(South)-Methanocarba-Thymidine

Identification

Generic Name
(South)-Methanocarba-Thymidine
DrugBank Accession Number
DB02921
Background

Not Available

Type
Small Molecule
Groups
Experimental
Structure
Weight
Average: 252.2664
Monoisotopic: 252.11100701
Chemical Formula
C12H16N2O4
Synonyms
  • (South)-methanocarbathymidine

Pharmacology

Indication

Not Available

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Pharmacodynamics

Not Available

Mechanism of action
TargetActionsOrganism
UThymidine kinase
inhibitor
HHV-1
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
Not Available

Interactions

Drug Interactions
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.
Not Available
Food Interactions
Not Available

Categories

Drug Categories
Not Available
Chemical TaxonomyProvided by Classyfire
Description
This compound belongs to the class of organic compounds known as cyclopentyl nucleosides. These are nucleoside analogues with a structure that consists of a cyclobutane that is substituted a the 1-position with a hydroxyl group and at the 2- or the 3- position with either a purine or pyrimidine base.
Kingdom
Organic compounds
Super Class
Nucleosides, nucleotides, and analogues
Class
Nucleoside and nucleotide analogues
Sub Class
Cyclopentyl nucleosides
Direct Parent
Cyclopentyl nucleosides
Alternative Parents
Pyrimidones / Hydropyrimidines / Vinylogous amides / Heteroaromatic compounds / Ureas / Secondary alcohols / Lactams / Cyclic alcohols and derivatives / Azacyclic compounds / Primary alcohols
show 4 more
Substituents
Alcohol / Aromatic heteropolycyclic compound / Azacycle / Cyclic alcohol / Cyclopentyl nucleoside / Heteroaromatic compound / Hydrocarbon derivative / Hydropyrimidine / Lactam / Organic nitrogen compound
show 12 more
Molecular Framework
Aromatic heteropolycyclic compounds
External Descriptors
secondary alcohol, pyrimidone, primary alcohol, carbobicyclic compound, C-glycosyl pyrimidine (CHEBI:45586)
Affected organisms
Not Available

Chemical Identifiers

UNII
Not Available
CAS number
Not Available
InChI Key
XRMLXZVSFIBRRJ-PEFMBERDSA-N
InChI
InChI=1S/C12H16N2O4/c1-6-4-14(11(18)13-10(6)17)12-2-8(12)7(5-15)9(16)3-12/h4,7-9,15-16H,2-3,5H2,1H3,(H,13,17,18)/t7-,8-,9-,12-/m0/s1
IUPAC Name
1-[(1S,3S,4R,5S)-3-hydroxy-4-(hydroxymethyl)bicyclo[3.1.0]hexan-1-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
SMILES
CC1=CN(C(=O)NC1=O)[C@]12C[C@H]1[C@H](CO)[C@@H](O)C2

References

General References
Not Available
PubChem Compound
447628
PubChem Substance
46504656
ChemSpider
394666
ChEBI
45586
ZINC
ZINC000003802232
PDBe Ligand
SCT
PDB Entries
1of1

Clinical Trials

Clinical Trials
PhaseStatusPurposeConditionsCount

Pharmacoeconomics

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

Properties

State
Solid
Experimental Properties
Not Available
Predicted Properties
PropertyValueSource
Water Solubility38.7 mg/mLALOGPS
logP-0.83ALOGPS
logP-1.6Chemaxon
logS-0.81ALOGPS
pKa (Strongest Acidic)10.3Chemaxon
pKa (Strongest Basic)-2.6Chemaxon
Physiological Charge0Chemaxon
Hydrogen Acceptor Count4Chemaxon
Hydrogen Donor Count3Chemaxon
Polar Surface Area89.87 Å2Chemaxon
Rotatable Bond Count2Chemaxon
Refractivity62.19 m3·mol-1Chemaxon
Polarizability25.29 Å3Chemaxon
Number of Rings3Chemaxon
Bioavailability1Chemaxon
Rule of FiveYesChemaxon
Ghose FilterNoChemaxon
Veber's RuleNoChemaxon
MDDR-like RuleNoChemaxon
Predicted ADMET Features
PropertyValueProbability
Human Intestinal Absorption+0.9615
Blood Brain Barrier-0.6291
Caco-2 permeable-0.7301
P-glycoprotein substrateSubstrate0.5431
P-glycoprotein inhibitor INon-inhibitor0.8165
P-glycoprotein inhibitor IINon-inhibitor0.9559
Renal organic cation transporterNon-inhibitor0.8762
CYP450 2C9 substrateNon-substrate0.6097
CYP450 2D6 substrateNon-substrate0.8368
CYP450 3A4 substrateSubstrate0.5464
CYP450 1A2 substrateNon-inhibitor0.8872
CYP450 2C9 inhibitorNon-inhibitor0.7536
CYP450 2D6 inhibitorNon-inhibitor0.8846
CYP450 2C19 inhibitorNon-inhibitor0.8414
CYP450 3A4 inhibitorNon-inhibitor0.9405
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9107
Ames testNon AMES toxic0.7139
CarcinogenicityNon-carcinogens0.721
BiodegradationNot ready biodegradable0.7848
Rat acute toxicity2.2640 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9721
hERG inhibition (predictor II)Non-inhibitor0.7551
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-MSsplash10-004i-3980000000-f45e8afde6c2ad6632ed
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSsplash10-0kdi-3970000000-37f833e161aa702ed9d1
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-0udi-0090000000-011c6886ae5d60e46af8
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-0560-8910000000-95d6bf52363a13bc8f70
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-001i-2940000000-550f0f4b5255fb3e93fd
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-0a4i-2920000000-49e9c73edd109a81ca8d
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-0f96-3950000000-8188cae8cf2c339ff81f
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]-155.41267
predicted
DeepCCS 1.0 (2019)
[M+H]+157.77066
predicted
DeepCCS 1.0 (2019)
[M+Na]+165.71884
predicted
DeepCCS 1.0 (2019)

Targets

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Kind
Protein
Organism
HHV-1
Pharmacological action
Unknown
Actions
Inhibitor
General Function
Thymidine kinase activity
Specific Function
In latent infection, may allow the virus to be reactivated and to grow in cells lacking a high concentration of phosphorylated nucleic acid precursors, such as nerve cells that do not replicate the...
Gene Name
TK
Uniprot ID
Q9QNF7
Uniprot Name
Thymidine kinase
Molecular Weight
40896.475 Da
References
  1. Schelling P, Claus MT, Johner R, Marquez VE, Schulz GE, Scapozza L: Biochemical and structural characterization of (South)-methanocarbathymidine that specifically inhibits growth of herpes simplex virus type 1 thymidine kinase-transduced osteosarcoma cells. J Biol Chem. 2004 Jul 30;279(31):32832-8. doi: 10.1074/jbc.M313343200. Epub 2004 May 25. [Article]

Drug created at June 13, 2005 13:24 / Updated at April 30, 2023 10:33