Thymidine-5'-Phosphate

Identification

Name
Thymidine-5'-Phosphate
Accession Number
DB01643  (EXPT03073, EXPT02988)
Type
Small Molecule
Groups
Experimental
Description

5-Thymidylic acid. A thymine nucleotide containing one phosphate group esterified to the deoxyribose moiety.

Structure
Thumb
Synonyms
  • 2'-Deoxythymidine 5'-monophosphate
  • 3'-Thymidylic acid
  • 3'-Tmp
  • 5-Methyl-dUMP
  • 5'-dTMP
  • 5'-Thymidylic acid
  • 5'-TMP
  • Deoxy TMP
  • Deoxyribosylthymine monophosphate
  • Deoxythymidine 5'-monophosphate
  • Deoxythymidine 5'-phosphate
  • Deoxythymidine monophosphate
  • Deoxythymidine phosphate
  • Deoxythymidylic acid
  • Deoxythymydilic acid
  • DTMP
  • Octothymidylate
  • Poly t
  • Poly(DT)
  • Poly(t)
  • Polydeoxyribothymidylic acid
  • Polydeoxythymidylic acid
  • Polythymidine
  • Polythymidylic acid
  • Thymidine 5'-(dihydrogen phosphate)
  • Thymidine 5'-phosphate
  • Thymidine 5'-phosphoric acid
  • Thymidine 5'MP
  • Thymidine mononucleotide
  • Thymidine monophosphate
  • Thymidine phosphate
  • Thymidine-5'-Monophosphate
  • Thymidine-5'-monophosphoric acid
  • Thymidylate
  • Thymidylic acid
  • Thymidylic acid polymer
Categories
UNII
43W3021X6C
CAS number
365-07-1
Weight
Average: 322.2085
Monoisotopic: 322.056601978
Chemical Formula
C10H15N2O8P
InChI Key
GYOZYWVXFNDGLU-XLPZGREQSA-N
InChI
InChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
IUPAC Name
{[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy}phosphonic acid
SMILES
CC1=CN([[email protected]]2C[[email protected]](O)[[email protected]@H](COP(O)(O)=O)O2)C(=O)NC1=O

Pharmacology

Indication
Not Available
Structured Indications
Not Available
Pharmacodynamics
Not Available
Mechanism of action
TargetActionsOrganism
UThymidylate kinaseNot AvailableMycobacterium tuberculosis
UThymidylate kinaseNot AvailableHuman
UThymidine kinaseNot AvailableHHV-1
UThymidylate synthaseNot AvailableHuman
UDNA topoisomerase 1Not AvailableEscherichia coli (strain K12)
UThymidylate synthaseNot AvailableLactobacillus casei
UPCZA361.16Not AvailableAmycolatopsis orientalis
UDNA polymerase III subunit epsilonNot AvailableEscherichia coli (strain K12)
UGlucose-1-phosphate thymidylyltransferaseNot AvailablePseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
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
PathwayCategory
Pyrimidine MetabolismMetabolic
MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy)Disease
Beta Ureidopropionase DeficiencyDisease
Dihydropyrimidinase DeficiencyDisease
UMP Synthase Deficiency (Orotic Aciduria)Disease
Pharmacogenomic Effects/ADRs
Not Available

Interactions

Drug Interactions
Not Available
Food Interactions
Not Available

References

Synthesis Reference

Timothy Benson, "Crystallization and structure determination of staphylococcus aureus thymidylate kinase." U.S. Patent US20040171050, issued September 02, 2004.

US20040171050
General References
Not Available
External Links
Human Metabolome Database
HMDB01227
KEGG Compound
C00364
PubChem Compound
9700
PubChem Substance
46504719
ChemSpider
9319
BindingDB
50332929
ChEBI
17013
ChEMBL
CHEMBL394429
HET
DT
PDB Entries
1cy1 / 1cy2 / 1cy4 / 1cy7 / 1cy8 / 1e2d / 1e2e / 1e2f / 1e2g / 1e2q
show 63 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 Solubility6.78 mg/mLALOGPS
logP-1.4ALOGPS
logP-1.2ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)1.23ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area145.63 Å2ChemAxon
Rotatable Bond Count4ChemAxon
Refractivity66.28 m3·mol-1ChemAxon
Polarizability27.56 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted ADMET features
PropertyValueProbability
Human Intestinal Absorption-0.6163
Blood Brain Barrier+0.7483
Caco-2 permeable-0.7958
P-glycoprotein substrateNon-substrate0.622
P-glycoprotein inhibitor INon-inhibitor0.7939
P-glycoprotein inhibitor IINon-inhibitor0.9698
Renal organic cation transporterNon-inhibitor0.9135
CYP450 2C9 substrateNon-substrate0.6352
CYP450 2D6 substrateNon-substrate0.8525
CYP450 3A4 substrateSubstrate0.5394
CYP450 1A2 substrateNon-inhibitor0.8991
CYP450 2C9 inhibitorNon-inhibitor0.8806
CYP450 2D6 inhibitorNon-inhibitor0.9153
CYP450 2C19 inhibitorNon-inhibitor0.8753
CYP450 3A4 inhibitorNon-inhibitor0.823
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9228
Ames testNon AMES toxic0.618
CarcinogenicityNon-carcinogens0.8044
BiodegradationNot ready biodegradable0.6481
Rat acute toxicity2.3169 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9424
hERG inhibition (predictor II)Non-inhibitor0.8058
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
GC-MS Spectrum - GC-EI-TOFGC-MSsplash10-01u0-0961000000-4380a23f8bec3c2dd015
GC-MS Spectrum - GC-EI-TOFGC-MSsplash10-03k9-0940000000-6238904f1b1f293aaf3a
MS/MS Spectrum - Quattro_QQQ 10V, PositiveLC-MS/MSsplash10-001i-9110000000-a45c0d5a58cdb0e5fee4
MS/MS Spectrum - Quattro_QQQ 25V, PositiveLC-MS/MSsplash10-001i-9000000000-624fe22ca203d0e6430e
MS/MS Spectrum - Quattro_QQQ 40V, PositiveLC-MS/MSsplash10-001i-9000000000-0c23943cc868acaaeda4
LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , NegativeLC-MS/MSsplash10-004i-9703000000-452b674ca61adb40209b
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
LC-MS/MS Spectrum - LC-ESI-QTOF , negativeLC-MS/MSsplash10-004i-9703000000-452b674ca61adb40209b
1H NMR Spectrum1D NMRNot Applicable
1H NMR Spectrum1D NMRNot Applicable
[1H,1H] 2D NMR Spectrum2D NMRNot Applicable
[1H,13C] 2D NMR Spectrum2D NMRNot Applicable

