NP-MRD: Showing NP-Card for (-)-Orcinol-3-O-beta-D-glycopyranoside (NP0072288)

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Record Information

Version

2.0

Created at

2022-04-28 17:39:10 UTC

Updated at

2022-04-28 17:39:10 UTC

NP-MRD ID

NP0072288

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Orcinol-3-O-beta-D-glycopyranoside

Description

Orcinol glucoside belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose. (-)-Orcinol-3-O-beta-D-glycopyranoside is found in Curculigo orchioides , Helichrysum arenarium, Molineria capitulata and Rumex nepalensis . (-)-Orcinol-3-O-beta-D-glycopyranoside was first documented in 2005 (PMID: 16079552). Based on a literature review a significant number of articles have been published on Orcinol glucoside (PMID: 25305598) (PMID: 34206443) (PMID: 35291616) (PMID: 34382261) (PMID: 31496649) (PMID: 30151753).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 38 39  0  0  0  0  0  0  0  0999 V2000
    5.4703   -0.6456    0.7220 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1731   -0.2609    0.0841 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2058    0.4382   -1.1122 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0320    0.8112   -1.7322 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0597    1.5135   -2.9340 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8300    0.4611   -1.1145 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7623   -0.2301    0.0691 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5871   -0.5886    0.7006 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6916   -0.3247    0.2683 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4012    0.5033    1.1765 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5025    0.9801    0.4450 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3046    1.9212    1.3207 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5190    2.9974    1.7224 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3745   -0.1622   -0.0033 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2847   -0.3292   -1.3942 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8549   -1.4332    0.6254 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8106   -1.2396    2.0032 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4458   -1.6554    0.1369 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4751   -2.0233   -1.2218 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9842   -0.5859    0.6587 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1598    0.2028    0.5742 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2574   -0.8510    1.7846 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8977   -1.5546    0.2247 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1241    0.7201   -1.6090 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0771    2.5158   -2.9672 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9272    0.7691   -1.6273 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7118    0.2276   -0.6790 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0986    1.5550   -0.4088 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1370    2.3454    0.7171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7613    1.4100    2.1748 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3160    3.6032    0.9883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4327   -0.0293    0.3021 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8541   -1.1172   -1.6351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5013   -2.3031    0.4121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7117   -1.0413    2.3801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9123   -2.4502    0.7109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4020   -3.0167   -1.2606 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9557   -1.1330    1.5951 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  4  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
  7 20  2  0
 20  2  1  0
 18  9  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  3 24  1  0
  5 25  1  0
  6 26  1  0
  9 27  1  6
 11 28  1  6
 12 29  1  0
 12 30  1  0
 13 31  1  0
 14 32  1  6
 15 33  1  0
 16 34  1  1
 17 35  1  0
 18 36  1  1
 19 37  1  0
 20 38  1  0
M  END


  Mrv1652304282219392D          

 20 21  0  0  1  0            999 V2000
    2.8579   -1.6500    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
    2.1434   -2.8875    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
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   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
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5724   -5.3625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -6.1875    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
  6  7  1  0  0  0  0
  4  8  1  0  0  0  0
  2  9  1  0  0  0  0
 10  9  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 10 15  1  0  0  0  0
 15 16  1  1  0  0  0
 14 17  1  6  0  0  0
 13 18  1  1  0  0  0
 12 19  1  6  0  0  0
 19 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0072288

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=CC(O)=CC(O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C13H18O7/c1-6-2-7(15)4-8(3-6)19-13-12(18)11(17)10(16)9(5-14)20-13/h2-4,9-18H,5H2,1H3/t9-,10-,11+,12-,13-/m1/s1

> <INCHI_KEY>
YTXIGTCAQNODGD-UJPOAAIJSA-N

> <FORMULA>
C13H18O7

> <MOLECULAR_WEIGHT>
286.28

> <EXACT_MASS>
286.10525292

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
28.120756745439067

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,3R,4S,5S,6R)-2-(3-hydroxy-5-methylphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
-1.03

> <JCHEM_LOGP>
-0.38853153133333346

> <ALOGPS_LOGS>
-1.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.201030856744811

