Thymidine (YMDB00507)

Identification
YMDB IDYMDB00507
NameThymidine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionThymidine, also known as deoxythymidine or DTHD, belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2. Thymidine is an extremely weak basic (essentially neutral) compound (based on its pKa). Thymidine exists in all living species, ranging from bacteria to humans. In yeast, thymidine is involved in the metabolic pathway called the pyrimidine metabolism pathway. Thymidine is a potentially toxic compound.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 1-(2-deoxy-beta-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione
  • 2-deoxythymidine
  • 2-Desoxy-thymidine
  • 2'-deoxy-5-methyl-Uridine
  • 2'-deoxy-5-methyluridine
  • 2'-Deoxythymidine
  • 2'-thymidine
  • 5-Methyl-2'-deoxyuridine
  • 5-Methyldeoxyuridine
  • 5-Methyldeoxyurindine
  • beta-D-Ribofuranoside, thymine-1 2-deoxy-
  • deoxyribosylthymine
  • Deoxyribothymidine
  • Deoxythymidin
  • deoxythymidine
  • Desoxy-thymidin
  • dT
  • dThd
  • DThyd
  • Thymidin
  • Thymidine
  • Thymidine, 2'-deoxy-
  • Thymine 2-desoxyriboside
  • thymine 2'-deoxyriboside
  • Thymine deoxyriboside
  • thymine-1 2-deoxy-b-D-Ribofuranoside
  • thymine-1 2-deoxy-beta-delta-Ribofuranoside
  • Thymine-2-deoxyriboside
  • Thymine-2-Desoxyriboside
  • Thyminedeoxyriboside
  • Uridine, 2'-deoxy-5-methyl-
  • T
  • 1-(2-Deoxy-b-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione
  • 1-(2-Deoxy-β-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione
  • 1-(2-Deoxy-b-D-erythro-pentofuranosyl)-5-methyl-2,4(1H,3H)-pyrimidinedione
  • 1-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-5-methyl-2,4(1H,3H)-pyrimidinedione
  • 1-[4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione
  • 2' Deoxythymidine
CAS number50-89-5
WeightAverage: 242.2286
Monoisotopic: 242.090271568
InChI KeyIQFYYKKMVGJFEH-XLPZGREQSA-N
InChIInChI=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 Name1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Namethymidine
Chemical FormulaC10H14N2O5
SMILESCC1=CN([C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)NC1=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassPyrimidine 2'-deoxyribonucleosides
Direct ParentPyrimidine 2'-deoxyribonucleosides
Alternative Parents
Substituents
  • Pyrimidine 2'-deoxyribonucleoside
  • Pyrimidone
  • Hydroxypyrimidine
  • Hydropyrimidine
  • Pyrimidine
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point186.5 °C
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogP-0.93 [SANGSTER (1993)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility66.8 g/LALOGPS
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 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity55.41 m³·mol⁻¹ChemAxon
Polarizability23.06 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • extracellular
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Pyrimidine metabolismPW002469 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Pyrimidine metabolismec00240 Map00240
SMPDB ReactionsNot Available
KEGG Reactions
water + 5-Thymidylic acid → phosphate + Thymidine
Adenosine triphosphate + Thymidine → hydron + ADP + 5-Thymidylic acid
phosphate + Thymidine ↔ Thymine + 2-deoxy-D-ribofuranose 1-phosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-MS (2 TMS)splash10-0udi-1900000000-8e769118bc877facb05fJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-0ue9-2910000000-823bcee487948a9c786fJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0udi-1900000000-8e769118bc877facb05fJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0ue9-2910000000-823bcee487948a9c786fJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-0900000000-996530d1ea081ac2a7c7JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0l6r-0900000000-4645a52830204c8ef5d0JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0zfr-0900000000-76b8a050c10b514ed50bJSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-9530000000-627a60bbe3e0b90f58cbJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-0g4i-7905000000-7b0c67709e3a5f91841aJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-004i-0900000000-1c2ba2f2aace4a76cdeaJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-004i-3900000000-d177672ef3f383adbb5dJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-01p9-9000000000-4483af567feecb34a651JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-0006-0090000000-435be9f03e969dbabb79JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-0006-5690000000-79b230d52929aa67bbf2JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-0006-9100000000-28a604508965067c85c5JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0006-9000000000-360e0667ff3d7d77e706JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0006-9000000000-b1fecd2d1fa166e22d5fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-004i-1920000000-1a2e609b8a19ef491964JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-004i-1900000000-5e4a733641fa285e7f74JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-004i-3900000000-f734d5813fecb7a31814JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-01t9-5900000000-53b0016c66aa014c2abcJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-03e9-9600000000-48f1a0d5512651a93e14JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-004i-1910000000-f02c2133ea475f4f838cJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-08i0-2900000000-ec21970768da0fbf8ce5JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-0002-9000000000-17c234cb0e8de5ae82f4JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-014i-9000000000-d7e5ed251a93758682ecJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-0090000000-435be9f03e969dbabb79JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-5690000000-79b230d52929aa67bbf2JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-9ad72ff6cb2e2dfab911JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-4900000000-3b1e6c50c2450e123648JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-6900000000-d30b05dfe1b6d25ebd2bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-052g-1940000000-ce16baa1ceb8a83565c2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0ufr-3920000000-c6ff3f238b6fed007635JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9200000000-104a4f5a4fe8a0ed5ca3JSpectraViewer
MSMass Spectrum (Electron Ionization)splash10-01dj-9300000000-6e24b5b6d36e07dd73d0JSpectraViewer | MoNA
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
Synthesis Reference:Herdewijn, P.; Kerremans, L.; Wigerinck, P.; Vandendriessche, F.; Van Aerschot, A. Synthesis of thymidine from 5-iodo-2'-deoxyuridine. Tetrahedron Letters (1991), 32(34), 4397-400.
External Links:
ResourceLink
CHEBI ID17748
HMDB IDHMDB00273
Pubchem Compound ID5789
Kegg IDC00214
ChemSpider ID23630337
FOODB IDFDB031201
WikipediaThymidine
BioCyc IDTHYMIDINE

Enzymes

Protein Details
1. Purine nucleoside phosphorylase
General function:
Involved in purine-nucleoside phosphorylase activity
Specific function:
Cleavage of guanosine or inosine to respective bases and sugar-1-phosphate molecules
Gene Name:
PNP1
Uniprot ID:
Q05788
Molecular weight:
33754.60156
Reactions
Purine nucleoside + phosphate → purine + alpha-D-ribose 1-phosphate.