NP-MRD: Showing NP-Card for (2s,3r,4s,5s)-2-(6-hydroxy-2-imino-3h-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol (NP0203663)

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Record Information

Version

2.0

Created at

2022-09-04 23:10:48 UTC

Updated at

2022-09-04 23:10:48 UTC

NP-MRD ID

NP0203663

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3r,4s,5s)-2-(6-hydroxy-2-imino-3h-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol

Description

(2S,3R,4S,5S)-2-(6-hydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol 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. (2s,3r,4s,5s)-2-(6-hydroxy-2-imino-3h-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol is found in Sauropus androgynus, Sinocrassula indica, Subergorgia suberosa and Zea mays. Based on a literature review very few articles have been published on (2S,3R,4S,5S)-2-(6-hydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 35  0  0  0  0  0  0  0  0999 V2000
   -4.1726    1.6031    2.3774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2139    1.3746    2.0404 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0016    0.7037    0.9688 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0690    0.2872    0.2655 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9036   -0.4219   -0.8690 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9906   -0.8572   -1.6032 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6175   -0.6889   -1.2576 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1234   -1.3564   -2.3149 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7951   -1.3416   -2.2492 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3859   -0.6633   -1.1459 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9790   -0.4630   -0.7808 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2653    0.8842   -0.4670 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5816    0.7412    0.0078 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1050    2.0423    0.5639 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0809    2.9811   -0.4592 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3623   -0.2908    1.1094 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6522    0.3367    2.1128 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4183   -1.2639    0.4162 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3846   -1.6620    1.2264 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5040   -0.2670   -0.5441 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7325    0.4308    0.5702 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9826   -1.6617   -2.2056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1450   -1.8065   -2.9758 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6607   -0.7167   -1.6188 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2734    0.3869   -0.7682 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5586    2.3789    1.4506 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1722    1.8754    0.8184 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1592    2.5945   -1.3540 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2945   -0.7637    1.4354 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2893   -0.3474    2.7182 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9979   -2.1695    0.1162 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3048   -2.6480    1.2758 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9022    0.7690    1.1401 H   0  0  0  0  0  0  0  0  0  0  0  0
 15 14  1  0
 14 13  1  0
 13 12  1  0
 12 11  1  0
 11 18  1  0
 18 19  1  0
 18 16  1  0
 16 17  1  0
 11 10  1  0
 10  9  1  0
  9  8  2  0
  8  7  1  0
  7 20  2  0
 20 21  1  0
 21  3  1  0
  3  2  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
 16 13  1  0
 20 10  1  0
  5  7  1  0
 15 28  1  0
 14 26  1  0
 14 27  1  0
 13 25  1  6
 11 24  1  6
 18 31  1  6
 19 32  1  0
 16 29  1  1
 17 30  1  0
  9 23  1  0
 21 33  1  0
  2  1  1  0
  6 22  1  0
M  END


  Mrv1652309052201102D          

 20 22  0  0  1  0            999 V2000
    4.0668    2.3479    0.0000 N   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 O   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  1  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  1  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  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
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  1  0  0  0
 13 14  1  0  0  0  0
 12 15  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  0  0  0  0
 10 17  1  0  0  0  0
 17 18  1  1  0  0  0
  9 19  1  0  0  0  0
  6 19  2  0  0  0  0
 19 20  1  0  0  0  0
  2 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0203663

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@@H]1O[C@@H]([C@H](O)[C@@H]1O)N1C=NC2=C1NC(=N)N=C2O

> <INCHI_IDENTIFIER>
InChI=1S/C10H13N5O5/c11-10-13-7-4(8(19)14-10)12-2-15(7)9-6(18)5(17)3(1-16)20-9/h2-3,5-6,9,16-18H,1H2,(H3,11,13,14,19)/t3-,5+,6+,9-/m0/s1

