Record Information
Version1.0
Created at2020-04-17 18:41:34 UTC
Updated at2020-12-07 19:11:03 UTC
CannabisDB IDCDB004834
Secondary Accession NumbersNot Available
Cannabis Compound Identification
Common NameThymidine
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 cell biology it is used to synchronize the cells in S phase. Within humans, thymidine participates in a number of enzymatic reactions. In particular, thymidine can be biosynthesized from 5-thymidylic acid through its interaction with the enzyme cytosolic purine 5'-nucleotidase. In addition, thymidine can be converted into 5-thymidylic acid; which is catalyzed by the enzyme thymidine kinase, cytosolic. In humans, thymidine is involved in the metabolic disorder called ump synthase deficiency (orotic aciduria). Outside of the human body, Thymidine has been detected, but not quantified in, several different foods, such as horned melons, asian pears, brassicas, japanese chestnuts, and apricots. This could make thymidine a potential biomarker for the consumption of these foods. Thymidine is a potentially toxic compound. Thymidine is non-toxic and is a naturally occurring compound that exists in all living organisms and DNA viruses. RNA does not have thymidine and has uridine instead. Thymidine is the DNA base T, which pairs with adenosine in double stranded DNA. 25% of DNA is composed of thymidine. Thymidine is a chemical compound which is a pyrimidine nucleoside. Thymidine is the DNA nucleoside T, which pairs with deoxyadenosine (A) in double-stranded DNA. Thymidine is a pyrimidine deoxynucleoside. Thymidine is expected to be in Cannabis as all living plants are known to produce and metabolize it.
Structure
Thumb
Synonyms
ValueSource
1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dioneChEBI
2'-Deoxy-5-methyluridineChEBI
2'-DeoxythymidineChEBI
2'-ThymidineChEBI
5-Methyl-2'-deoxyuridineChEBI
DeoxythymidineChEBI
DTHDChEBI
TChEBI
Thymine 2'-deoxyribosideChEBI
1-(2-Deoxy-b-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dioneGenerator
1-(2-Deoxy-β-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dioneGenerator
1-(2-Deoxy-b-D-erythro-pentofuranosyl)-5-methyl-2,4(1H,3H)-pyrimidinedioneHMDB
1-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-5-methyl-2,4(1H,3H)-pyrimidinedioneHMDB
1-[4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-pyrimidine-2,4-dioneHMDB
2'-Deoxy-5-methyl-uridineHMDB
5-MethyldeoxyuridineHMDB
DeoxyribothymidineHMDB
DTHMDB
DThydHMDB
ThymidinHMDB
Thymine 2-desoxyribosideHMDB
Thymine deoxyribosideHMDB
Thymine-1 2-deoxy-b-D-ribofuranosideHMDB
Thymine-1 2-deoxy-beta-delta-ribofuranosideHMDB
2' DeoxythymidineHMDB
Chemical FormulaC10H14N2O5
Average Molecular Weight242.23
Monoisotopic Molecular Weight242.0903
IUPAC Name1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Namethymidine
CAS Registry Number50-89-5
SMILES
CC1=CN([C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)NC1=O
InChI Identifier
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
InChI KeyIQFYYKKMVGJFEH-XLPZGREQSA-N
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
Ontology
Physiological effect

Health effect:

Disposition

Route of exposure:

Source:

Biological location:

Role

Biological role:

Industrial application:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility73.5 mg/mLNot Available
logP-0.93SANGSTER (1993)
Predicted Properties
PropertyValueSource
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
EI-MSMass Spectrum (Electron Ionization)splash10-01dj-9300000000-6e24b5b6d36e07dd73d0Spectrum
GC-MSThymidine, 2 TMS, GC-MS Spectrumsplash10-0udi-1900000000-8e769118bc877facb05fSpectrum
GC-MSThymidine, 3 TMS, GC-MS Spectrumsplash10-0ue9-2910000000-823bcee487948a9c786fSpectrum
GC-MSThymidine, non-derivatized, GC-MS Spectrumsplash10-0udi-1900000000-8e769118bc877facb05fSpectrum
GC-MSThymidine, non-derivatized, GC-MS Spectrumsplash10-0ue9-2910000000-823bcee487948a9c786fSpectrum
GC-MSThymidine, non-derivatized, GC-MS Spectrumsplash10-0udi-0900000000-996530d1ea081ac2a7c7Spectrum
GC-MSThymidine, non-derivatized, GC-MS Spectrumsplash10-0l6r-0900000000-4645a52830204c8ef5d0Spectrum
GC-MSThymidine, non-derivatized, GC-MS Spectrumsplash10-0zfr-0900000000-76b8a050c10b514ed50bSpectrum
Predicted GC-MSThymidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-004i-9530000000-627a60bbe3e0b90f58cbSpectrum
Predicted GC-MSThymidine, 2 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0g4i-7905000000-7b0c67709e3a5f91841aSpectrum
Predicted GC-MSThymidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSThymidine, TMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSThymidine, TMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSThymidine, TMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSThymidine, TMS_2_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSThymidine, TMS_2_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSThymidine, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSThymidine, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSThymidine, TBDMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSThymidine, TBDMS_2_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSThymidine, TBDMS_2_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSThymidine, TBDMS_2_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-004i-0900000000-1c2ba2f2aace4a76cdeaSpectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-004i-3900000000-d177672ef3f383adbb5dSpectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-01p9-9000000000-4483af567feecb34a651Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-0006-0090000000-435be9f03e969dbabb79Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-0006-5690000000-79b230d52929aa67bbf2Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-0006-9100000000-28a604508965067c85c5Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0006-9000000000-360e0667ff3d7d77e706Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0006-9000000000-b1fecd2d1fa166e22d5fSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-004i-1920000000-1a2e609b8a19ef491964Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-004i-1900000000-5e4a733641fa285e7f74Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-004i-3900000000-f734d5813fecb7a31814Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-01t9-5900000000-53b0016c66aa014c2abcSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-03e9-9600000000-48f1a0d5512651a93e14Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-004i-1910000000-f02c2133ea475f4f838cSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-08i0-2900000000-ec21970768da0fbf8ce5Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-0002-9000000000-17c234cb0e8de5ae82f4Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-014i-9000000000-d7e5ed251a93758682ecSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-0090000000-435be9f03e969dbabb79Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-5690000000-79b230d52929aa67bbf2Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-9ad72ff6cb2e2dfab911Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-4900000000-3b1e6c50c2450e123648Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-6900000000-d30b05dfe1b6d25ebd2bSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-052g-1940000000-ce16baa1ceb8a83565c2Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0ufr-3920000000-c6ff3f238b6fed007635Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9200000000-104a4f5a4fe8a0ed5ca3Spectrum
NMR
TypeDescriptionView
1D NMR1H NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
2D NMR[1H,1H] 2D NMR SpectrumSpectrum
2D NMR[1H,13C] 2D NMR SpectrumSpectrum
Pathways
Pathways
Protein Targets
Enzymes
Protein NameGene NameLocusUniprot IDDetails
5'-nucleotidaseNT5E6q14-q21P21589 details
Cytosolic 5'-nucleotidase 1BNT5C1B2p24.2Q96P26 details
Cytosolic 5'-nucleotidase 1ANT5C1A1p34.3-p33Q9BXI3 details
5'(3')-deoxyribonucleotidase, cytosolic typeNT5CQ8TCD5 details
5'(3')-deoxyribonucleotidase, mitochondrialNT5MQ9NPB1 details
Cytosolic 5'-nucleotidase 3NT5C37p14.3Q9H0P0 details
Cytosolic purine 5'-nucleotidaseNT5C210q24.32P49902 details
Thymidine kinase, cytosolicTK117q23.2-q25.3P04183 details
Thymidine kinase 2, mitochondrialTK216q22-q23.1O00142 details
Thymidine phosphorylaseTYMP22q13.33P19971 details
Thymidine kinaseQ8IZR3 details
Transporters
Protein NameGene NameLocusUniprot IDDetails
Solute carrier family 22 member 1SLC22A16q26O15245 details
Solute carrier family 28 member 3SLC28A39q22.2Q9HAS3 details
Metal Bindings
Protein NameGene NameLocusUniprot IDDetails
5'-nucleotidaseNT5E6q14-q21P21589 details
Cytosolic 5'-nucleotidase 1BNT5C1B2p24.2Q96P26 details
Cytosolic 5'-nucleotidase 1ANT5C1A1p34.3-p33Q9BXI3 details
5'(3')-deoxyribonucleotidase, cytosolic typeNT5CQ8TCD5 details
5'(3')-deoxyribonucleotidase, mitochondrialNT5MQ9NPB1 details
Cytosolic 5'-nucleotidase 3NT5C37p14.3Q9H0P0 details
Cytosolic purine 5'-nucleotidaseNT5C210q24.32P49902 details
Thymidine kinase, cytosolicTK117q23.2-q25.3P04183 details
Receptors
Protein NameGene NameLocusUniprot IDDetails
Thymidine phosphorylaseTYMP22q13.33P19971 details
Transcriptional FactorsNot Available
Concentrations Data
Not Available
HMDB IDHMDB0000273
DrugBank IDDB04485
Phenol Explorer Compound IDNot Available
FoodDB IDFDB031201
KNApSAcK IDC00019698
Chemspider ID5585
KEGG Compound IDC00214
BioCyc IDTHYMIDINE
BiGG ID50348
Wikipedia LinkThymidine
METLIN ID3375
PubChem Compound5789
PDB IDNot Available
ChEBI ID17748
References
General ReferencesNot Available

