NP-MRD: Showing NP-Card for (2r,3r,4s,5r)-2-(6-amino-2-methoxypurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol (NP0271655)

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Record Information

Version

2.0

Created at

2022-09-08 18:01:28 UTC

Updated at

2022-09-08 18:01:28 UTC

NP-MRD ID

NP0271655

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3r,4s,5r)-2-(6-amino-2-methoxypurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol

Description

Spongosine belongs to the class of organic compounds known as purine nucleosides. Purine nucleosides are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety. (2r,3r,4s,5r)-2-(6-amino-2-methoxypurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol was first documented in 2011 (PMID: 21534931). Based on a literature review very few articles have been published on Spongosine (PMID: 25668560).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 38  0  0  0  0  0  0  0  0999 V2000
    5.2062    0.1151    2.1549 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8437    0.4322    2.1040 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0902    0.2263    0.9462 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7061   -0.2889   -0.1328 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0166   -0.5041   -1.2716 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6488   -1.0428   -2.4083 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6907   -0.1852   -1.2905 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7653   -0.2813   -2.2480 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4368    0.1671   -1.7929 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2657    0.5548   -0.5196 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2627    1.0941    0.3536 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6635    0.2364    1.3479 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7822   -0.4435    0.9328 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3454   -1.8808    0.6357 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4036   -2.6503    0.2087 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3392    0.2271   -0.2762 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.6878    0.5465   -0.1573 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5267    1.4816   -0.3842 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1742    2.4862    0.3222 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0204    0.3522   -0.1853 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7816    0.5355    0.9114 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.5441   -0.4757    1.2548 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3856   -0.5092    3.0548 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8634    1.0067    2.2199 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2887   -0.4603   -2.9646 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4695   -2.0184   -2.6808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3088    0.1712   -2.4145 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9137    2.0380    0.8649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5758   -0.4690    1.7069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4715   -1.8960   -0.0359 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9934   -2.3199    1.6035 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1860   -2.1182   -0.0835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2398   -0.4543   -1.1340 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8396    1.5270   -0.1133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3329    1.7934   -1.4249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5717    3.0064    0.8960 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  5  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 13 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 10 20  1  0
 20 21  2  0
 21  3  1  0
 20  7  1  0
 18 11  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  6 25  1  0
  6 26  1  0
  9 27  1  0
 11 28  1  1
 13 29  1  1
 14 30  1  0
 14 31  1  0
 15 32  1  0
 16 33  1  6
 17 34  1  0
 18 35  1  6
 19 36  1  0
M  END


  Mrv1652309082220012D          

 21 23  0  0  1  0            999 V2000
    4.7812    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    2.3479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -0.1271    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    2.9750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0992    3.2299    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992    4.0549    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5683    4.5399    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3220    4.2043    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    4.3099    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1387    5.0945    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3687    3.6424    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1937    3.6424    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  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  1  0  0  0  0
  5  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 11 10  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  6  0  0  0
 14 15  1  0  0  0  0
 13 16  1  0  0  0  0
 16 17  1  1  0  0  0
 16 18  1  0  0  0  0
 11 18  1  0  0  0  0
 18 19  1  1  0  0  0
 10 20  1  0  0  0  0
  7 20  1  0  0  0  0
 20 21  2  0  0  0  0
  3 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0271655

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=NC(N)=C2N=CN([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)C2=N1

> <INCHI_IDENTIFIER>
InChI=1S/C11H15N5O5/c1-20-11-14-8(12)5-9(15-11)16(3-13-5)10-7(19)6(18)4(2-17)21-10/h3-4,6-7,10,17-19H,2H2,1H3,(H2,12,14,15)/t4-,6-,7-,10-/m1/s1

> <INCHI_KEY>
AJACDNCVEGIBNA-KQYNXXCUSA-N

> <FORMULA>
C11H15N5O5

> <MOLECULAR_WEIGHT>
297.271

> <EXACT_MASS>
297.107318603

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
28.368656310176938

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5R)-2-(6-amino-2-methoxy-9H-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol

