Thymidine-3',5'-Diphosphate
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Identification
- Generic Name
- Thymidine-3',5'-Diphosphate
- DrugBank Accession Number
- DB04205
- Background
Not Available
- Type
- Small Molecule
- Groups
- Experimental
- Structure
- Weight
- Average: 402.1884
Monoisotopic: 402.022932388 - Chemical Formula
- C10H16N2O11P2
- Synonyms
- Not Available
Pharmacology
- Indication
Not Available
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- Pharmacodynamics
Not Available
- Mechanism of action
Target Actions Organism UDNA topoisomerase 1 Not Available Escherichia coli (strain K12) UThermonuclease Not Available Staphylococcus aureus - 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 pyrimidine deoxyribonucleoside 3',5'-bisphosphates. These are pyrimidine ribobucleotides with one phosphate group attached to each of two different hydroxyl groups of the ribose moiety, which lacks a hydroxyl group at position 2.
- Kingdom
- Organic compounds
- Super Class
- Nucleosides, nucleotides, and analogues
- Class
- Pyrimidine nucleotides
- Sub Class
- Pyrimidine deoxyribonucleotides
- Direct Parent
- Pyrimidine deoxyribonucleoside 3',5'-bisphosphates
- Alternative Parents
- Ribonucleoside 3'-phosphates / Pyrimidones / Monoalkyl phosphates / Hydropyrimidines / Vinylogous amides / Heteroaromatic compounds / Tetrahydrofurans / Ureas / Lactams / Azacyclic compounds show 6 more
- Substituents
- Alkyl phosphate / Aromatic heteromonocyclic compound / Azacycle / Heteroaromatic compound / Hydrocarbon derivative / Hydropyrimidine / Lactam / Monoalkyl phosphate / Organic nitrogen compound / Organic oxide show 15 more
- Molecular Framework
- Aromatic heteromonocyclic compounds
- External Descriptors
- Not Available
- Affected organisms
- Not Available
Chemical Identifiers
- UNII
- Not Available
- CAS number
- Not Available
- InChI Key
- CSNCBOPUCJOHLS-XLPZGREQSA-N
- InChI
- InChI=1S/C10H16N2O11P2/c1-5-3-12(10(14)11-9(5)13)8-2-6(23-25(18,19)20)7(22-8)4-21-24(15,16)17/h3,6-8H,2,4H2,1H3,(H,11,13,14)(H2,15,16,17)(H2,18,19,20)/t6-,7+,8+/m0/s1
- IUPAC Name
- {[(2R,3S,5R)-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3-(phosphonooxy)oxolan-2-yl]methoxy}phosphonic acid
- SMILES
- [H][C@@]1(C[C@@]([H])(O[C@]1([H])COP(O)(O)=O)N1C=C(C)C(=O)NC1=O)OP(O)(O)=O
References
- General References
- Not Available
- External Links
- PubChem Compound
- 121976
- PubChem Substance
- 46509069
- ChemSpider
- 108812
- ChEMBL
- CHEMBL1235491
- ZINC
- ZINC000011422512
- PDBe Ligand
- THP
- PDB Entries
- 1a2t / 1a2u / 1a3t / 1a3u / 1a3v / 1aex / 1cy1 / 1enc / 1jok / 1joq … show 192 more
Clinical Trials
- Clinical Trials
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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 7.73 mg/mL ALOGPS logP -0.96 ALOGPS logP -1.4 Chemaxon logS -1.7 ALOGPS pKa (Strongest Acidic) 0.85 Chemaxon pKa (Strongest Basic) -4.2 Chemaxon Physiological Charge -4 Chemaxon Hydrogen Acceptor Count 9 Chemaxon Hydrogen Donor Count 5 Chemaxon Polar Surface Area 192.16 Å2 Chemaxon Rotatable Bond Count 6 Chemaxon Refractivity 77.16 m3·mol-1 Chemaxon Polarizability 32.71 Å3 Chemaxon Number of Rings 2 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 - 0.6635 Blood Brain Barrier + 0.8252 Caco-2 permeable - 0.801 P-glycoprotein substrate Non-substrate 0.6737 P-glycoprotein inhibitor I Non-inhibitor 0.8053 P-glycoprotein inhibitor II Non-inhibitor 0.9697 Renal organic cation transporter Non-inhibitor 0.8886 CYP450 2C9 substrate Non-substrate 0.6356 CYP450 2D6 substrate Non-substrate 0.8565 CYP450 3A4 substrate Substrate 0.5398 CYP450 1A2 substrate Non-inhibitor 0.9003 CYP450 2C9 inhibitor Non-inhibitor 0.8723 CYP450 2D6 inhibitor Non-inhibitor 0.9184 CYP450 2C19 inhibitor Non-inhibitor 0.8626 CYP450 3A4 inhibitor Non-inhibitor 0.8381 CYP450 inhibitory promiscuity Low CYP Inhibitory Promiscuity 0.8995 Ames test Non AMES toxic 0.6229 Carcinogenicity Non-carcinogens 0.831 Biodegradation Not ready biodegradable 0.6662 Rat acute toxicity 2.3253 LD50, mol/kg Not applicable hERG inhibition (predictor I) Weak inhibitor 0.9342 hERG inhibition (predictor II) Non-inhibitor 0.8033
Spectra
- Mass Spec (NIST)
- Not Available
- Spectra
Spectrum Spectrum Type Splash Key Predicted GC-MS Spectrum - GC-MS Predicted GC-MS splash10-0002-9343000000-dc4b8b2aafcca918fd7b Predicted MS/MS Spectrum - 10V, Positive (Annotated) Predicted LC-MS/MS splash10-0udi-0220900000-e4fa44f9af38c8f42cb9 Predicted MS/MS Spectrum - 10V, Negative (Annotated) Predicted LC-MS/MS splash10-0ufr-9000600000-354dddf75320d7d11845 Predicted MS/MS Spectrum - 20V, Positive (Annotated) Predicted LC-MS/MS splash10-0059-2429200000-eb32410a51b1d9dea590 Predicted MS/MS Spectrum - 20V, Negative (Annotated) Predicted LC-MS/MS splash10-004i-9004000000-14264e8e1eb86815635b Predicted MS/MS Spectrum - 40V, Positive (Annotated) Predicted LC-MS/MS splash10-053r-5943000000-9dc5d72c601d0c686b15 Predicted MS/MS Spectrum - 40V, Negative (Annotated) Predicted LC-MS/MS splash10-004i-9101000000-f73ee57de09d353985b9 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]- 162.51476 predictedDeepCCS 1.0 (2019) [M+H]+ 164.91031 predictedDeepCCS 1.0 (2019) [M+Na]+ 170.82283 predictedDeepCCS 1.0 (2019)
Targets
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1. DetailsDNA topoisomerase 1
- Kind
- Protein
- Organism
- Escherichia coli (strain K12)
- Pharmacological action
- Unknown
- General Function
- Magnesium ion binding
- Specific Function
- Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introdu...
- Gene Name
- topA
- Uniprot ID
- P06612
- Uniprot Name
- DNA topoisomerase 1
- Molecular Weight
- 97349.0 Da
References
2. DetailsThermonuclease
- Kind
- Protein
- Organism
- Staphylococcus aureus
- Pharmacological action
- Unknown
- General Function
- Nucleic acid binding
- Specific Function
- Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond.
- Gene Name
- nuc
- Uniprot ID
- P00644
- Uniprot Name
- Thermonuclease
- Molecular Weight
- 25471.16 Da
References
Drug created at June 13, 2005 13:24 / Updated at June 12, 2020 16:52