Vidarabine (CED0005896)

Record Information

Version

1.0

Creation Date

2016-05-25 18:18:56 UTC

Update Date

2026-05-14 16:24:36 UTC

Accession Number

CHEM022064

Identification

Common Name

Vidarabine

Class

Small Molecule

Description

Vidarabine belongs to the purine nucleosides, a class of nucleosides, nucleotides, and analogues within the organic compounds. This compound has the chemical formula C10H13N5O4 and an average molecular weight of 267.24 g/mol. The substance is found in or released from 12 recorded sources. These sources include healthcare, pharmaceuticals, and veterinary products, specifically antivirals and antiinfectives. It is also associated with electrical and electronic equipment, such as antennas, amplifiers, and adjustable resistors, as well as building and construction materials, including ladders, roofs, floors, ceilings, sunshades awnings or outside screens, and two additional sources. The recorded route of exposure for this compound is topical. Vidarabine interacts with three recorded protein targets. It acts as an inducer, inhibitor, or modulator of the DNA polymerase catalytic subunit. Additionally, it targets thymidine kinase (TK) and the adenosine receptor A2b (ADORA2B).

Contaminant Type

Not Available

Chemical Structure

MOL SDF PDB SMILES InChI

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
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 Molecular Mass

267.241 g/mol

Monoisotopic Mass

267.097 g/mol

CAS Registry Number

24356-66-9

IUPAC Name

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

Traditional Name

armes

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

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 )

Biological Properties

Status

Detected and Not Quantified

Origin

Not Available

Cellular Locations

Not Available

Biofluid Locations

Not Available

Tissue Locations

Not Available

Applications

Not Available

Biological Roles

Not Available

Chemical Roles

Not Available

Organoleptic Effects

Not Available

Physical Properties

State

Not Available

Appearance

Not Available

Experimental Properties

Property	Value
Melting Point	Not Available
Boiling Point	Not Available
Solubility	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	14 g/L	ALOGPS
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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum	splash10-0a4l-9350000000-ed8639e5b54e46825628	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	splash10-014i-1492400000-1fe7f0d7ca11fdb4800f	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-000i-2910000000-e18a8d00eb0e73aa6dec	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-000i-2910000000-e18a8d00eb0e73aa6dec	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-000i-0940000000-42bee9785f9b55b32eea	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-000i-0900000000-c8cda6a661ace060572c	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-000i-2900000000-0304a85c3951aa1cb41a	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-0159-0690000000-0258e5851611884483d9	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-001i-0900000000-e6b8fc6980387f646d64	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-053r-2900000000-1e0cad8d044715d90f12	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-001i-0910000000-83e24e24fe97518d665a	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-001i-0900000000-291c06f7d909185dce29	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-053r-1900000000-1401974aef47ea042a5c	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-000i-0920000000-c89adfa0ec9ccc01f131	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-000i-0900000000-c1ee2199364d0258bae1	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-000i-1900000000-fd986996dd15b2469008	Not Available	View Spectrum
1D NMR	¹H NMR Spectrum (1D, D₂O, predicted)	Not Available	Not Available	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, D₂O, predicted)	Not Available	Not Available	View Spectrum

Toxicity Profile

Mechanism of Toxicity

Not Available

Carcinogenicity (IARC Classification)

Not Available

Minimum Risk Level

Not Available

Symptoms

Not Available

Treatment

Not Available

Toxicity Values

Toxicity Value	Unit	Value Range	Organism	Dose Descriptor	Route of Exposure	Predicted or Experimental	Reference
953.0	Log mg/kg	[540:1700]	Rat	LD50	oral	predicted	Not Available

