NP-MRD: Showing NP-Card for (2r,3s,4r,5s)-2-(hydroxymethyl)-5-{4-imino-3h,5h-pyrrolo[3,2-d]pyrimidin-7-yl}oxolane-3,4-diol (NP0195311)

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Record Information

Version

2.0

Created at

2022-09-04 13:08:43 UTC

Updated at

2022-09-04 13:08:43 UTC

NP-MRD ID

NP0195311

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3s,4r,5s)-2-(hydroxymethyl)-5-{4-imino-3h,5h-pyrrolo[3,2-d]pyrimidin-7-yl}oxolane-3,4-diol

Description

9-Deazaadenosine, also known as C9ADO, belongs to the class of organic compounds known as c-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a C-glycosidic bond. (2r,3s,4r,5s)-2-(hydroxymethyl)-5-{4-imino-3h,5h-pyrrolo[3,2-d]pyrimidin-7-yl}oxolane-3,4-diol was first documented in 2008 (PMID: 18788044). Based on a literature review a small amount of articles have been published on 9-Deazaadenosine (PMID: 34781859) (PMID: 26467263) (PMID: 26398671) (PMID: 25710354).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 35  0  0  0  0  0  0  0  0999 V2000
    4.9301   -0.1675   -2.1214 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1246   -0.3860   -1.1405 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1706   -0.2929   -0.2610 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3592   -0.5656    1.0413 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3675   -0.4688    1.9534 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1360   -0.0877    1.5704 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8966    0.1943    0.2894 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7231    0.6033   -0.3410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5846    0.8293    0.2809 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0766   -0.3044    0.9247 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4482   -0.3187    0.7189 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0681   -1.6564    0.9886 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4395   -1.5426    0.7480 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5117    0.0525   -0.7538 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.7768    0.3239   -1.1980 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6397    1.3162   -0.6760 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4797    2.2728   -0.0544 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0622    0.7442   -1.6628 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3734    0.4366   -1.8251 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9044    0.0994   -0.6565 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3405   -0.8635    1.3120 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5905   -0.7062    2.9981 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5270    1.6123    1.0955 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8801    0.4988    1.2976 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9476   -1.9841    2.0345 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6862   -2.3895    0.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9607   -2.2682    1.1858 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9758   -0.7314   -1.3457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0792   -0.4811   -1.7276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2915    1.6486   -1.6460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9526    3.0834    0.1184 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4319    1.0467   -2.4859 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9149    0.4520   -2.7206 H   0  0  0  0  0  0  0  0  0  0  0  0
 13 12  1  0
 12 11  1  0
 11 10  1  0
 10  9  1  0
  9 16  1  0
 16 17  1  0
 16 14  1  0
 14 15  1  0
  9  8  1  0
  8 18  2  0
 18 19  1  0
 19 20  1  0
 20  7  2  0
  7  6  1  0
  6  5  2  0
  5  4  1  0
  4  3  1  0
  3  2  2  0
 14 11  1  0
  7  8  1  0
  3 20  1  0
 13 27  1  0
 12 25  1  0
 12 26  1  0
 11 24  1  1
  9 23  1  1
 16 30  1  6
 17 31  1  0
 14 28  1  6
 15 29  1  0
 18 32  1  0
 19 33  1  0
  5 22  1  0
  4 21  1  0
  2  1  1  0
M  END


  Mrv1652309042215082D          

 19 21  0  0  1  0            999 V2000
    3.2789    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249   -1.0396    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0098   -1.7070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249   -2.3744    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7798   -3.1591    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5868   -3.3306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7403   -2.1195    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0728   -2.6044    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7403   -1.2945    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0728   -0.8096    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   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  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  8  7  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  6  0  0  0
 11 12  1  0  0  0  0
 10 13  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  0  0  0  0
  8 15  1  0  0  0  0
 15 16  1  1  0  0  0
  7 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
  2 19  1  0  0  0  0
  6 19  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0195311

