NAV

Thymidine-3',5'-Diphosphate

Identification

Generic Name
Thymidine-3',5'-Diphosphate
DrugBank Accession Number
DB04205
Background

Not Available

Type
Small Molecule
Groups
Experimental
Structure
3D
Similar Structures
Weight
Average: 402.1884
Monoisotopic: 402.022932388
Chemical Formula
C10H16N2O11P2
Synonyms
Not Available
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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
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

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 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
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 186 more

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 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-MSsplash10-0002-9343000000-dc4b8b2aafcca918fd7b
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSsplash10-0udi-0220900000-e4fa44f9af38c8f42cb9
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-0ufr-9000600000-354dddf75320d7d11845
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-0059-2429200000-eb32410a51b1d9dea590
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-004i-9004000000-14264e8e1eb86815635b
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-053r-5943000000-9dc5d72c601d0c686b15
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-004i-9101000000-f73ee57de09d353985b9
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]-162.51476
predicted
DeepCCS 1.0 (2019)
[M+H]+164.91031
predicted
DeepCCS 1.0 (2019)
[M+Na]+170.82283
predicted
DeepCCS 1.0 (2019)

Targets

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Details1. DNA 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
  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]
Details2. Thermonuclease
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. [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