Only showing the first 10 proteins. There are 22 proteins in total.

Enzymes

General function:
Involved in hydrolase activity
Specific function:
Hydrolyzes extracellular nucleotides into membrane permeable nucleosides.
Gene Name:
NT5E
Uniprot ID:
P21589
Molecular weight:
57948.125
General function:
Involved in nucleotide binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides. Helps to regulate adenosine levels (By similarity).
Gene Name:
NT5C1B
Uniprot ID:
Q96P26
Molecular weight:
68803.055
General function:
Involved in nucleotide binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides and has a broad substrate specificity. Helps to regulate adenosine levels in heart during ischemia and hypoxia.
Gene Name:
NT5C1A
Uniprot ID:
Q9BXI3
Molecular weight:
41020.145
General function:
Involved in metal ion binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides, with a preference for dUMP and dTMP, intermediate activity towards dGMP, and low activity towards dCMP and dAMP.
Gene Name:
NT5C
Uniprot ID:
Q8TCD5
Molecular weight:
Not Available
General function:
Involved in phosphatase activity
Specific function:
Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.
Gene Name:
NT5M
Uniprot ID:
Q9NPB1
Molecular weight:
Not Available
General function:
Involved in magnesium ion binding
Specific function:
Can act both as nucleotidase and as phosphotransferase.
Gene Name:
NT5C3
Uniprot ID:
Q9H0P0
Molecular weight:
33914.91
General function:
Involved in 5'-nucleotidase activity
Specific function:
May have a critical role in the maintenance of a constant composition of intracellular purine/pyrimidine nucleotides in cooperation with other nucleotidases. Preferentially hydrolyzes inosine 5'-monophosphate (IMP) and other purine nucleotides.
Gene Name:
NT5C2
Uniprot ID:
P49902
Molecular weight:
64969.2
General function:
Nucleotide transport and metabolism
Specific function:
Not Available
Gene Name:
TK1
Uniprot ID:
P04183
Molecular weight:
25468.455
General function:
Involved in ATP binding
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
Molecular weight:
27561.495
General function:
Involved in transferase activity, transferring glycosyl groups
Specific function:
May have a role in maintaining the integrity of the blood vessels. Has growth promoting activity on endothelial cells, angiogenic activity in vivo and chemotactic activity on endothelial cells in vitro. Catalyzes the reversible phosphorolysis of thymidine. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
Gene Name:
TYMP
Uniprot ID:
P19971
Molecular weight:
49954.965

Transporters

General function:
Involved in ion 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, and metformin. The transport of organic cations is inhibited by a broad array of compounds like tetramethylammonium (TMA), cocaine, lidocaine, NMDA receptor antagonists, atropine, prazosin, cimetidine, TEA and NMN, guanidine, cimetidine, choline, procainamide, quinine, tetrabutylammonium, and tetrapentylammonium. Translocates organic cations in an electrogenic and pH-independent manner. Translocates organic cations across the plasma membrane in both directions. Transports the polyamines spermine and spermidine. Transports pramipexole across the basolateral membrane of the proximal tubular epithelial cells. The choline transport is activated by MMTS. Regulated by various intracellular signaling pathways including inhibition by protein kinase A activation, and endogenously activation by the calmodulin complex, the calmodulin- dependent kinase II and LCK tyrosine kinase
Gene Name:
SLC22A1
Uniprot ID:
O15245
Molecular weight:
61187.4
General function:
Involved in nucleoside: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-deazauridine
Gene Name:
SLC28A3
Uniprot ID:
Q9HAS3
Molecular weight:
76929.6

Only showing the first 10 proteins. There are 22 proteins in total.