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Record Information
Version3.6
Creation Date2012-09-06 15:16:49 UTC
Update Date2016-02-11 01:28:10 UTC
HMDB IDHMDB14340
Secondary Accession NumbersNone
Metabolite Identification
Common NameVidarabine
DescriptionA nucleoside antibiotic isolated from Streptomyces antibioticus. It has some antineoplastic properties and has broad spectrum activity against DNA viruses in cell cultures and significant antiviral activity against infections caused by a variety of viruses such as the herpes viruses, the vaccinia VIRUS and varicella zoster virus. [PubChem]
Structure
Thumb
Synonyms
ValueSource
2-(6-amino-PURIN-9-yl)-5-hydroxymethyl-tetrahydro-furan-3,4-diolChEBI
9-beta-D-Arabinofuranosyl-9H-purin-6-amineChEBI
9-beta-D-ArabinofuranosyladenineChEBI
SpongoadenosineChEBI
9-b-D-Arabinofuranosyl-9H-purin-6-amineGenerator
9-β-D-arabinofuranosyl-9H-purin-6-amineGenerator
9-b-D-ArabinofuranosyladenineGenerator
9-β-D-arabinofuranosyladenineGenerator
9-beta-D-Arabinofuranosyl-adenineHMDB
Adenine arabinosideHMDB
Ara-aHMDB
Ara-ATPHMDB
AraadenosineHMDB
Arabinoside adenineHMDB
Arabinosyl adenineHMDB
ArabinosyladenineHMDB
Chemical FormulaC10H13N5O4
Average Molecular Weight267.2413
Monoisotopic Molecular Weight267.096753929
IUPAC Name(2R,3S,4S,5R)-2-(6-amino-9H-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol
Traditional Namearmes
CAS Registry Number24356-66-9
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 KeyInChIKey=OIRDTQYFTABQOQ-UHTZMRCNSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as purine nucleosides. These are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleosides
Sub ClassNot Available
Direct ParentPurine nucleosides
Alternative Parents
Substituents
  • Purine ribonucleoside
  • N-glycosyl compound
  • Glycosyl compound
  • 6-aminopurine
  • Purine
  • Imidazopyrimidine
  • Aminopyrimidine
  • Imidolactam
  • Pyrimidine
  • Primary aromatic amine
  • N-substituted imidazole
  • Monosaccharide
  • Heteroaromatic compound
  • Oxolane
  • Imidazole
  • Azole
  • Secondary alcohol
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
StatusExpected but not Quantified
Origin
  • Drug
Biofunction
  • Antimetabolites
  • Antiviral Agents
Application
  • Pharmaceutical
Cellular locations
  • Cytoplasm
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility1.40e+01 g/LNot Available
LogP-2.115Not Available
Predicted Properties
PropertyValueSource
Water Solubility14.0 mg/mLALOGPS
logP-1.2ALOGPS
logP-2.1ChemAxon
logS-1.3ALOGPS
pKa (Strongest Acidic)12.45ChemAxon
pKa (Strongest Basic)4.99ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area139.54 Å2ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity63.2 m3·mol-1ChemAxon
Polarizability24.49 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
SpectraNot Available
Biological Properties
Cellular Locations
  • Cytoplasm
Biofluid Locations
  • Blood
  • Urine
Tissue LocationNot Available
PathwaysNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot ApplicableNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00194
  • Not Applicable
details
UrineExpected but not QuantifiedNot ApplicableNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00194
  • Not Applicable
details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00194
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID20400
KEGG Compound IDC07195
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkVidarabine
NuGOwiki LinkHMDB14340
Metagene LinkHMDB14340
METLIN IDNot Available
PubChem Compound21704
PDB IDRAB
ChEBI ID45327
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Feher Z, Mishra NC: An aphidicolin-resistant mutant of Chinese hamster ovary cell with altered DNA polymerase and 3' exonuclease activities. Biochim Biophys Acta. 1995 Aug 22;1263(2):141-6. [7640304 ]
  2. Russell RR 3rd, Bergeron R, Shulman GI, Young LH: Translocation of myocardial GLUT-4 and increased glucose uptake through activation of AMPK by AICAR. Am J Physiol. 1999 Aug;277(2 Pt 2):H643-9. [10444490 ]
  3. Moore CL, Chiaramonte M, Higgins T, Kuchta RD: Synthesis of nucleotide analogues that potently and selectively inhibit human DNA primase. Biochemistry. 2002 Nov 26;41(47):14066-75. [12437364 ]
  4. Kuchta RD, Ilsley D, Kravig KD, Schubert S, Harris B: Inhibition of DNA primase and polymerase alpha by arabinofuranosylnucleoside triphosphates and related compounds. Biochemistry. 1992 May 19;31(19):4720-8. [1581321 ]
  5. Chen J, Hudson E, Chi MM, Chang AS, Moley KH, Hardie DG, Downs SM: AMPK regulation of mouse oocyte meiotic resumption in vitro. Dev Biol. 2006 Mar 15;291(2):227-38. Epub 2006 Jan 26. [16443210 ]
  6. Thompson HC, Kuchta RD: Arabinofuranosyl nucleotides are not chain-terminators during initiation of new strands of DNA by DNA polymerase alpha-primase. Biochemistry. 1995 Sep 5;34(35):11198-203. [7545435 ]
  7. Feher Z, Mishra NC: Aphidicolin-resistant Chinese hamster ovary cells possess altered DNA polymerases of the alpha-family. Biochim Biophys Acta. 1994 May 17;1218(1):35-47. [7514891 ]

Enzymes

General function:
Involved in deaminase activity
Specific function:
Catalyzes the hydrolytic deamination of adenosine and 2-deoxyadenosine. Plays an important role in purine metabolism and in adenosine homeostasis. Modulates signaling by extracellular adenosine, and so contributes indirectly to cellular signaling events. Acts as a positive regulator of T-cell coactivation, by binding DPP4. Its interaction with DPP4 regulates lymphocyte-epithelial cell adhesion.
Gene Name:
ADA
Uniprot ID:
P00813
Molecular weight:
40764.13
References
  1. Agarwal RP, Blatt J, Miser J, Sallan S, Lipton JM, Reaman GH, Holcenberg J, Poplack DG: Clinical pharmacology of 9-beta-D-arabinofuranosyladenine in combination with 2'-deoxycoformycin. Cancer Res. 1982 Sep;42(9):3884-6. [6980706 ]
  2. Balzarini J, De Clercq E: The antiviral activity of 9-beta-D-arabinofuranosyladenine is enhanced by the 2',3'-dideoxyriboside, the 2',3'-didehydro-2',3'-dideoxyriboside and the 3'-azido-2',3'-dideoxyriboside of 2,6-diaminopurine. Biochem Biophys Res Commun. 1989 Feb 28;159(1):61-7. [2538128 ]
  3. Cristalli G, Franchetti P, Grifantini M, Vittori S, Lupidi G, Riva F, Bordoni T, Geroni C, Verini MA: Adenosine deaminase inhibitors. Synthesis and biological activity of deaza analogues of erythro-9-(2-hydroxy-3-nonyl)adenine. J Med Chem. 1988 Feb;31(2):390-3. [3339608 ]