Taxonomy

Description
This compound belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside monophosphates. These are pyrimidine nucleotides with a monophosphate group linked to the ribose moiety lacking 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 2'-deoxyribonucleoside monophosphates
Alternative Parents
Pyrimidones / Monoalkyl phosphates / Hydropyrimidines / Vinylogous amides / Tetrahydrofurans / Heteroaromatic compounds / Ureas / Secondary alcohols / Lactams / Oxacyclic compounds
show 5 more
Substituents
Pyrimidine 2'-deoxyribonucleoside monophosphate / Pyrimidone / Monoalkyl phosphate / Hydropyrimidine / Organic phosphoric acid derivative / Phosphoric acid ester / Pyrimidine / Alkyl phosphate / Heteroaromatic compound / Vinylogous amide
show 16 more
Molecular Framework
Aromatic heteromonocyclic compounds
External Descriptors
thymidine 5'-monophosphate (CHEBI:17013) / Deoxyribonucleotides (C00364)

Targets

Details
1. Thymidylate kinase
Kind
Protein
Organism
Mycobacterium tuberculosis
Pharmacological action
Unknown
General Function
Catalyzes the reversible phosphorylation of deoxythymidine monophosphate (dTMP) to deoxythymidine diphosphate (dTDP), using ATP as its preferred phosphoryl donor. Situated at the junction of both de novo and salvage pathways of deoxythymidine triphosphate (dTTP) synthesis, is essential for DNA synthesis and cellular growth. Has a broad specificity for nucleoside triphosphates, being highly active with ATP or dATP as phosphate donors, and less active with ITP, GTP, CTP and UTP.
Specific Function
Atp binding
Gene Name
tmk
Uniprot ID
P9WKE1
Uniprot Name
Thymidylate kinase
Molecular Weight
22634.285 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
Human
Pharmacological action
Unknown
General Function
Uridylate kinase activity
Specific Function
Catalyzes the conversion of dTMP to dTDP.
Gene Name
DTYMK
Uniprot ID
P23919
Uniprot Name
Thymidylate kinase
Molecular Weight
23819.105 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]
  3. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235]
Kind
Protein
Organism
HHV-1
Pharmacological action
Unknown
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
P03176
Uniprot Name
Thymidine kinase
Molecular Weight
40971.555 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
Human
Pharmacological action
Unknown
General Function
Thymidylate synthase activity
Specific Function
Contributes to the de novo mitochondrial thymidylate biosynthesis pathway.
Gene Name
TYMS
Uniprot ID
P04818
Uniprot Name
Thymidylate synthase
Molecular Weight
35715.65 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
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
Lactobacillus casei
Pharmacological action
Unknown
General Function
Thymidylate synthase activity
Specific Function
Provides the sole de novo source of dTMP for DNA biosynthesis.
Gene Name
thyA
Uniprot ID
P00469
Uniprot Name
Thymidylate synthase
Molecular Weight
36579.235 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
Amycolatopsis orientalis
Pharmacological action
Unknown
General Function
Dtdp-4-dehydrorhamnose 3,5-epimerase activity
Specific Function
Not Available
Gene Name
Not Available
Uniprot ID
O52806
Uniprot Name
PCZA361.16
Molecular Weight
22488.53 Da
Kind
Protein
Organism
Escherichia coli (strain K12)
Pharmacological action
Unknown
General Function
Metal ion binding
Specific Function
DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The epsilon subunit contain the editing function and is a proofreading 3'-5' exonuc...
Gene Name
dnaQ
Uniprot ID
P03007
Uniprot Name
DNA polymerase III subunit epsilon
Molecular Weight
27098.7 Da
Kind
Protein
Organism
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Pharmacological action
Unknown
General Function
Nucleotide binding
Specific Function
Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis.
Gene Name
rmlA
Uniprot ID
Q9HU22
Uniprot Name
Glucose-1-phosphate thymidylyltransferase
Molecular Weight
32456.65 Da

Drug created on June 13, 2005 07:24 / Updated on November 09, 2017 03:02