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C1=CNC2=C1N=CNC2=N

> <INCHI_IDENTIFIER>
InChI=1S/C11H14N4O4/c12-11-7-6(14-3-15-11)4(1-13-7)10-9(18)8(17)5(2-16)19-10/h1,3,5,8-10,13,16-18H,2H2,(H2,12,14,15)/t5-,8-,9-,10+/m1/s1

> <INCHI_KEY>
KEHFJRVBOUROMM-KBHCAIDQSA-N

> <FORMULA>
C11H14N4O4

> <MOLECULAR_WEIGHT>
266.257

> <EXACT_MASS>
266.101504947

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
25.89543553763285

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4R,5S)-2-(hydroxymethyl)-5-{4-imino-3H,4H,5H-pyrrolo[3,2-d]pyrimidin-7-yl}oxolane-3,4-diol

> <JCHEM_LOGP>
-2.2785974200000005

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.702023156548737

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.712992595219632

> <JCHEM_PKA_STRONGEST_BASIC>
5.254184162387003

> <JCHEM_POLAR_SURFACE_AREA>
133.95000000000002

> <JCHEM_REFRACTIVITY>
77.16350000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4R,5S)-2-(hydroxymethyl)-5-{4-imino-3H,5H-pyrrolo[3,2-d]pyrimidin-7-yl}oxolane-3,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  N   UNK     0       6.121   3.850   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       7.454   1.540   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       6.121  -0.770   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.322  -0.476   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.846  -1.941   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       3.752  -3.186   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.846  -4.432   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.322  -5.897   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       4.829  -6.217   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       1.382  -3.956   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       0.136  -4.862   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       1.382  -2.416   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.136  -1.511   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0       3.322   2.016   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   19                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   19                                                  
CONECT    7    6    8   17                                                  
CONECT    8    7    9   15                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   13                                                  
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13   10   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    8   16                                                  
CONECT   16   15                                                            
CONECT   17    7   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18    2    6                                                  
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

View in JSmol

Synonyms

Value	Source
C9Ado	MeSH

Chemical Formula

C₁₁H₁₄N₄O₄

Average Mass

266.2570 Da

Monoisotopic Mass

266.10150 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C1=CNC2=C1N=CNC2=N

InChI Identifier

InChI=1S/C11H14N4O4/c12-11-7-6(14-3-15-11)4(1-13-7)10-9(18)8(17)5(2-16)19-10/h1,3,5,8-10,13,16-18H,2H2,(H2,12,14,15)/t5-,8-,9-,10+/m1/s1

InChI Key

KEHFJRVBOUROMM-KBHCAIDQSA-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 c-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a C-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

C-glycosyl compounds

Alternative Parents

Substituents

C-glycosyl compound
Pentose monosaccharide
Pyrrolopyrimidine
Aminopyrimidine
Monosaccharide
Pyrimidine
Imidolactam
Substituted pyrrole
Heteroaromatic compound
Pyrrole
Tetrahydrofuran
Secondary alcohol
Dialkyl ether
Ether
Oxacycle
Azacycle
Organoheterocyclic compound
Organonitrogen compound
Hydrocarbon derivative
Amine
Alcohol
Organic nitrogen compound
Primary alcohol
Primary amine
Organopnictogen compound
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	-2.3	ChemAxon
pKa (Strongest Acidic)	9.71	ChemAxon
pKa (Strongest Basic)	5.25	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00018714

