NP-MRD: Showing NP-Card for purine nucleoside (NP0153424)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

1.0

Created at

2022-09-02 10:04:41 UTC

Updated at

2022-09-02 10:04:41 UTC

NP-MRD ID

NP0153424

Secondary Accession Numbers

None

Natural Product Identification

Common Name

purine nucleoside

Description

purine nucleoside is found in Medicago sativa, Phellinus igniarius and Streptomyces yokosukanensis. It was first documented in 1953 (PMID: 13117878).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 30 32  0  0  0  0  0  0  0  0999 V2000
    4.5210    0.4943   -0.5363 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3020    1.1554   -0.4817 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2996    0.4519    0.3885 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1225    1.1980    0.3700 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1183    0.3638    0.8439 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1311    0.8057    0.3108 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4033    2.0866    0.0055 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6536    2.1687   -0.4699 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2016    0.9542   -0.4784 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4487    0.5041   -0.8673 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6939   -0.8090   -0.7479 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7519   -1.6460   -0.2659 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5362   -1.2053    0.1129 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2327    0.0966    0.0168 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4969   -1.0351    0.5187 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7533   -1.7517    1.7052 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8502   -0.8667   -0.1572 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6603   -1.9260    0.1795 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4817   -0.4230   -0.1939 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4962    2.1482   -0.0155 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9152    1.3247   -1.5142 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6997    0.3913    1.4065 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0812    0.5027    1.9460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7614    2.9614    0.1030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2117    1.1650   -1.2550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0345   -2.6939   -0.2027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2016   -1.6023   -0.0853 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5574   -1.4015    2.1651 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6990   -0.7681   -1.2515 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2077   -2.6441    0.6572 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0
  2  1  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
  5 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17  3  1  0
 14  6  1  0
 14  9  1  0
  3 22  1  1
  2 20  1  0
  2 21  1  0
  1 19  1  0
  5 23  1  1
  7 24  1  0
 10 25  1  0
 12 26  1  0
 15 27  1  6
 16 28  1  0
 17 29  1  6
 18 30  1  0
M  END


  Mrv0541 10101211232D          

 22 24  0  0  0  0            999 V2000
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -3.7149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -3.2299    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8838   -3.4849    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3687   -2.8174    0.0000 C   0  0  2  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
    0.8838   -2.1500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4820   -4.5353    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -4.2695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1937   -2.8174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -2.4049    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4991   -3.9515    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5351   -4.2326    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7432   -3.5525    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6986   -2.0209    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  2  0  0  0  0
  6  2  1  1  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  5  1  0  0  0  0
 10  8  1  0  0  0  0
 11  1  1  0  0  0  0
 11  3  2  0  0  0  0
 12  3  1  0  0  0  0
 12  9  2  0  0  0  0
 13  4  2  0  0  0  0
 13  5  1  0  0  0  0
 14  4  1  0  0  0  0
 14  9  1  0  0  0  0
 10 14  1  1  0  0  0
 15  2  1  0  0  0  0
  7 16  1  6  0  0  0
  8 17  1  6  0  0  0
 18  6  1  0  0  0  0
 18 10  1  0  0  0  0
  6 19  1  6  0  0  0
  7 20  1  1  0  0  0
  8 21  1  1  0  0  0
 10 22  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0153424

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]1(CO)O[C@@]([H])(N2C=NC3=CN=CN=C23)[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C10H12N4O4/c15-2-6-7(16)8(17)10(18-6)14-4-13-5-1-11-3-12-9(5)14/h1,3-4,6-8,10,15-17H,2H2/t6-,7-,8-,10-/m1/s1

> <INCHI_KEY>
MRWXACSTFXYYMV-FDDDBJFASA-N

> <FORMULA>
C10H12N4O4

> <MOLECULAR_WEIGHT>
252.2267

> <EXACT_MASS>
252.085854892

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
23.514367899578446

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.99

> <JCHEM_LOGP>
-1.8564954476666669

> <ALOGPS_LOGS>
-1.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.891226311459594

