NP-MRD: Showing NP-Card for (2r,3s,4r,5s)-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol (NP0263874)

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Record Information

Version

2.0

Created at

2022-09-08 07:12:11 UTC

Updated at

2022-09-08 07:12:11 UTC

NP-MRD ID

NP0263874

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

Lopac-A-9251 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,3s,4r,5s)-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol is found in Acanthus ebracteatus, Acanthus ilicifolius, Allium tuberosum, Arabidopsis thaliana, Atractylodes lancea, Cassytha filiformis, Codonopsis pilosula, Crocus sativus, Cucumis sativus, Dioscorea oppositifolia, Gastrodia elata, Junceella juncea, Oxytropis myriophylla, Strychnos lucida, Subergorgia suberosa and Zea mays. Based on a literature review very few articles have been published on Lopac-A-9251.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 34  0  0  0  0  0  0  0  0999 V2000
    5.3176    0.1571    0.4248 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1207    0.0642   -0.3295 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1447   -0.1244   -1.6629 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0283   -0.2176   -2.4132 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8218   -0.1207   -1.8245 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7049    0.0668   -0.5068 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8646    0.1596    0.2441 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4760    0.3417    1.5014 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1298    0.3615    1.5328 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6218    0.1928    0.2973 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7752    0.1535   -0.0940 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5558    0.9556    0.7385 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8556    0.5273    0.6128 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4562    1.1724   -0.6059 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3910    2.5672   -0.3907 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7479   -0.9539    0.5267 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8000   -1.4763    1.8243 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3565   -1.2369   -0.0051 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6153   -2.0272    0.8506 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0183    0.8838    0.1806 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4892   -0.4941    1.2110 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1227   -0.3722   -3.4993 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4817    0.4933    2.4132 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9294    0.5007   -1.1342 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4351    0.8728    1.4928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5076    0.9000   -0.7806 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8819    0.9834   -1.5300 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0623    3.0467   -1.1675 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5365   -1.4328   -0.0833 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9837   -1.2788    2.3391 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4405   -1.7303   -1.0035 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0116   -2.9353    0.8413 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  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  6  1  0
  6  5  2  0
  5  4  1  0
  4  3  2  0
  3  2  1  0
  6  7  1  0
 18 11  1  0
  1 20  1  0
  1 21  1  0
  9 23  1  0
 11 24  1  6
 13 25  1  1
 14 26  1  0
 14 27  1  0
 15 28  1  0
 16 29  1  6
 17 30  1  0
 18 31  1  6
 19 32  1  0
  4 22  1  0
M  END


  Mrv1652309082209122D          

 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
    2.5645    0.8250    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
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 N   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  1  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  2  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  2  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  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  2  0  0  0  0
  6  7  1  0  0  0  0
  2  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
  6 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  1  0  0  0
 14 15  1  0  0  0  0
 13 16  1  0  0  0  0
 16 17  1  6  0  0  0
 16 18  1  0  0  0  0
 11 18  1  0  0  0  0
 18 19  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0263874

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=C2N=CN([C@@H]3O[C@@H](CO)[C@H](O)[C@@H]3O)C2=NC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6-,7-,10+/m0/s1

> <INCHI_KEY>
OIRDTQYFTABQOQ-SXVXDFOESA-N

> <FORMULA>
C10H13N5O4

> <MOLECULAR_WEIGHT>
267.245

> <EXACT_MASS>
267.096753919

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
25.028070044136815

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-2.0909638716666668

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.891216626641981

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.45400327595609

> <JCHEM_PKA_STRONGEST_BASIC>
3.921276940416587

> <JCHEM_POLAR_SURFACE_AREA>
139.54000000000002

> <JCHEM_REFRACTIVITY>
63.195600000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4R,5S)-2-(6-aminopurin-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  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       4.787   1.540   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       3.322   2.016   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       3.322  -0.476   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       2.846  -1.941   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       3.752  -3.186   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       2.846  -4.432   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.322  -5.897   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       4.829  -6.217   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       1.382  -3.956   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       0.136  -4.862   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       1.382  -2.416   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       0.136  -1.511   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   10                                                  
CONECT    7    6    2    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    6   11                                                  
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                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₁₃N₅O₄

Average Mass

267.2450 Da

Monoisotopic Mass

267.09675 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

NC1=C2N=CN([C@@H]3O[C@@H](CO)[C@H](O)[C@@H]3O)C2=NC=N1

InChI Identifier

InChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6-,7-,10+/m0/s1

InChI Key

OIRDTQYFTABQOQ-SXVXDFOESA-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

Species Name	Source	Reference
Acanthus ebracteatus	LOTUS Database	35616633
Acanthus ilicifolius	LOTUS Database	35616633
Allium tuberosum	LOTUS Database	35616633
Arabidopsis thaliana	LOTUS Database	35616633
Atractylodes lancea	LOTUS Database	35616633
Cassytha filiformis	LOTUS Database	35616633
Codonopsis pilosula	LOTUS Database	35616633
Crocus sativus	LOTUS Database	35616633
Cucumis sativus	LOTUS Database	35616633
Dioscorea oppositifolia	LOTUS Database	35616633
Gastrodia elata	LOTUS Database	35616633
Junceella juncea	LOTUS Database	35616633
Oxytropis myriophylla	LOTUS Database	35616633
Strychnos lucida	LOTUS Database	35616633
Subergorgia suberosa	LOTUS Database	35616633
Zea mays	LOTUS Database	35616633

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
Aminopyrimidine
Monosaccharide
N-substituted imidazole
Pyrimidine
Imidolactam
Tetrahydrofuran
Azole
Imidazole
Heteroaromatic compound
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Organic oxygen compound
Organic nitrogen compound
Alcohol
Organonitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Organooxygen compound
Amine
Primary alcohol
Primary amine
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

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

395197

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

448378

PDB ID

Not Available

ChEBI ID

140569

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2r,3s,4r,5s)-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol (NP0263874)

MOL for NP0263874 ((2r,3s,4r,5s)-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

3D MOL for NP0263874 ((2r,3s,4r,5s)-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

3D SDF for NP0263874 ((2r,3s,4r,5s)-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

3D-SDF for NP0263874 ((2r,3s,4r,5s)-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

PDB for NP0263874 ((2r,3s,4r,5s)-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

3D PDB for NP0263874 ((2r,3s,4r,5s)-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

SMILES for NP0263874 ((2r,3s,4r,5s)-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

INCHI for NP0263874 ((2r,3s,4r,5s)-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

Structure for NP0263874 ((2r,3s,4r,5s)-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

3D Structure for NP0263874 ((2r,3s,4r,5s)-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)