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.556790812059726

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810923437263277

> <JCHEM_POLAR_SURFACE_AREA>
119.61000000000001

> <JCHEM_REFRACTIVITY>
67.2054

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.37e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5S,6R)-2-(3-hydroxy-5-methylphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       8.002  -7.700   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       4.001 -10.010   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       6.668 -11.550   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       9.336 -10.010   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       9.336 -11.550   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    8                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    4                                                            
CONECT    9    2   10                                                       
CONECT   10    9   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   19                                                  
CONECT   13   12   14   18                                                  
CONECT   14   13   15   17                                                  
CONECT   15   14   10   16                                                  
CONECT   16   15                                                            
CONECT   17   14                                                            
CONECT   18   13                                                            
CONECT   19   12   20                                                       
CONECT   20   19                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₃H₁₈O₇

Average Mass

286.2800 Da

Monoisotopic Mass

286.10525 Da

IUPAC Name

(2S,3R,4S,5S,6R)-2-(3-hydroxy-5-methylphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

(2S,3R,4S,5S,6R)-2-(3-hydroxy-5-methylphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

CC1=CC(O)=CC(O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)=C1

InChI Identifier

InChI=1S/C13H18O7/c1-6-2-7(15)4-8(3-6)19-13-12(18)11(17)10(16)9(5-14)20-13/h2-4,9-18H,5H2,1H3/t9-,10-,11+,12-,13-/m1/s1

InChI Key

YTXIGTCAQNODGD-UJPOAAIJSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Curculigo orchioides	Plant	KNApSAcK
Helichrysum arenarium	LOTUS Database	35616633
Molineria capitulata	LOTUS Database	35616633
Rumex nepalensis	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Phenolic glycosides

Alternative Parents

Substituents

Phenolic glycoside
Hexose monosaccharide
O-glycosyl compound
Phenoxy compound
M-cresol
Phenol ether
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Toluene
Phenol
Monocyclic benzene moiety
Benzenoid
Monosaccharide
Oxane
Secondary alcohol
Acetal
Oxacycle
Organoheterocyclic compound
Polyol
Alcohol
Primary alcohol
Hydrocarbon derivative
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	ALOGPS
logP	-0.39	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	9.56	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	119.61 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	67.21 m³·mol⁻¹	ChemAxon
Polarizability	28.12 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00032097

Chemspider ID

22913150

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

12315192

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

He Y, Dong X, Jia X, Li M, Yuan T, Xu H, Qin L, Han T, Zhang Q: Qualitative and quantitative analysis on chemical constituents from Curculigo orchioides using ultra high performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry. J Pharm Biomed Anal. 2015 Jan;102:236-45. doi: 10.1016/j.jpba.2014.09.024. Epub 2014 Sep 28. [PubMed:25305598 ]
Shovo MARB, Tona MR, Mouah J, Islam F, Chowdhury MHU, Das T, Paul A, Agagunduz D, Rahman MM, Emran TB, Capasso R, Simal-Gandara J: Computational and Pharmacological Studies on the Antioxidant, Thrombolytic, Anti-Inflammatory, and Analgesic Activity of Molineria capitulata. Curr Issues Mol Biol. 2021 Jun 22;43(2):434-456. doi: 10.3390/cimb43020035. [PubMed:34206443 ]
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Showing NP-Card for (-)-Orcinol-3-O-beta-D-glycopyranoside (NP0072288)

MOL for NP0072288 ((-)-Orcinol-3-O-beta-D-glycopyranoside)

3D MOL for NP0072288 ((-)-Orcinol-3-O-beta-D-glycopyranoside)

3D SDF for NP0072288 ((-)-Orcinol-3-O-beta-D-glycopyranoside)

3D-SDF for NP0072288 ((-)-Orcinol-3-O-beta-D-glycopyranoside)

PDB for NP0072288 ((-)-Orcinol-3-O-beta-D-glycopyranoside)

3D PDB for NP0072288 ((-)-Orcinol-3-O-beta-D-glycopyranoside)

SMILES for NP0072288 ((-)-Orcinol-3-O-beta-D-glycopyranoside)

INCHI for NP0072288 ((-)-Orcinol-3-O-beta-D-glycopyranoside)

Structure for NP0072288 ((-)-Orcinol-3-O-beta-D-glycopyranoside)

3D Structure for NP0072288 ((-)-Orcinol-3-O-beta-D-glycopyranoside)