Identification

Name
Deoxythymidine
Accession Number
DB04485  (EXPT03053)
Type
Small Molecule
Groups
Experimental, Investigational
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
Categories
UNII
VC2W18DGKR
CAS number
50-89-5
Weight
Average: 242.2286
Monoisotopic: 242.090271568
Chemical Formula
C10H14N2O5
InChI Key
IQFYYKKMVGJFEH-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

Indication
Not Available
Structured Indications
Not Available
Pharmacodynamics
Not Available
Mechanism of action
TargetActionsOrganism
UThymidylate kinaseNot AvailableMycobacterium tuberculosis
UThymidine kinaseNot AvailableHHV-1
UUridine phosphorylaseNot AvailableEscherichia coli (strain K12)
UThymidine kinaseNot AvailableEHV-4
UThymidine kinase 2, mitochondrialNot AvailableHuman
UNucleoside-specific channel-forming protein tsxNot 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

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

US4921950
General References
Not Available
External Links
Human Metabolome Database
HMDB00273
KEGG Compound
C00214
PubChem Compound
5789
PubChem Substance
46507598
ChemSpider
5585
BindingDB
1
ChEBI
17748
ChEMBL
CHEMBL52609
HET
THM
Wikipedia
Thymidine
PDB Entries
1e2j / 1g0r / 1h5r / 1kim / 1ot3 / 1p6x / 1p72 / 1p7c / 1rxu / 1tlw
show 35 more

Clinical Trials

Clinical Trials
PhaseStatusPurposeConditionsCount
2CompletedTreatment5'-Nucleotidase Syndrome1

Pharmacoeconomics

Manufacturers
Not Available
Packagers
Not Available
Dosage forms
Not Available
Prices
Not Available
Patents
Not Available

Properties

State
Solid
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
SpectrumSpectrum TypeSplash Key
GC-MS Spectrum - GC-MS (2 TMS)GC-MSsplash10-0udi-1900000000-8e769118bc877facb05f
GC-MS Spectrum - GC-MS (3 TMS)GC-MSsplash10-0ue9-2910000000-823bcee487948a9c786f
Predicted GC-MS Spectrum - GC-MSPredicted GC-MSNot Available
GC-MS Spectrum - GC-MSGC-MSsplash10-0udi-1900000000-8e769118bc877facb05f
GC-MS Spectrum - GC-MSGC-MSsplash10-0ue9-2910000000-823bcee487948a9c786f
GC-MS Spectrum - GC-EI-TOFGC-MSsplash10-0udi-0900000000-996530d1ea081ac2a7c7
GC-MS Spectrum - GC-EI-TOFGC-MSsplash10-0l6r-0900000000-4645a52830204c8ef5d0
GC-MS Spectrum - GC-EI-TOFGC-MSsplash10-0zfr-0900000000-76b8a050c10b514ed50b
MS/MS Spectrum - Quattro_QQQ 10V, PositiveLC-MS/MSsplash10-004i-0900000000-1c2ba2f2aace4a76cdea
MS/MS Spectrum - Quattro_QQQ 25V, PositiveLC-MS/MSsplash10-004i-3900000000-d177672ef3f383adbb5d
MS/MS Spectrum - Quattro_QQQ 40V, PositiveLC-MS/MSsplash10-01p9-9000000000-4483af567feecb34a651
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, NegativeLC-MS/MSsplash10-0006-0090000000-435be9f03e969dbabb79
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, NegativeLC-MS/MSsplash10-0006-5690000000-79b230d52929aa67bbf2
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, NegativeLC-MS/MSsplash10-0006-9100000000-28a604508965067c85c5
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, NegativeLC-MS/MSsplash10-0006-9000000000-360e0667ff3d7d77e706
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, NegativeLC-MS/MSsplash10-0006-9000000000-b1fecd2d1fa166e22d5f
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, PositiveLC-MS/MSsplash10-004i-1920000000-1a2e609b8a19ef491964
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, PositiveLC-MS/MSsplash10-004i-1900000000-5e4a733641fa285e7f74
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, PositiveLC-MS/MSsplash10-004i-3900000000-f734d5813fecb7a31814
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, PositiveLC-MS/MSsplash10-01t9-5900000000-53b0016c66aa014c2abc
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, PositiveLC-MS/MSsplash10-03e9-9600000000-48f1a0d5512651a93e14
LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , PositiveLC-MS/MSsplash10-004i-1910000000-f02c2133ea475f4f838c
LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , PositiveLC-MS/MSsplash10-08i0-2900000000-ec21970768da0fbf8ce5
LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , PositiveLC-MS/MSsplash10-0002-9000000000-17c234cb0e8de5ae82f4
LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , PositiveLC-MS/MSsplash10-014i-9000000000-d7e5ed251a93758682ec
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-QQ , negativeLC-MS/MSsplash10-0006-0090000000-435be9f03e969dbabb79
LC-MS/MS Spectrum - LC-ESI-QQ , negativeLC-MS/MSsplash10-0006-5690000000-79b230d52929aa67bbf2
LC-MS/MS Spectrum - LC-ESI-QQ , negativeLC-MS/MSsplash10-0006-9100000000-28a604508965067c85c5
LC-MS/MS Spectrum - LC-ESI-QQ , negativeLC-MS/MSsplash10-0006-9000000000-360e0667ff3d7d77e706
LC-MS/MS Spectrum - LC-ESI-QQ , negativeLC-MS/MSsplash10-0006-9000000000-b1fecd2d1fa166e22d5f
LC-MS/MS Spectrum - LC-ESI-QQ , positiveLC-MS/MSsplash10-004i-1920000000-1a2e609b8a19ef491964
LC-MS/MS Spectrum - LC-ESI-QQ , positiveLC-MS/MSsplash10-004i-1900000000-9d8e0993092f578cc8f6
LC-MS/MS Spectrum - LC-ESI-QQ , positiveLC-MS/MSsplash10-004i-3900000000-e0521f9b56ef22bf8b3f
LC-MS/MS Spectrum - LC-ESI-QQ , positiveLC-MS/MSsplash10-01t9-5900000000-50dfea3f53e01a5eb616
LC-MS/MS Spectrum - LC-ESI-QQ , positiveLC-MS/MSsplash10-03e9-9600000000-c9ba28b7314a771703b3
LC-MS/MS Spectrum - LC-ESI-IT , positiveLC-MS/MSsplash10-004i-1900000000-7b67aad6f6257db9d603
1H NMR Spectrum1D NMRNot Applicable
1H NMR Spectrum1D NMRNot Applicable
13C 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'-deoxyribonucleosides. These are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.
Kingdom
Organic compounds
Super Class
Nucleosides, nucleotides, and analogues
Class
Pyrimidine nucleosides
Sub Class
Pyrimidine 2'-deoxyribonucleosides
Direct Parent
Pyrimidine 2'-deoxyribonucleosides
Alternative Parents
Pyrimidones / Hydroxypyrimidines / Hydropyrimidines / Tetrahydrofurans / Heteroaromatic compounds / Secondary alcohols / Oxacyclic compounds / Azacyclic compounds / Primary alcohols / Organopnictogen compounds
show 3 more
Substituents
Pyrimidine 2'-deoxyribonucleoside / Pyrimidone / Hydroxypyrimidine / Hydropyrimidine / Pyrimidine / Heteroaromatic compound / Tetrahydrofuran / Secondary alcohol / Oxacycle / Azacycle
show 11 more
Molecular Framework
Aromatic heteromonocyclic compounds
External Descriptors
pyrimidine 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 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
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 ...
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 the...
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-methylnico...
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 subtyp...
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 November 09, 2017 03:42