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Identification
NameThymidine-5'-Phosphate
Accession NumberDB01643  (EXPT03073, EXPT02988)
TypeSmall Molecule
GroupsExperimental
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
External Identifiers Not Available
Approved Prescription ProductsNot Available
Approved Generic Prescription ProductsNot Available
Approved Over the Counter ProductsNot Available
Unapproved/Other Products Not Available
International BrandsNot Available
Brand mixturesNot Available
SaltsNot Available
CategoriesNot Available
UNII43W3021X6C
CAS number365-07-1
WeightAverage: 322.2085
Monoisotopic: 322.056601978
Chemical FormulaC10H15N2O8P
InChI KeyInChIKey=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)[C@@H](COP(O)(O)=O)O2)C(=O)NC1=O
Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as pyrimidine deoxyribonucleotides. These are pyrimidine nucleotides where the purine moiety is linked to a ribose lacking a hydroxyl group at one or more positions.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassPyrimidine deoxyribonucleotides
Direct ParentPyrimidine deoxyribonucleotides
Alternative Parents
Substituents
  • Pyrimidine deoxyribonucleotide
  • Monoalkyl phosphate
  • Pyrimidone
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Hydropyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Oxolane
  • Urea
  • Secondary alcohol
  • Lactam
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Pharmacology
IndicationNot Available
PharmacodynamicsNot Available
Mechanism of actionNot Available
Related Articles
AbsorptionNot Available
Volume of distributionNot Available
Protein bindingNot Available
MetabolismNot Available
Route of eliminationNot Available
Half lifeNot Available
ClearanceNot Available
ToxicityNot Available
Affected organismsNot Available
Pathways
PathwayCategorySMPDB ID
Pyrimidine MetabolismMetabolicSMP00046
MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy)DiseaseSMP00202
Beta Ureidopropionase DeficiencyDiseaseSMP00172
Dihydropyrimidinase DeficiencyDiseaseSMP00178
UMP Synthase Deiciency (Orotic Aciduria)DiseaseSMP00219
SNP Mediated EffectsNot Available
SNP Mediated Adverse Drug ReactionsNot Available
ADMET
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 )
Pharmacoeconomics
ManufacturersNot Available
PackagersNot Available
Dosage formsNot Available
PricesNot Available
PatentsNot Available
Properties
StateSolid
Experimental PropertiesNot 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 FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Mass Spec (NIST)Not Available
Spectra
Spectrum TypeDescriptionSplash Key
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-001i-9110000000-a45c0d5a58cdb0e5fee4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-001i-9000000000-624fe22ca203d0e6430eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-001i-9000000000-0c23943cc868acaaeda4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-004i-9703000000-452b674ca61adb40209bView in MoNA
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,1H] 2D NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot 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 ReferencesNot Available
External Links
ATC CodesNot Available
AHFS CodesNot Available
PDB Entries
FDA labelNot Available
MSDSNot Available
Interactions
Drug InteractionsNot Available
Food InteractionsNot Available

Targets

Kind
Protein
Organism
Mycobacterium tuberculosis
Pharmacological action
unknown
General Function:
Nucleotide transport and metabolism
Specific 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 acti...
Gene Name:
tmk
Uniprot ID:
O05891
Molecular Weight:
22635.0 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
Human
Pharmacological action
unknown
General Function:
Uridylate kinase activity
Specific Function:
Catalyzes the conversion of dTMP to dTDP.
Gene Name:
DTYMK
Uniprot ID:
P23919
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 their genome.
Gene Name:
TK
Uniprot ID:
P03176
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
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. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(...
Gene Name:
topA
Uniprot ID:
P06612
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
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
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' exonuclease.
Gene Name:
dnaQ
Uniprot ID:
P03007
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
Molecular Weight:
32456.65 Da
Comments
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Drug created on June 13, 2005 07:24 / Updated on September 16, 2013 17:15