> <INCHI_KEY>
NYHBQMYGNKIUIF-PXMDKTAGSA-N

> <FORMULA>
C10H13N5O5

> <MOLECULAR_WEIGHT>
283.244

> <EXACT_MASS>
283.091668539

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
25.872278660608757

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-2.009869935

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.362468028200354

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.9781416348512435

> <JCHEM_PKA_STRONGEST_BASIC>
2.963918293515141

> <JCHEM_POLAR_SURFACE_AREA>
156.21

> <JCHEM_REFRACTIVITY>
75.2022

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  N   UNK     0       7.591   4.383   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       6.258   2.073   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.924  -0.237   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       2.126   1.597   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       1.650   5.553   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.185   6.029   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.185   7.569   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.061   8.474   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -2.468   7.848   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       1.650   8.045   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       2.126   9.510   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       2.555   6.799   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.095   6.799   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0       4.924   4.383   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   20                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   19                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   19                                                  
CONECT   10    9   11   17                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15   12   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   10   18                                                  
CONECT   18   17                                                            
CONECT   19    9    6   20                                                  
CONECT   20   19    2                                                       
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₁₃N₅O₅

Average Mass

283.2440 Da

Monoisotopic Mass

283.09167 Da

IUPAC Name

(2S,3R,4S,5S)-2-(6-hydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol

Traditional Name

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

CAS Registry Number

Not Available

SMILES

OC[C@@H]1O[C@@H]([C@H](O)[C@@H]1O)N1C=NC2=C1NC(=N)N=C2O

InChI Identifier

InChI=1S/C10H13N5O5/c11-10-13-7-4(8(19)14-10)12-2-15(7)9-6(18)5(17)3(1-16)20-9/h2-3,5-6,9,16-18H,1H2,(H3,11,13,14,19)/t3-,5+,6+,9-/m0/s1

InChI Key

NYHBQMYGNKIUIF-PXMDKTAGSA-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
Sauropus androgynus	LOTUS Database	35616633
Sinocrassula indica	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-oxopurine
Pentose monosaccharide
Hypoxanthine
Purinone
Imidazopyrimidine
Purine
Aminopyrimidine
Pyrimidone
N-substituted imidazole
Monosaccharide
Primary aromatic amine
Pyrimidine
Oxolane
Vinylogous amide
Imidazole
Heteroaromatic compound
Azole
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Primary amine
Amine
Alcohol
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Primary alcohol
Organonitrogen compound
Organooxygen 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	ChemAxon
pKa (Strongest Acidic)	5.98	ChemAxon
pKa (Strongest Basic)	2.96	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	156.21 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	75.2 m³·mol⁻¹	ChemAxon
Polarizability	25.87 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

5415634

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

7059425

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s,3r,4s,5s)-2-(6-hydroxy-2-imino-3h-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol (NP0203663)

MOL for NP0203663 ((2s,3r,4s,5s)-2-(6-hydroxy-2-imino-3h-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

3D MOL for NP0203663 ((2s,3r,4s,5s)-2-(6-hydroxy-2-imino-3h-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

3D SDF for NP0203663 ((2s,3r,4s,5s)-2-(6-hydroxy-2-imino-3h-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

3D-SDF for NP0203663 ((2s,3r,4s,5s)-2-(6-hydroxy-2-imino-3h-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

PDB for NP0203663 ((2s,3r,4s,5s)-2-(6-hydroxy-2-imino-3h-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

3D PDB for NP0203663 ((2s,3r,4s,5s)-2-(6-hydroxy-2-imino-3h-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

SMILES for NP0203663 ((2s,3r,4s,5s)-2-(6-hydroxy-2-imino-3h-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

INCHI for NP0203663 ((2s,3r,4s,5s)-2-(6-hydroxy-2-imino-3h-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

Structure for NP0203663 ((2s,3r,4s,5s)-2-(6-hydroxy-2-imino-3h-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)

3D Structure for NP0203663 ((2s,3r,4s,5s)-2-(6-hydroxy-2-imino-3h-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol)