Thymidine

Details

• Internal ID: 38ee8912-ec0c-4579-89e6-9ea78ca744c1
• Taxonomy: Nucleosides, nucleotides, and analogues > Pyrimidine nucleosides > Pyrimidine 2-deoxyribonucleosides
• IUPAC Name: 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione
• SMILES (Canonical): CC1=CN(C(=O)NC1=O)C2CC(C(O2)CO)O
• SMILES (Isomeric): CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O
• 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
• InChI Key: IQFYYKKMVGJFEH-XLPZGREQSA-N
• Popularity: 67,345 references in papers

Physical and Chemical Properties

• Molecular Formula: C₁₀H₁₄N₂O₅
• Molecular Weight: 242.23 g/mol
• Exact Mass: 242.09027155 g/mol
• Topological Polar Surface Area (TPSA): 99.10 Ų
• XlogP: -1.20
• Atomic LogP (AlogP): -1.51
• H-Bond Acceptor: 6
• H-Bond Donor: 3
• Rotatable Bonds: 2

Synonyms

• 50-89-5
• 2'-Deoxythymidine
• Thymidin
• DThyd
• 5-Methyl-2'-deoxyuridine
• Thymine-2-desoxyriboside
• Thyminedeoxyriboside
• dThd
• Deoxyribothymidine
• 2'-thymidine
• Doxribtimine
• thymine 2'-deoxyriboside
• 2'-deoxy-5-methyluridine
• 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
• DTXSID5023661
• CHEBI:17748
• VC2W18DGKR
• 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione
• NSC-21548
• DTXCID703661
• MT-1621 COMPONENT 2'-DEOXYTHYMIDINE
• 1-(2-deoxy-beta-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione
• 2' Deoxythymidine
• 1-((2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl)-5-methylpyrimidine-2,4-dione
• 1-((2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl)-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
• RefChem:189836
• 200-070-4
• deoxythymidine
• 5-Methyldeoxyuridine
• 5-Methyldeoxyurindine
• Thymine-2-deoxyriboside
• Thymine deoxyriboside
• Uridine, 2'-deoxy-5-methyl-
• MFCD00006537
• 1-((2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-5-methylpyrimidine-2,4(1H,3H)-dione
• 157049-39-3
• dT
• AI3-52267
• beta-D-Ribofuranoside, thymine-1 2-deoxy-
• Beta-Thymidine
• 1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-5-methyl-2,4(1H,3H)-pyrimidinedione
• 2,4(1H,3H)-Pyrimidinedione, 1-(2-deoxy-beta-D-erythro-pentofuranosyl)-5-methyl-
• Thymine 2-desoxyriboside
• [3H]-Thymidine
• NCGC00142484-03
• alpha-tritiated thymidine
• 146183-25-7
• THM
• 1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione (Thymidine)
• 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-5-methyl-pyrimidine-2,4-dione
• 1-[(4S,2R,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,3-dihydropyri midine-2,4-dione
• 157049-40-6
• CCRIS 1283
• EINECS 200-070-4
• UNII-VC2W18DGKR
• NSC 21548
• 2'deoxythymidine
• deoxyribosylthymine
• 4qsv
• Thymidinedeoxyriboside
• Thymidine (Standard)
• 30819-56-8
• beta-Methyldeoxyuridine
• 1w2g
• Thymidine, >=99%
• BDBM1
• THYMIDINE [MI]
• Thymidine (8CI,9CI)
• Doxribtimine (USAN/INN)
• DOXRIBTIMINE [INN]
• bmse000244
• Epitope ID:138113
• THYMIDINE [MART.]
• DOXRIBTIMINE [USAN]
• EC 200-070-4
• THYMIDINE [WHO-DD]
• THYMIDINE [WHO-IP]
• 2'-deoxy-5-methyl-Uridine
• 1-(2-Deoxy-beta-D-ribofuranosyl)-5-methyluracil
• SCHEMBL19894
• 50-88-4
• 2'-dT
• CHEMBL52609
• SCHEMBL655193
• SCHEMBL932666
• Thymidine,labeledwithcarbon-14
• GTPL4718
• orb1296048
• SCHEMBL2722555
• HY-N1150R
• IMPURITY C [EP IMPURITY]
• MSK6808
• MT1621 (dT)
• HY-N1150
• STR05630
• Thymidine, >=99.0% (HPLC)
• dT;2-dT;Deoxythymidine;Doxribtimine
• Tox21_111560
• HG1139
• s4803
• SBB003204
• AKOS015895360
• STAVUDINE IMPURITY C [WHO-IP]
• thymine-1 2-deoxy-b-D-Ribofuranoside
• AC-1475
• CCG-266886
• CS-W019644
• DB04485
• NT02592
• CAS-50-89-5
• DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE
• NCGC00142484-01
• 1-((2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)tetrahydro-furan-2-yl)-5-methylpyrimidine-2,4(1H,3H)-dione
• 1-(2-Deoxy-beta-D-ribofuranosyl)thymine
• BP-58693
• ST056941
• SY005232
• STAVUDINE IMPURITY C [EP IMPURITY]
• Thymidine, Vetec(TM) reagent grade, 99%
• DB-030432
• ZIDOVUDINE IMPURITY E [EP IMPURITY]
• NS00068173
• T0233
• thymine-1 2-deoxy-beta-delta-Ribofuranoside
• 1-(2-Deoxy-beta-ribofuranosyl)-5-methyluracil
• C00214
• D12466
• EN300-378408
• F078885
• Q422464
• SR-01000883981
• 1-(2-Deoxy-.beta.-D-ribofuranosyl)-5-methyluracil
• SR-01000883981-1
• BRD-K28309349-001-02-4
• Q27124084
• D7E43A69-265B-4DAA-BC8F-193FB357140F
• Thymidine, powder, BioReagent, suitable for cell culture
• Z1741976665
• 1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-pyrimidine-2,4-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-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione
• 1-(2-DEOXY-.BETA.-D-ERYTHRO-PENTOFURANOSYL)-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE [WHO-IP]
• 1211376-53-2

2D Structure

ADMET Properties (via admetSAR 2)

Target	Value	Probability (raw)	Probability (%)
Human Intestinal Absorption	+	0.7162	71.62%
Caco-2	-	0.9390	93.90%
Blood Brain Barrier	-	0.5250	52.50%
Human oral bioavailability	+	0.8143	81.43%
Subcellular localzation	Nucleus	0.6071	60.71%
OATP2B1 inhibitior	-	0.8707	87.07%
OATP1B1 inhibitior	+	0.9526	95.26%
OATP1B3 inhibitior	+	0.9475	94.75%
MATE1 inhibitior	-	1.0000	100.00%
OCT2 inhibitior	-	1.0000	100.00%
BSEP inhibitior	-	0.9479	94.79%
P-glycoprotein inhibitior	-	0.9441	94.41%
P-glycoprotein substrate	-	0.9565	95.65%
CYP3A4 substrate	-	0.5381	53.81%
CYP2C9 substrate	-	0.7864	78.64%
CYP2D6 substrate	-	0.8747	87.47%
CYP3A4 inhibition	-	0.9308	93.08%
CYP2C9 inhibition	-	0.9392	93.92%
CYP2C19 inhibition	-	0.9479	94.79%
CYP2D6 inhibition	-	0.9491	94.91%
CYP1A2 inhibition	-	0.9529	95.29%
CYP2C8 inhibition	-	0.9638	96.38%
CYP inhibitory promiscuity	-	0.9415	94.15%
UGT catelyzed	+	0.6000	60.00%
Carcinogenicity (binary)	-	0.8200	82.00%
Carcinogenicity (trinary)	Non-required	0.5003	50.03%
Eye corrosion	-	0.9901	99.01%
Eye irritation	-	0.9540	95.40%
Skin irritation	-	0.8722	87.22%
Skin corrosion	-	0.9640	96.40%
Ames mutagenesis	-	0.8600	86.00%
Human Ether-a-go-go-Related Gene inhibition	-	0.6156	61.56%
Micronuclear	+	1.0000	100.00%
Hepatotoxicity	+	0.5931	59.31%
skin sensitisation	-	0.9435	94.35%
Respiratory toxicity	+	0.9222	92.22%
Reproductive toxicity	+	0.9667	96.67%
Mitochondrial toxicity	+	0.9625	96.25%
Nephrotoxicity	+	0.5538	55.38%
Acute Oral Toxicity (c)	III	0.4665	46.65%
Estrogen receptor binding	+	0.5481	54.81%
Androgen receptor binding	+	0.7553	75.53%
Thyroid receptor binding	+	0.6009	60.09%
Glucocorticoid receptor binding	+	0.6282	62.82%
Aromatase binding	-	0.8514	85.14%
PPAR gamma	+	0.7197	71.97%
Honey bee toxicity	-	0.8919	89.19%
Biodegradation	-	0.7000	70.00%
Crustacea aquatic toxicity	-	0.5600	56.00%
Fish aquatic toxicity	-	0.6264	62.64%

