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Showing metabocard for Vidarabine (HMDB0014340)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
enzymes (1) Show 1 protein
Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:49 UTC
Update Date2020-02-26 21:39:27 UTC
HMDB IDHMDB0014340
Secondary Accession Numbers
  • HMDB14340
Metabolite Identification
Common NameVidarabine
DescriptionVidarabine, 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. Vidarabine is a synthetic purine nucleoside analogue with in vitro and in vivo inhibitory activity against herpes simplex virus types 1 (HSV-1), 2 (HSV-2), and varicella-zoster virus (VZV). By acting as a substrate for viral DNA polymerase, ara-ATP competitively inhibits dATP leading to the formation of ‘faulty’ DNA. Vidarabine is a drug which is used for treatment of chickenpox - varicella, herpes zoster and herpes simplex. The inhibitory activity of Vidarabine is highly selective due to its affinity for the enzyme thymidine kinase (TK) encoded by HSV and VZV. 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. Vidarabine is a strong basic compound (based on its pKa). A nucleoside antibiotic isolated from Streptomyces antibioticus. No untoward effects should result from ingestion of the entire contents of the tube.
Structure
Data?1582753167
MOLSDFPDBSMILESInChI
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
Vidarabine anhydrousKegg
ARA-aKegg
ArmesKegg
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-ATPHMDB
AraadenosineHMDB
Arabinoside adenineHMDB
Arabinosyl adenineHMDB
ArabinosyladenineHMDB
a, alpha-AraHMDB
Ara aHMDB
ArabinofuranosyladenineHMDB
Monarch brand OF vidarabineHMDB
ViraAHMDB
alpha Ara aHMDB
alpha D ArabinofuranosyladenineHMDB
alpha-Ara aHMDB
9 beta ArabinofuranosyladenineHMDB
9 beta D ArabinofuranosyladenineHMDB
a, AraHMDB
beta Ara aHMDB
Arabinoside, adenineHMDB
alpha-D-ArabinofuranosyladenineHMDB
9-beta-ArabinofuranosyladenineHMDB
a, beta-AraHMDB
Parke davis brand OF vidarabineHMDB
Vira aHMDB
Vira-aHMDB
beta-Ara aHMDB
VidarabineChEBI
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 KeyOIRDTQYFTABQOQ-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.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleosides
Sub ClassNot Available
Direct ParentPurine 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 FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Disposition

Biological location:

Role

Industrial application:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility14 g/LNot Available
LogP-2.115Not Available
Predicted Properties
PropertyValueSource
Water Solubility14 g/LALOGPS
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 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity63.2 m³·mol⁻¹ChemAxon
Polarizability24.49 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a4l-9350000000-ed8639e5b54e46825628Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-014i-1492400000-1fe7f0d7ca11fdb4800fSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-qTof , Positivesplash10-000i-2910000000-e18a8d00eb0e73aa6decSpectrum
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-000i-2910000000-e18a8d00eb0e73aa6decSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0940000000-42bee9785f9b55b32eeaSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0900000000-c8cda6a661ace060572cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-2900000000-0304a85c3951aa1cb41aSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0159-0690000000-0258e5851611884483d9Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-0900000000-e6b8fc6980387f646d64Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-053r-2900000000-1e0cad8d044715d90f12Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not Quantified Not AvailableNot AvailableTaking drug identified by DrugBank entry DB00194 details
UrineExpected but not Quantified Not AvailableNot AvailableTaking drug identified by DrugBank entry DB00194 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00194
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID20400
KEGG Compound IDC07195
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkVidarabine
METLIN IDNot Available
PubChem Compound21704
PDB IDRAB
ChEBI ID45327
Food Biomarker OntologyNot Available
VMH IDNot Available
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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed:7514891 ]

Enzymes

Enzyme Details
1. Adenosine deaminase
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. [PubMed: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. [PubMed: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. [PubMed:3339608 ]