Identification
NameDeoxythymidine
Accession NumberDB04485  (EXPT03053)
TypeSmall Molecule
GroupsExperimental
Description

Deoxythymidine is a pyrimidine deoxynucleoside. Deoxythymidine is the DNA nucleoside T, which pairs with deoxyadenosine (A) in double-stranded DNA. In cell biology it is used to synchronize the cells in S phase.

Structure
Thumb
Synonyms
2'-Deoxythymidine
deoxyribosylthymine
Thymidine
thymine deoxyriboside
External IDs NSC-21548
Product Ingredients 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
Categories
UNIIVC2W18DGKR
CAS number50-89-5
WeightAverage: 242.2286
Monoisotopic: 242.090271568
Chemical FormulaC10H14N2O5
InChI KeyIQFYYKKMVGJFEH-XLPZGREQSA-N
InChI
InChI=1S/C10H14N2O5/c1-5-3-12(10(16)11-9(5)15)8-2-6(14)7(4-13)17-8/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16)/t6-,7+,8+/m0/s1
IUPAC Name
1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
SMILES
CC1=CN([[email protected]]2C[[email protected]](O)[[email protected]@H](CO)O2)C(=O)NC1=O
Pharmacology
IndicationNot Available
Structured Indications Not Available
PharmacodynamicsNot Available
Mechanism of action
TargetKindPharmacological actionActionsOrganismUniProt ID
Thymidylate kinaseProteinunknownNot AvailableMycobacterium tuberculosisP9WKE1 details
Thymidine kinaseProteinunknownNot AvailableHHV-1P03176 details
Uridine phosphorylaseProteinunknownNot AvailableEscherichia coli (strain K12)P12758 details
Thymidine kinaseProteinunknownNot AvailableEHV-4P24425 details
Thymidine kinase 2, mitochondrialProteinunknownNot AvailableHumanO00142 details
Nucleoside-specific channel-forming protein tsxProteinunknownNot AvailableEscherichia coli (strain K12)P0A927 details
Glucose-1-phosphate thymidylyltransferaseProteinunknownNot AvailablePseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)Q9HU22 details
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
Pharmacogenomic Effects/ADRs Not Available
Interactions
Drug Interactions Not Available
Food InteractionsNot Available
References
Synthesis Reference

Jeffrey D. Wilson, "Preparation of 3'azido-3-'-deoxythymidine." U.S. Patent US4921950, issued October, 1986.

US4921950
General ReferencesNot Available
External Links
ATC CodesNot Available
AHFS CodesNot Available
PDB Entries
FDA labelNot Available
MSDSNot Available
Clinical Trials
Clinical Trials
PhaseStatusPurposeConditionsCount
2CompletedTreatment5'-Nucleotidase Syndrome1
Pharmacoeconomics
ManufacturersNot Available
PackagersNot Available
Dosage formsNot Available
PricesNot Available
PatentsNot Available
Properties
StateSolid
Experimental Properties
PropertyValueSource
melting point (°C)186.5 °CPhysProp
logP-0.93SANGSTER (1993)
Predicted Properties
PropertyValueSource
Water Solubility66.8 mg/mLALOGPS
logP-1.3ALOGPS
logP-1.1ChemAxon
logS-0.56ALOGPS
pKa (Strongest Acidic)9.96ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area99.1 Å2ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity55.41 m3·mol-1ChemAxon
Polarizability23.06 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted ADMET features
PropertyValueProbability
Human Intestinal Absorption+0.971
Blood Brain Barrier+0.5902
Caco-2 permeable-0.8851
P-glycoprotein substrateNon-substrate0.6468
P-glycoprotein inhibitor INon-inhibitor0.8872
P-glycoprotein inhibitor IINon-inhibitor0.9128
Renal organic cation transporterNon-inhibitor0.9072
CYP450 2C9 substrateNon-substrate0.6893
CYP450 2D6 substrateNon-substrate0.8834
CYP450 3A4 substrateNon-substrate0.5083
CYP450 1A2 substrateNon-inhibitor0.9529
CYP450 2C9 inhibitorNon-inhibitor0.9392
CYP450 2D6 inhibitorNon-inhibitor0.9491
CYP450 2C19 inhibitorNon-inhibitor0.9479
CYP450 3A4 inhibitorNon-inhibitor0.9308
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9415
Ames testNon AMES toxic0.9133
CarcinogenicityNon-carcinogens0.7872
BiodegradationNot ready biodegradable0.5131
Rat acute toxicity1.8754 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9358
hERG inhibition (predictor II)Non-inhibitor0.8734
ADMET data is predicted using admetSAR, a free tool for evaluating chemical ADMET properties. (23092397 )
Spectra
Mass Spec (NIST)Not Available
Spectra
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-MS (2 TMS)splash10-0udi-1900000000-8e769118bc877facb05fView in MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-0ue9-2910000000-823bcee487948a9c786fView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MSNot Available
GC-MSGC-MS Spectrum - GC-MSsplash10-0udi-1900000000-8e769118bc877facb05fView in MoNA
GC-MSGC-MS Spectrum - GC-MSsplash10-0ue9-2910000000-823bcee487948a9c786fView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOFsplash10-0udi-0900000000-996530d1ea081ac2a7c7View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOFsplash10-0l6r-0900000000-4645a52830204c8ef5d0View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOFsplash10-0zfr-0900000000-76b8a050c10b514ed50bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-004i-0900000000-1c2ba2f2aace4a76cdeaView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-004i-3900000000-d177672ef3f383adbb5dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-01p9-9000000000-4483af567feecb34a651View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-0006-0090000000-435be9f03e969dbabb79View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-0006-5690000000-79b230d52929aa67bbf2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-0006-9100000000-28a604508965067c85c5View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0006-9000000000-360e0667ff3d7d77e706View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0006-9000000000-b1fecd2d1fa166e22d5fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-004i-1920000000-1a2e609b8a19ef491964View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-004i-1900000000-5e4a733641fa285e7f74View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-004i-3900000000-f734d5813fecb7a31814View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-01t9-5900000000-53b0016c66aa014c2abcView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-03e9-9600000000-48f1a0d5512651a93e14View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-004i-1910000000-f02c2133ea475f4f838cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-08i0-2900000000-ec21970768da0fbf8ce5View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-0002-9000000000-17c234cb0e8de5ae82f4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-014i-9000000000-d7e5ed251a93758682ecView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-0090000000-435be9f03e969dbabb79View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-5690000000-79b230d52929aa67bbf2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR13C NMR SpectrumNot Available
2D NMR[1H,1H] 2D NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
Taxonomy
DescriptionThis compound belongs to the class of chemical entities known as pyrimidine 2'-deoxyribonucleosides. These are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.
KingdomChemical entities
Super ClassOrganic compounds
ClassNucleosides, nucleotides, and analogues
Sub ClassPyrimidine nucleosides
Direct ParentPyrimidine 2'-deoxyribonucleosides
Alternative ParentsPyrimidones / Hydroxypyrimidines / Hydropyrimidines / Oxolanes / Heteroaromatic compounds / Secondary alcohols / Oxacyclic compounds / Azacyclic compounds / Primary alcohols / Organopnictogen compounds
SubstituentsPyrimidine 2'-deoxyribonucleoside / Hydroxypyrimidine / Pyrimidone / Hydropyrimidine / Pyrimidine / Oxolane / Heteroaromatic compound / Secondary alcohol / Azacycle / Organoheterocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptorspyrimidine 2'-deoxyribonucleoside (CHEBI:17748 ) / Deoxyribonucleosides (C00214 )

