Thymidine-3',5'-Diphosphate

Identification

Name
Thymidine-3',5'-Diphosphate
Accession Number
DB04205  (EXPT03055)
Type
Small Molecule
Groups
Experimental
Description
Not Available
Structure
Thumb
Synonyms
Not Available
Categories
Not Available
UNII
Not Available
CAS number
Not Available
Weight
Average: 402.1884
Monoisotopic: 402.022932388
Chemical Formula
C10H16N2O11P2
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

Pharmacology

Indication
Not Available
Pharmacodynamics
Not Available
Mechanism of action
TargetActionsOrganism
UDNA topoisomerase 1Not AvailableEscherichia coli (strain K12)
UThermonucleaseNot AvailableStaphylococcus 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
Toxicity
Not Available
Affected organisms
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

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 190 more

Clinical Trials

Clinical Trials
Not Available

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 Solubility7.73 mg/mLALOGPS
logP-0.96ALOGPS
logP-1.4ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)0.85ChemAxon
pKa (Strongest Basic)-4.2ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area192.16 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity77.16 m3·mol-1ChemAxon
Polarizability32.71 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted ADMET features
PropertyValueProbability
Human Intestinal Absorption-0.6635
Blood Brain Barrier+0.8252
Caco-2 permeable-0.801
P-glycoprotein substrateNon-substrate0.6737
P-glycoprotein inhibitor INon-inhibitor0.8053
P-glycoprotein inhibitor IINon-inhibitor0.9697
Renal organic cation transporterNon-inhibitor0.8886
CYP450 2C9 substrateNon-substrate0.6356
CYP450 2D6 substrateNon-substrate0.8565
CYP450 3A4 substrateSubstrate0.5398
CYP450 1A2 substrateNon-inhibitor0.9003
CYP450 2C9 inhibitorNon-inhibitor0.8723
CYP450 2D6 inhibitorNon-inhibitor0.9184
CYP450 2C19 inhibitorNon-inhibitor0.8626
CYP450 3A4 inhibitorNon-inhibitor0.8381
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.8995
Ames testNon AMES toxic0.6229
CarcinogenicityNon-carcinogens0.831
BiodegradationNot ready biodegradable0.6662
Rat acute toxicity2.3253 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9342
hERG inhibition (predictor II)Non-inhibitor0.8033
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-MSNot Available
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSNot Available

Taxonomy

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

Targets

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
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284]
  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. [PubMed:17016423]
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
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284]
  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. [PubMed:17016423]

Drug created on June 13, 2005 07:24 / Updated on June 12, 2020 10:52

Logo pink
Are you a
new drug developer?
Contact us to learn more about our customized products and solutions.
Logo pink
Stay in the know!
As part of our commitment to providing the most up-to-date drug information, we will be releasing #DrugBankUpdates with our newly added curated drug pages.
#DrugBankUpdates