NP-MRD: Showing NP-Card for vidarabine (NP0181883)

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Record Information

Version

2.0

Created at

2022-09-03 20:28:57 UTC

Updated at

2022-09-03 20:28:58 UTC

NP-MRD ID

NP0181883

Secondary Accession Numbers

None

Natural Product Identification

Common Name

vidarabine

Description

Vidarabine, also known as ara a or spongoadenosine, 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. A purine nucleoside in which adenine is attached to arabinofuranose via a beta-N(9)-glycosidic bond. Vidarabine is a drug which is used for treatment of chickenpox - varicella, herpes zoster and herpes simplex. vidarabine is found in Apis cerana, Daucus carota, Eunicella cavolini, Streptomyces herbaceus and Tillandsia usneoides. Vidarabine is a strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 34  0  0  0  0  0  0  0  0999 V2000
    5.3035   -0.5021   -0.9887 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2212   -0.2595   -0.1233 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3433   -0.2483    1.2103 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3026   -0.0159    2.0130 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0903    0.2157    1.4968 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8641    0.2253    0.1558 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9556   -0.0173   -0.6454 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4877    0.0431   -1.9199 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1718    0.3107   -1.8768 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7775    0.4249   -0.6053 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5226    0.7030   -0.0531 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9828   -0.3814    0.7259 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3205   -0.1652    0.9295 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0772   -1.4730    1.0636 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4258   -1.2444    1.2688 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8380    0.6766   -0.2089 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0767    1.9607    0.2834 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5981    0.7738   -1.1002 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5701   -0.3300   -1.9576 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2638   -1.2962   -1.6433 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1344    0.1541   -0.9331 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4057   -0.0076    3.0950 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5000    0.4235   -2.7394 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5692    1.5909    0.5716 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4278    0.3624    1.9127 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6482   -2.0231    1.9129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9852   -2.0734    0.1327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6145   -1.1451    2.2558 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6942    0.2457   -0.7326 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5429    2.5412   -0.3541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5780    1.6880   -1.6909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3497   -1.1572   -1.4549 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  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
  7  2  1  0
 18 11  1  0
 10  6  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  9 23  1  0
 11 24  1  1
 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
M  END

32326
  Mrv0541 02231214302D          

 19 21  0  0  1  0            999 V2000
    3.6940    3.6075    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6001    4.0236    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6576    5.4739    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1168    4.5794    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6526    2.5697    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6526    1.2419    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1575    2.7308    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4430    1.4933    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1575    0.2558    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4251    4.0222    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9089    3.3538    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9112    4.6888    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6954    4.4325    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.3637    4.9163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8720    2.3183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1341    1.9058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8720    1.4933    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1575    1.0808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4430    2.3183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 11  1  0  0  0  0
  1 13  1  0  0  0  0
 10  2  1  1  0  0  0
 12  3  1  6  0  0  0
  4 14  1  0  0  0  0
 11  5  1  1  0  0  0
  5 15  1  0  0  0  0
  5 16  1  0  0  0  0
  6 16  2  0  0  0  0
  6 17  1  0  0  0  0
  7 15  1  0  0  0  0
  7 19  2  0  0  0  0
  8 18  2  0  0  0  0
  8 19  1  0  0  0  0
  9 18  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
 15 17  2  0  0  0  0
 17 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0181883

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O

> <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-/m1/s1

> <INCHI_KEY>
OIRDTQYFTABQOQ-UHTZMRCNSA-N

> <FORMULA>
C10H13N5O4

> <MOLECULAR_WEIGHT>
267.2413

> <EXACT_MASS>
267.096753929

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
24.491812595571652

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.21

> <JCHEM_LOGP>
-2.0909638716666668

> <ALOGPS_LOGS>
-1.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.891216627250436

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.454003289052789

> <JCHEM_PKA_STRONGEST_BASIC>
4.9884408144871495

> <JCHEM_POLAR_SURFACE_AREA>
139.54

> <JCHEM_REFRACTIVITY>
63.1956

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.40e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
armes