> <JCHEM_LOGP>
-1.5698491153333332

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.891193118946578

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.454001083601781

> <JCHEM_PKA_STRONGEST_BASIC>
3.2552885845364843

> <JCHEM_POLAR_SURFACE_AREA>
148.77000000000004

> <JCHEM_REFRACTIVITY>
69.6048

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S,5R)-2-(6-amino-2-methoxypurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0       8.925   3.613   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       7.591   4.383   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       6.258   2.073   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       4.924  -0.237   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       2.126   1.597   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       1.650   5.553   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       0.185   6.029   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.185   7.569   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.061   8.474   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -2.468   7.848   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       1.650   8.045   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       2.126   9.510   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       2.555   6.799   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       4.095   6.799   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       4.924   4.383   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   21                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   20                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   20                                                  
CONECT   11   10   12   18                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16   13   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   11   19                                                  
CONECT   19   18                                                            
CONECT   20   10    7   21                                                  
CONECT   21   20    3                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₁₅N₅O₅

Average Mass

297.2710 Da

Monoisotopic Mass

297.10732 Da

IUPAC Name

(2R,3R,4S,5R)-2-(6-amino-2-methoxy-9H-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol

Traditional Name

(2R,3R,4S,5R)-2-(6-amino-2-methoxypurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol

CAS Registry Number

Not Available

SMILES

COC1=NC(N)=C2N=CN([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)C2=N1

InChI Identifier

InChI=1S/C11H15N5O5/c1-20-11-14-8(12)5-9(15-11)16(3-13-5)10-7(19)6(18)4(2-17)21-10/h3-4,6-7,10,17-19H,2H2,1H3,(H2,12,14,15)/t4-,6-,7-,10-/m1/s1

InChI Key

AJACDNCVEGIBNA-KQYNXXCUSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine nucleosides. Purine nucleosides are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleosides

Sub Class

Not Available

Direct Parent

Purine nucleosides

Alternative Parents

Substituents

Purine nucleoside
Glycosyl compound
N-glycosyl compound
6-aminopurine
Pentose monosaccharide
Imidazopyrimidine
Purine
Alkyl aryl ether
Aminopyrimidine
Monosaccharide
N-substituted imidazole
Imidolactam
Pyrimidine
Oxolane
Azole
Heteroaromatic compound
Imidazole
Secondary alcohol
Organoheterocyclic compound
Ether
Oxacycle
Azacycle
Amine
Organic nitrogen compound
Alcohol
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Primary amine
Organic oxygen compound
Primary alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	-1.6	ChemAxon
pKa (Strongest Acidic)	12.45	ChemAxon
pKa (Strongest Basic)	3.26	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	148.77 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	69.6 m³·mol⁻¹	ChemAxon
Polarizability	28.37 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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

Not Available

Chemspider ID

7971993

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9796227

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Bertin MJ, Schwartz SL, Lee J, Korobeynikov A, Dorrestein PC, Gerwick L, Gerwick WH: Spongosine production by a Vibrio harveyi strain associated with the sponge Tectitethya crypta. J Nat Prod. 2015 Mar 27;78(3):493-9. doi: 10.1021/np5009762. Epub 2015 Feb 10. [PubMed:25668560 ]
Ebada SS, Proksch P: Chemical and pharmacological significance of natural guanidines from marine invertebrates. Mini Rev Med Chem. 2011 Mar;11(3):225-46. doi: 10.2174/138955711795049862. [PubMed:21534931 ]
LOTUS database [Link]

Showing NP-Card for (2r,3r,4s,5r)-2-(6-amino-2-methoxypurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol (NP0271655)

MOL for NP0271655 ((2r,3r,4s,5r)-2-(6-amino-2-methoxypurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

3D MOL for NP0271655 ((2r,3r,4s,5r)-2-(6-amino-2-methoxypurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

3D SDF for NP0271655 ((2r,3r,4s,5r)-2-(6-amino-2-methoxypurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

3D-SDF for NP0271655 ((2r,3r,4s,5r)-2-(6-amino-2-methoxypurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

PDB for NP0271655 ((2r,3r,4s,5r)-2-(6-amino-2-methoxypurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

3D PDB for NP0271655 ((2r,3r,4s,5r)-2-(6-amino-2-methoxypurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

SMILES for NP0271655 ((2r,3r,4s,5r)-2-(6-amino-2-methoxypurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

INCHI for NP0271655 ((2r,3r,4s,5r)-2-(6-amino-2-methoxypurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

Structure for NP0271655 ((2r,3r,4s,5r)-2-(6-amino-2-methoxypurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

3D Structure for NP0271655 ((2r,3r,4s,5r)-2-(6-amino-2-methoxypurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)