NAV

Tubercidin

Identification

Generic Name
Tubercidin
DrugBank Accession Number
DB03172
Background

An antibiotic purine ribonucleoside that readily substitutes for adenosine in the biological system, but its incorporation into DNA and RNA has an inhibitory effect on the metabolism of these nucleic acids.

Type
Small Molecule
Groups
Experimental
Structure
3D
Similar Structures
Weight
Average: 266.2533
Monoisotopic: 266.101504956
Chemical Formula
C11H14N4O4
Synonyms
  • 7-deazaadenosine
  • Sparsomycin A
  • Tubercidine
External IDs
  • Antibiotic 155B2T
  • Antibiotic XK 101-1
  • U-10071
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Pharmacology

Indication

Not Available

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Contraindications & Blackbox Warnings
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Pharmacodynamics

Not Available

Mechanism of action
TargetActionsOrganism
UPurine nucleoside phosphorylase DeoD-typeNot AvailableEscherichia coli (strain K12)
Absorption

Not Available

Volume of distribution

Not Available

Protein binding

Not Available

Metabolism
Not Available
Route of elimination

Not Available

Half-life

Not Available

Clearance

Not Available

Adverse Effects
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Toxicity

Not Available

Pathways
Not Available
Pharmacogenomic Effects/ADRs Browse all" title="About SNP Mediated Effects/ADRs" id="snp-actions-info" class="drug-info-popup" href="javascript:void(0);">
Not Available

Interactions

Drug Interactions Learn More" title="About Drug Interactions" id="structured-interactions-info" class="drug-info-popup" href="javascript:void(0);">
This information should not be interpreted without the help of a healthcare provider. If you believe you are experiencing an interaction, contact a healthcare provider immediately. The absence of an interaction does not necessarily mean no interactions exist.
DrugInteraction
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interactions in your software
AmbroxolThe risk or severity of methemoglobinemia can be increased when Tubercidin is combined with Ambroxol.
ArticaineThe risk or severity of methemoglobinemia can be increased when Tubercidin is combined with Articaine.
BenzocaineThe risk or severity of methemoglobinemia can be increased when Tubercidin is combined with Benzocaine.
Benzyl alcoholThe risk or severity of methemoglobinemia can be increased when Tubercidin is combined with Benzyl alcohol.
BupivacaineThe risk or severity of methemoglobinemia can be increased when Tubercidin is combined with Bupivacaine.
Food Interactions
Not Available

Categories

Drug Categories
Chemical TaxonomyProvided by Classyfire
Description
This compound belongs to the class of organic compounds known as pyrrolopyrimidine nucleosides and nucleotides. These are nucleoside derivatives containing a ribose derivative which is n-glycosylated to a pyrrolopyrimidine. Also called deazapurine nucleosides, they are analogs of purine nucleosides with the N atom of the purine being replaced by a C atom at position 7.
Kingdom
Organic compounds
Super Class
Nucleosides, nucleotides, and analogues
Class
Pyrrolopyrimidine nucleosides and nucleotides
Sub Class
Not Available
Direct Parent
Pyrrolopyrimidine nucleosides and nucleotides
Alternative Parents
Glycosylamines / Pentoses / Pyrrolo[2,3-d]pyrimidines / Aminopyrimidines and derivatives / Substituted pyrroles / Imidolactams / Tetrahydrofurans / Heteroaromatic compounds / Secondary alcohols / Oxacyclic compounds
show 5 more
Substituents
Alcohol / Amine / Aminopyrimidine / Aromatic heteropolycyclic compound / Azacycle / Glycosyl compound / Heteroaromatic compound / Hydrocarbon derivative / Imidolactam / Monosaccharide
show 19 more
Molecular Framework
Aromatic heteropolycyclic compounds
External Descriptors
N-glycosylpyrrolopyrimidine (CHEBI:45836)
Affected organisms
Not Available

Chemical Identifiers

UNII
M351LCX45Y
CAS number
69-33-0
InChI Key
HDZZVAMISRMYHH-KCGFPETGSA-N
InChI
InChI=1S/C11H14N4O4/c12-9-5-1-2-15(10(5)14-4-13-9)11-8(18)7(17)6(3-16)19-11/h1-2,4,6-8,11,16-18H,3H2,(H2,12,13,14)/t6-,7-,8-,11-/m1/s1
IUPAC Name
(2R,3R,4S,5R)-2-{4-amino-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-5-(hydroxymethyl)oxolane-3,4-diol
SMILES
NC1=NC=NC2=C1C=CN2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O

References

Synthesis Reference

Charles G. Smith, "Tubercidin preparation." U.S. Patent US4065556, issued December 27, 1977.