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 32326                                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       6.895   6.734   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0       2.987   7.511   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       4.961  10.218   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       9.551   8.548   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       4.952   4.797   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       4.952   2.318   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0       2.161   5.097   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0       0.827   2.787   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0       2.161   0.477   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       4.527   7.508   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.430   6.260   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.434   8.752   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.898   8.274   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.146   9.177   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.494   4.327   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.850   3.557   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.494   2.787   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.161   2.017   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.827   4.327   0.000  0.00  0.00           C+0
CONECT    1   11   13                                                       
CONECT    2   10                                                            
CONECT    3   12                                                            
CONECT    4   14                                                            
CONECT    5   11   15   16                                                  
CONECT    6   16   17                                                       
CONECT    7   15   19                                                       
CONECT    8   18   19                                                       
CONECT    9   18                                                            
CONECT   10    2   11   12                                                  
CONECT   11    1    5   10                                                  
CONECT   12    3   10   13                                                  
CONECT   13    1   12   14                                                  
CONECT   14    4   13                                                       
CONECT   15    5    7   17                                                  
CONECT   16    5    6                                                       
CONECT   17    6   15   18                                                  
CONECT   18    8    9   17                                                  
CONECT   19    7    8                                                       
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

View in JSmol

Synonyms

Value	Source
2-(6-AMINO-purin-9-yl)-5-hydroxymethyl-tetrahydro-furan-3,4-diol	ChEBI
9-beta-D-Arabinofuranosyl-9H-purin-6-amine	ChEBI
9-beta-D-Arabinofuranosyladenine	ChEBI
Spongoadenosine	ChEBI
Vidarabine anhydrous	Kegg
ARA-a	Kegg
Armes	Kegg
9-b-D-Arabinofuranosyl-9H-purin-6-amine	Generator
9-Β-D-arabinofuranosyl-9H-purin-6-amine	Generator
9-b-D-Arabinofuranosyladenine	Generator
9-Β-D-arabinofuranosyladenine	Generator
9-beta-D-Arabinofuranosyl-adenine	HMDB
Adenine arabinoside	HMDB
Ara-ATP	HMDB
Araadenosine	HMDB
Arabinoside adenine	HMDB
Arabinosyl adenine	HMDB
Arabinosyladenine	HMDB
a, alpha-Ara	HMDB
Ara a	HMDB
Arabinofuranosyladenine	HMDB
Monarch brand OF vidarabine	HMDB
ViraA	HMDB
alpha Ara a	HMDB
alpha D Arabinofuranosyladenine	HMDB
alpha-Ara a	HMDB
9 beta Arabinofuranosyladenine	HMDB
9 beta D Arabinofuranosyladenine	HMDB
a, Ara	HMDB
beta Ara a	HMDB
Arabinoside, adenine	HMDB
alpha-D-Arabinofuranosyladenine	HMDB
9-beta-Arabinofuranosyladenine	HMDB
a, beta-Ara	HMDB
Parke davis brand OF vidarabine	HMDB
Vira a	HMDB
Vira-a	HMDB
beta-Ara a	HMDB
Vidarabine	ChEBI

Chemical Formula

C₁₀H₁₃N₅O₄

Average Mass

267.2413 Da

Monoisotopic Mass

267.09675 Da

IUPAC Name

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

Traditional Name

armes

CAS Registry Number

Not Available

SMILES

NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O

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-/m1/s1

InChI Key

OIRDTQYFTABQOQ-UHTZMRCNSA-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
Apis cerana	LOTUS Database	35616633
Daucus carota	LOTUS Database	35616633
Eunicella cavolini	LOTUS Database	35616633
Streptomyces herbaceus	LOTUS Database	35616633
Tillandsia usneoides	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

purine nucleoside (CHEBI:45327 )
beta-D-arabinoside (CHEBI:45327 )

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	-1.2	ALOGPS
logP	-2.1	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	12.45	ChemAxon
pKa (Strongest Basic)	4.99	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	139.54 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	63.2 m³·mol⁻¹	ChemAxon
Polarizability	24.49 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