Health Effects

Health Effect	Relationship	Direction	Reference

Exposure Sources

Source ID	Source	Sector	Reference
351	Antivirals	Healthcare, pharmaceuticals & veterinary products	Not Available
395	Antiinfectives	Healthcare, pharmaceuticals & veterinary products	Not Available
495	Ceilings	Building & Construction	Not Available
497	Floors	Building & Construction	Not Available
498	Ladders	Building & Construction	Not Available
499	Roofs	Building & Construction	Not Available
501	Sunshades Awnings Or Outside Screens	Building & Construction	Not Available
502	Sunshades Awnings Or Outside Screens	Building & Construction	Not Available
503	Tents Or Canopies	Building & Construction	Not Available
504	Adjustable Resistors	Electrical & Electronic Equipment	Not Available
505	Amplifiers	Electrical & Electronic Equipment	Not Available
506	Antennas	Electrical & Electronic Equipment	Not Available

Pathways

0 pathways

No pathways found

No metabolic pathways have been associated with this synthetic chemical

Targets

Structure	Protein	UniProt ID	Organism	Relationship	Details
Click to view 3D structure	Adenosine receptor A2a	P30543	Rattus norvegicus	Predicted (SEA)	0.0778492
Click to view 3D structure	Adenosine receptor A1	P25099	Rattus norvegicus	Predicted (SEA)	0.0778492
Click to view 3D structure	Adenosine receptor A3	P0DMS8	Humans	Predicted (SEA)	0.467095
Click to view 3D structure	Adenosine receptor A3	P28647	Rattus norvegicus	Predicted (SEA)	0.0778492
Click to view 3D structure	Heat shock protein HSP 90-alpha	P07900	Humans	Predicted (SEA)	0.0778492
Click to view 3D structure	Endoplasmin	P14625	Humans	Predicted (SEA)	0.0778492
Click to view 3D structure	Adenosine receptor A2a	P29274	Humans	Predicted (SEA)	0.389246
Click to view 3D structure	Adenosine receptor A1	P30542	Humans	Predicted (SEA)	0.778492
Click to view 3D structure	Adenosine receptor A1	P47745	Cavia porcellus	Predicted (SEA)	0.0778492
Click to view 3D structure	S-methyl-5'-thioadenosine phosphorylase	Q9CQ65	Mus musculus	Predicted (SEA)	0.311397
Click to view 3D structure	Adenosine receptor A2b	P29275	Humans	Predicted (SEA)	1.55698
Click to view 3D structure	Adenosine kinase	P55263	Humans	Predicted (SEA)	0.155698
Click to view 3D structure	P2Y purinoceptor 1	P47900	Humans	Predicted (SEA)	1.08989
Click to view 3D structure	P2Y purinoceptor 2	P41231	Humans	Predicted (SEA)	3.03612
Click to view 3D structure	Adenosine kinase	P9WID5	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Predicted (SEA)	0.0778492
Click to view 3D structure	High affinity choline transporter 1	Q9GZV3	Humans	Predicted (SEA)	0.155698
Click to view 3D structure	ADP-ribose glycohydrolase MACROD1	Q9BQ69	Humans	Predicted (SEA)	0.700643
Click to view 3D structure	ADP-ribose glycohydrolase MACROD2	A1Z1Q3	Humans	Predicted (SEA)	0.700643
Click to view 3D structure	NAD kinase	Q5HH78	Staphylococcus aureus (strain COL)	Predicted (SEA)	0.0778492
Click to view 3D structure	NAD kinase 1	Q8Y8D7	Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)	Predicted (SEA)	0.0778492
Click to view 3D structure	P2Y purinoceptor 1	P49652	Meleagris gallopavo	Predicted (SEA)	1.08989
Click to view 3D structure	Heat shock cognate 71 kDa protein	P19120	Bos taurus	Predicted (SEA)	0.934191
Click to view 3D structure	Sensor protein kinase WalK	Q9RDT3	Staphylococcus aureus	Predicted (SEA)	0.934191
Click to view 3D structure	P2X purinoceptor 1	P51575	Humans	Predicted (SEA)	0.934191
Click to view 3D structure	Histone-lysine N-methyltransferase, H3 lysine-79 specific	Q8TEK3	Humans	Predicted (SEA)	0.622794