(South)-Methanocarba-Thymidine
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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
Target Actions Organism UThymidine kinase inhibitorHHV-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
- Improve decision support & research outcomesWith structured adverse effects data, including: blackbox warnings, adverse reactions, warning & precautions, & incidence rates. View sample adverse effects data in our new Data Library!Improve decision support & research outcomes with our structured adverse effects data.
- 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
- External Links
- PDB Entries
- 1of1
Clinical Trials
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
Property Value Source Water Solubility 38.7 mg/mL ALOGPS logP -0.83 ALOGPS logP -1.6 Chemaxon logS -0.81 ALOGPS pKa (Strongest Acidic) 10.3 Chemaxon pKa (Strongest Basic) -2.6 Chemaxon Physiological Charge 0 Chemaxon Hydrogen Acceptor Count 4 Chemaxon Hydrogen Donor Count 3 Chemaxon Polar Surface Area 89.87 Å2 Chemaxon Rotatable Bond Count 2 Chemaxon Refractivity 62.19 m3·mol-1 Chemaxon Polarizability 25.29 Å3 Chemaxon Number of Rings 3 Chemaxon Bioavailability 1 Chemaxon Rule of Five Yes Chemaxon Ghose Filter No Chemaxon Veber's Rule No Chemaxon MDDR-like Rule No Chemaxon - Predicted ADMET Features
Property Value Probability Human Intestinal Absorption + 0.9615 Blood Brain Barrier - 0.6291 Caco-2 permeable - 0.7301 P-glycoprotein substrate Substrate 0.5431 P-glycoprotein inhibitor I Non-inhibitor 0.8165 P-glycoprotein inhibitor II Non-inhibitor 0.9559 Renal organic cation transporter Non-inhibitor 0.8762 CYP450 2C9 substrate Non-substrate 0.6097 CYP450 2D6 substrate Non-substrate 0.8368 CYP450 3A4 substrate Substrate 0.5464 CYP450 1A2 substrate Non-inhibitor 0.8872 CYP450 2C9 inhibitor Non-inhibitor 0.7536 CYP450 2D6 inhibitor Non-inhibitor 0.8846 CYP450 2C19 inhibitor Non-inhibitor 0.8414 CYP450 3A4 inhibitor Non-inhibitor 0.9405 CYP450 inhibitory promiscuity Low CYP Inhibitory Promiscuity 0.9107 Ames test Non AMES toxic 0.7139 Carcinogenicity Non-carcinogens 0.721 Biodegradation Not ready biodegradable 0.7848 Rat acute toxicity 2.2640 LD50, mol/kg Not applicable hERG inhibition (predictor I) Weak inhibitor 0.9721 hERG inhibition (predictor II) Non-inhibitor 0.7551
Spectra
- Mass Spec (NIST)
- Not Available
- Spectra
Spectrum Spectrum Type Splash Key Predicted GC-MS Spectrum - GC-MS Predicted GC-MS splash10-004i-3980000000-f45e8afde6c2ad6632ed Predicted MS/MS Spectrum - 10V, Positive (Annotated) Predicted LC-MS/MS splash10-0kdi-3970000000-37f833e161aa702ed9d1 Predicted MS/MS Spectrum - 10V, Negative (Annotated) Predicted LC-MS/MS splash10-0udi-0090000000-011c6886ae5d60e46af8 Predicted MS/MS Spectrum - 20V, Positive (Annotated) Predicted LC-MS/MS splash10-0560-8910000000-95d6bf52363a13bc8f70 Predicted MS/MS Spectrum - 20V, Negative (Annotated) Predicted LC-MS/MS splash10-001i-2940000000-550f0f4b5255fb3e93fd Predicted MS/MS Spectrum - 40V, Positive (Annotated) Predicted LC-MS/MS splash10-0a4i-2920000000-49e9c73edd109a81ca8d Predicted MS/MS Spectrum - 40V, Negative (Annotated) Predicted LC-MS/MS splash10-0f96-3950000000-8188cae8cf2c339ff81f Predicted 1H NMR Spectrum 1D NMR Not Applicable Predicted 13C NMR Spectrum 1D NMR Not Applicable - Chromatographic Properties
Collision Cross Sections (CCS)
Adduct CCS Value (Å2) Source type Source [M-H]- 155.41267 predictedDeepCCS 1.0 (2019) [M+H]+ 157.77066 predictedDeepCCS 1.0 (2019) [M+Na]+ 165.71884 predictedDeepCCS 1.0 (2019)
Targets
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1. DetailsThymidine kinase
- 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
- 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