Ketone
Oxacycle
Organoheterocyclic compound
Polyol
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic 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	1.15	ALOGPS
logP	2.02	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	7.87	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	156.91 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	104.31 m³·mol⁻¹	ChemAxon
Polarizability	41.6 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	Yes	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

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

162990468

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Glycyphyllin (NP0050585)

MOL for NP0050585 (Glycyphyllin)

3D MOL for NP0050585 (Glycyphyllin)

3D SDF for NP0050585 (Glycyphyllin)

3D-SDF for NP0050585 (Glycyphyllin)

PDB for NP0050585 (Glycyphyllin)

3D PDB for NP0050585 (Glycyphyllin)

SMILES for NP0050585 (Glycyphyllin)

INCHI for NP0050585 (Glycyphyllin)

Structure for NP0050585 (Glycyphyllin)

3D Structure for NP0050585 (Glycyphyllin)