Targets

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
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
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
Escherichia coli (strain K12)
Pharmacological action
unknown
General Function:
Uridine phosphorylase activity
Specific Function:
Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
Gene Name:
udp
Uniprot ID:
P12758
Uniprot Name:
Uridine phosphorylase
Molecular Weight:
27158.88 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
EHV-4
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:
P24425
Uniprot Name:
Thymidine kinase
Molecular Weight:
38784.035 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:
Thymidine kinase activity
Specific Function:
Deoxyribonucleoside kinase that phosphorylates thymidine, deoxycytidine, and deoxyuridine. Also phosphorylates anti-viral and anti-cancer nucleoside analogs.
Gene Name:
TK2
Uniprot ID:
O00142
Uniprot Name:
Thymidine kinase 2, mitochondrial
Molecular Weight:
31004.53 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
Escherichia coli (strain K12)
Pharmacological action
unknown
General Function:
Nucleoside-specific channel forming porin activity
Specific Function:
Constitutes the receptor for colicin K and phage T6, and functions as substrate-specific channel for nucleosides and deoxynucleosides.
Gene Name:
tsx
Uniprot ID:
P0A927
Uniprot Name:
Nucleoside-specific channel-forming protein tsx
Molecular Weight:
33588.835 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
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

Transporters

Kind
Protein
Organism
Human
Pharmacological action
unknown
Actions
inhibitor
General Function:
Secondary active organic cation transmembrane transporter activity
Specific Function:
Translocates a broad array of organic cations with various structures and molecular weights including the model compounds 1-methyl-4-phenylpyridinium (MPP), tetraethylammonium (TEA), N-1-methylnicotinamide (NMN), 4-(4-(dimethylamino)styryl)-N-methylpyridinium (ASP), the endogenous compounds choline, guanidine, histamine, epinephrine, adrenaline, noradrenaline and dopamine, and the drugs quinine...
Gene Name:
SLC22A1
Uniprot ID:
O15245
Uniprot Name:
Solute carrier family 22 member 1
Molecular Weight:
61153.345 Da
References
  1. Zhang L, Dresser MJ, Gray AT, Yost SC, Terashita S, Giacomini KM: Cloning and functional expression of a human liver organic cation transporter. Mol Pharmacol. 1997 Jun;51(6):913-21. [PubMed:9187257 ]
Kind
Protein
Organism
Human
Pharmacological action
unknown
General Function:
Pyrimidine- and adenine-specific:sodium symporter activity
Specific Function:
Sodium-dependent, pyrimidine- and purine-selective. Involved in the homeostasis of endogenous nucleosides. Exhibits the transport characteristics of the nucleoside transport system cib or N3 subtype (N3/cib) (with marked transport of both thymidine and inosine). Employs a 2:1 sodium/nucleoside ratio. Also able to transport gemcitabine, 3'-azido-3'-deoxythymidine (AZT), ribavirin and 3-deazaurid...
Gene Name:
SLC28A3
Uniprot ID:
Q9HAS3
Uniprot Name:
Solute carrier family 28 member 3
Molecular Weight:
76929.61 Da
References
  1. Badagnani I, Chan W, Castro RA, Brett CM, Huang CC, Stryke D, Kawamoto M, Johns SJ, Ferrin TE, Carlson EJ, Burchard EG, Giacomini KM: Functional analysis of genetic variants in the human concentrative nucleoside transporter 3 (CNT3; SLC28A3). Pharmacogenomics J. 2005;5(3):157-65. [PubMed:15738947 ]
Drug created on June 13, 2005 07:24 / Updated on September 01, 2017 11:17