Chemspider ID

432618

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

494271

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Haraguchi K, Kumamoto H, Tanaka H: 4-Thiofuranoid Glycal: Versatile Glycosyl Donor for the Selective Synthesis of beta-anomer of 4'-thionucleoside and its Biological Activities. Curr Med Chem. 2022;29(21):3684-3731. doi: 10.2174/0929867328666211115121434. [PubMed:34781859 ]
Kim S, Hong JH: Synthesis and Biological Evaluation of 9-Deazaadenine 5'-Deoxy-6',6'-Difluoro-Carbocyclic C-Nucleoside Phosphonic Acid Derivatives. Nucleosides Nucleotides Nucleic Acids. 2015;34(10):708-28. doi: 10.1080/15257770.2015.1071847. Epub 2015 Oct 15. [PubMed:26467263 ]
Kim E, Hong JH: Synthesis and potent anti-leukemic activity of novel 5'-deoxycarbocyclic C-nucleoside phosphonic acids. Nucleosides Nucleotides Nucleic Acids. 2015;34(11):737-52. doi: 10.1080/15257770.2015.1072636. Epub 2015 Sep 23. [PubMed:26398671 ]
Kim S, Kim E, Hong JH: The first synthesis of 4'-branched 5'-deoxycarbocyclic 9-deazaadenosine and phosphonic acids as antiviral agents. Nucleosides Nucleotides Nucleic Acids. 2015;34(3):163-79. doi: 10.1080/15257770.2014.975245. [PubMed:25710354 ]
Oh CH, Liu LJ, Hong JH: First synthesis and anti-HIV evaluation of 4'-methyl-cyclopentanyl 9-deazaadenosine. Nucleosides Nucleotides Nucleic Acids. 2008 Oct;27(10):1144-52. doi: 10.1080/15257770802341392. [PubMed:18788044 ]
LOTUS database [Link]

Showing NP-Card for (2r,3s,4r,5s)-2-(hydroxymethyl)-5-{4-imino-3h,5h-pyrrolo[3,2-d]pyrimidin-7-yl}oxolane-3,4-diol (NP0195311)

MOL for NP0195311 ((2r,3s,4r,5s)-2-(hydroxymethyl)-5-{4-imino-3h,5h-pyrrolo[3,2-d]pyrimidin-7-yl}oxolane-3,4-diol)

3D MOL for NP0195311 ((2r,3s,4r,5s)-2-(hydroxymethyl)-5-{4-imino-3h,5h-pyrrolo[3,2-d]pyrimidin-7-yl}oxolane-3,4-diol)

3D SDF for NP0195311 ((2r,3s,4r,5s)-2-(hydroxymethyl)-5-{4-imino-3h,5h-pyrrolo[3,2-d]pyrimidin-7-yl}oxolane-3,4-diol)

3D-SDF for NP0195311 ((2r,3s,4r,5s)-2-(hydroxymethyl)-5-{4-imino-3h,5h-pyrrolo[3,2-d]pyrimidin-7-yl}oxolane-3,4-diol)

PDB for NP0195311 ((2r,3s,4r,5s)-2-(hydroxymethyl)-5-{4-imino-3h,5h-pyrrolo[3,2-d]pyrimidin-7-yl}oxolane-3,4-diol)

3D PDB for NP0195311 ((2r,3s,4r,5s)-2-(hydroxymethyl)-5-{4-imino-3h,5h-pyrrolo[3,2-d]pyrimidin-7-yl}oxolane-3,4-diol)

SMILES for NP0195311 ((2r,3s,4r,5s)-2-(hydroxymethyl)-5-{4-imino-3h,5h-pyrrolo[3,2-d]pyrimidin-7-yl}oxolane-3,4-diol)

INCHI for NP0195311 ((2r,3s,4r,5s)-2-(hydroxymethyl)-5-{4-imino-3h,5h-pyrrolo[3,2-d]pyrimidin-7-yl}oxolane-3,4-diol)

Structure for NP0195311 ((2r,3s,4r,5s)-2-(hydroxymethyl)-5-{4-imino-3h,5h-pyrrolo[3,2-d]pyrimidin-7-yl}oxolane-3,4-diol)

3D Structure for NP0195311 ((2r,3s,4r,5s)-2-(hydroxymethyl)-5-{4-imino-3h,5h-pyrrolo[3,2-d]pyrimidin-7-yl}oxolane-3,4-diol)