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.45400449058085

> <JCHEM_PKA_STRONGEST_BASIC>
3.774993845986062

> <JCHEM_POLAR_SURFACE_AREA>
113.52000000000001

> <JCHEM_REFRACTIVITY>
58.1817

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.68e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
purine nucleoside

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-OCT-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    5   11                                                       
CONECT    2    6   15                                                       
CONECT    3   11   12                                                       
CONECT    4   13   14                                                       
CONECT    5    1    9   13                                                  
CONECT    6    2    7   18   19                                             
CONECT    7    6    8   16   20                                             
CONECT    8    7   10   17   21                                             
CONECT    9    5   12   14                                                  
CONECT   10    8   14   18   22                                             
CONECT   11    1    3                                                       
CONECT   12    3    9                                                       
CONECT   13    4    5                                                       
CONECT   14    4    9   10                                                  
CONECT   15    2                                                            
CONECT   16    7                                                            
CONECT   17    8                                                            
CONECT   18    6   10                                                       
CONECT   19    6                                                            
CONECT   20    7                                                            
CONECT   21    8                                                            
CONECT   22   10                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

View in JSmol

Synonyms

Value	Source
N-D-Ribosylpurine	ChEBI
Purine nucleoside	ChEBI
Purine riboside	ChEBI
Purine ribonucleoside	Kegg
9-(beta-D-Ribofuranosyl)purine	MeSH
Purine-1-D-ribofuranoside	MeSH

Chemical Formula

C₁₀H₁₂N₄O₄

Average Mass

252.2267 Da

Monoisotopic Mass

252.08585 Da

IUPAC Name

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

Traditional Name

purine nucleoside

CAS Registry Number

Not Available

SMILES

[H][C@]1(CO)O[C@@]([H])(N2C=NC3=CN=CN=C23)[C@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C10H12N4O4/c15-2-6-7(16)8(17)10(18-6)14-4-13-5-1-11-3-12-9(5)14/h1,3-4,6-8,10,15-17H,2H2/t6-,7-,8-,10-/m1/s1

InChI Key

MRWXACSTFXYYMV-FDDDBJFASA-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
Medicago sativa	LOTUS Database	35616633
Phellinus igniarius	LOTUS Database	35616633
Streptomyces yokosukanensis	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
Pentose monosaccharide
Imidazopyrimidine
Purine
Monosaccharide
N-substituted imidazole
Pyrimidine
Heteroaromatic compound
Azole
Imidazole
Tetrahydrofuran
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Primary alcohol
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Alcohol
Organic oxygen compound
Hydrocarbon derivative
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

purine ribonucleoside (CHEBI:18255 )

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	-0.99	ALOGPS
logP	-1.9	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	12.45	ChemAxon
pKa (Strongest Basic)	3.77	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	113.52 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	58.18 m³·mol⁻¹	ChemAxon
Polarizability	23.51 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

DB04440

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00018685

Chemspider ID

Not Available

KEGG Compound ID

C15586

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

68368

PDB ID

Not Available

ChEBI ID

18255

Good Scents ID

Not Available

References

General References

BROWN GB, WELIKY VS: The synthesis of 9-beta-D-ribofuranosylpurine and the identity of nebularine. J Biol Chem. 1953 Oct;204(2):1019-24. [PubMed:13117878 ]
Rahman MS, Humayun MZ: Nebularine (9-2'-deoxy-beta-D-ribofuranosylpurine) has the template characteristics of adenine in vivo and in vitro. Mutat Res. 1997 Jul 3;377(2):263-8. doi: 10.1016/s0027-5107(97)00084-5. [PubMed:9247623 ]
LOTUS database [Link]

Showing NP-Card for purine nucleoside (NP0153424)

MOL for NP0153424 (purine nucleoside)

3D MOL for NP0153424 (purine nucleoside)

3D SDF for NP0153424 (purine nucleoside)

3D-SDF for NP0153424 (purine nucleoside)

PDB for NP0153424 (purine nucleoside)

3D PDB for NP0153424 (purine nucleoside)

SMILES for NP0153424 (purine nucleoside)

INCHI for NP0153424 (purine nucleoside)

Structure for NP0153424 (purine nucleoside)

3D Structure for NP0153424 (purine nucleoside)