US4065556
General References
  1. Zimmerman TP, Wolberg G, Duncan GS: Metabolism of tubercidin and formycin to their 3':5'-cyclic nucleotides in mammalian cells. J Biol Chem. 1978 Dec 25;253(24):8792-7. [Article]
PubChem Compound
6245
PubChem Substance
46505938
ChemSpider
6009
BindingDB
50000298
ChEBI
48267
ChEMBL
CHEMBL267099
ZINC
ZINC000003832269
Therapeutic Targets Database
DNC001412
PharmGKB
PA152530738
PDBe Ligand
TBN
PDB Entries
1pr5 / 3uq9 / 4dar / 4l5a / 5f7x / 5tbv / 6g38 / 8bsd

Clinical Trials

Clinical Trials Learn More" title="About Clinical Trials" id="clinical-trials-info" class="drug-info-popup" href="javascript:void(0);">
PhaseStatusPurposeConditionsCount

Pharmacoeconomics

Manufacturers
Not Available
Packagers
Not Available
Dosage Forms
Not Available
Prices
Not Available
Patents
Not Available

Properties

State
Solid
Experimental Properties
PropertyValueSource
water solubility3000 mg/LMERCK INDEX (1996)
logP-0.80HANSCH,C ET AL. (1995)
Predicted Properties
PropertyValueSource
Water Solubility16.6 mg/mLALOGPS
logP-0.83ALOGPS
logP-1.3Chemaxon
logS-1.2ALOGPS
pKa (Strongest Acidic)12.46Chemaxon
pKa (Strongest Basic)6.51Chemaxon
Physiological Charge1Chemaxon
Hydrogen Acceptor Count7Chemaxon
Hydrogen Donor Count4Chemaxon
Polar Surface Area126.65 Å2Chemaxon
Rotatable Bond Count2Chemaxon
Refractivity65.37 m3·mol-1Chemaxon
Polarizability25.65 Å3Chemaxon
Number of Rings3Chemaxon
Bioavailability1Chemaxon
Rule of FiveYesChemaxon
Ghose FilterNoChemaxon
Veber's RuleNoChemaxon
MDDR-like RuleNoChemaxon
Predicted ADMET Features
PropertyValueProbability
Human Intestinal Absorption+0.9411
Blood Brain Barrier+0.9544
Caco-2 permeable-0.8848
P-glycoprotein substrateNon-substrate0.7783
P-glycoprotein inhibitor INon-inhibitor0.9643
P-glycoprotein inhibitor IINon-inhibitor0.9007
Renal organic cation transporterNon-inhibitor0.9438
CYP450 2C9 substrateNon-substrate0.8419
CYP450 2D6 substrateNon-substrate0.8362
CYP450 3A4 substrateNon-substrate0.5788
CYP450 1A2 substrateNon-inhibitor0.9688
CYP450 2C9 inhibitorNon-inhibitor0.9479
CYP450 2D6 inhibitorNon-inhibitor0.9743
CYP450 2C19 inhibitorNon-inhibitor0.9397
CYP450 3A4 inhibitorNon-inhibitor0.9559
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9623
Ames testNon AMES toxic0.8976
CarcinogenicityNon-carcinogens0.9253
BiodegradationNot ready biodegradable0.9382
Rat acute toxicity2.6214 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9907
hERG inhibition (predictor II)Non-inhibitor0.9027
ADMET data is predicted using admetSAR, a free tool for evaluating chemical ADMET properties. (23092397)

Spectra

Mass Spec (NIST)
Not Available
Spectra
SpectrumSpectrum TypeSplash Key
Predicted GC-MS Spectrum - GC-MSPredicted GC-MSsplash10-00bm-9550000000-16876c0a7138908cbdda
LC-MS/MS Spectrum - LC-ESI-qTof , PositiveLC-MS/MSsplash10-000i-0900000000-36d410d303827e6de6d9
MS/MS Spectrum - , positiveLC-MS/MSsplash10-000i-0900000000-36d410d303827e6de6d9
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSsplash10-014i-0090000000-c9aca04d34f45255712d
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-000i-0910000000-a360ed2339f59b9e4012
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-001i-0900000000-805c499ba70bc93e3e86
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-052o-5900000000-ecf83a5f8b4b028f5270
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-001i-0900000000-3050fc189690cd1c4865
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-001i-1900000000-e15b2dfa8c3bad91b745
Predicted 1H NMR Spectrum1D NMRNot Applicable
Predicted 13C NMR Spectrum1D NMRNot Applicable
Chromatographic Properties
Collision Cross Sections (CCS)
AdductCCS Value (Å2)Source typeSource
[M-H]-165.9492468
predicted
DarkChem Lite v0.1.0
[M-H]-158.2498
predicted
DeepCCS 1.0 (2019)
[M+H]+165.9332468
predicted
DarkChem Lite v0.1.0
[M+H]+160.64537
predicted
DeepCCS 1.0 (2019)
[M+Na]+165.9842468
predicted
DarkChem Lite v0.1.0
[M+Na]+168.48773
predicted
DeepCCS 1.0 (2019)

Targets

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Details1. Purine nucleoside phosphorylase DeoD-type
Kind
Protein
Organism
Escherichia coli (strain K12)
Pharmacological action
Unknown
General Function
Purine-nucleoside phosphorylase activity
Specific Function
Cleavage of guanosine or inosine to respective bases and sugar-1-phosphate molecules.
Gene Name
deoD
Uniprot ID
P0ABP8
Uniprot Name
Purine nucleoside phosphorylase DeoD-type
Molecular Weight
25949.68 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [Article]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [Article]

Drug created at June 13, 2005 13:24 / Updated at June 12, 2020 16:52