Targets

Proven Targets:

CHEMBL ID	UniProt ID	Name	Min activity	Assay type	Source
CHEMBL2883	P04183	Thymidine kinase, cytosolic	26 nM; 16 nM	IC50; IC50	PMID: 12213066; PMID: 12213066
CHEMBL1947	P10828	Thyroid hormone receptor beta-1	0.7 nM	Potency	via Super-PRED

Predicted Targets (via Super-PRED):

CHEMBL ID	UniProt ID	Name	Probability	Model accuracy
CHEMBL3251	P19838	Nuclear factor NF-kappa-B p105 subunit	96.30%	96.09%
CHEMBL4016	P42262	Glutamate receptor ionotropic, AMPA 2	96.22%	86.92%
CHEMBL4261	Q16665	Hypoxia-inducible factor 1 alpha	94.47%	85.14%
CHEMBL3137262	O60341	LSD1/CoREST complex	92.56%	97.09%
CHEMBL3108638	O15164	Transcription intermediary factor 1-alpha	92.29%	95.56%
CHEMBL4203	Q9HAZ1	Dual specificity protein kinase CLK4	91.55%	94.45%
CHEMBL2581	P07339	Cathepsin D	90.62%	98.95%
CHEMBL3401	O75469	Pregnane X receptor	85.84%	94.73%
CHEMBL1806	P11388	DNA topoisomerase II alpha	85.06%	89.00%
CHEMBL2635	P51452	Dual specificity protein phosphatase 3	84.54%	94.00%
CHEMBL3351	Q13085	Acetyl-CoA carboxylase 1	84.12%	93.04%
CHEMBL3038477	P67870	Casein kinase II alpha/beta	83.43%	99.23%
CHEMBL220	P22303	Acetylcholinesterase	81.71%	94.45%

Plants that contains it

• Alisma plantago-aquatica subsp. orientale
• Allium tuberosum
• Anethum graveolens
• Arabidopsis thaliana
• Aralidium pinnatifidum
• Artemisia dracunculus
• Astilbe rubra
• Bersama swinnyi
• Blainvillea acmella
• Boronia muelleri
• Colchicum macedonicum
• Conioselinum anthriscoides
• Coprosma acerosa
• Coptis deltoidea
• Cranfillia vulcanica
• Dalbergia frutescens
• Dicliptera riparia
• Dillenia papuana
• Eleutherococcus senticosus
• Equisetum ramosissimum var. huegelii
• Euphorbia caducifolia
• Euphorbia resinifera
• Euryale ferox
• Eurycoma longifolia
• Ficus elastica
• Foeniculum vulgare
• Fritillaria cirrhosa
• Fritillaria delavayi
• Fritillaria monantha
• Fritillaria pallidiflora
• Fritillaria przewalskii
• Fritillaria taipaiensis
• Fritillaria thunbergii
• Fritillaria unibracteata
• Fritillaria verticillata
• Fritillaria walujewii
• Geigeria schinzii
• Ginkgo biloba
• Goniothalamus undulatus
• Gymnadenia conopsea
• Gymnospermium kiangnanensis
• Helichrysum sutherlandii
• Hydrangea macrophylla
• Hypericum papuanum
• Ilex kaushue
• Inula thapsoides
• Kaunia longipetiolata
• Limeum pterocarpum
• Lophocereus marginatus
• Lupinus formosus
• Neltuma kuntzei
• Nemuaron vieillardii
• Ophryosporus charua
• Oreomecon radicata
• Oxandra xylopioides
• Pachycereus pringlei
• Palicourea alpina
• Paragymnopteris marantae subsp. marantae
• Peucedanum japonicum
• Picea glauca
• Pinellia ternata
• Polygonum thunbergii
• Posoqueria latifolia
• Pteris leptophylla
• Rhodomyrtus tomentosa
• Salix sieboldiana
• Salvia xalapensis
• Sambucus ebulus
• Saussurea medusa
• Scrophularia smithii
• Senna spectabilis var. spectabilis
• Solanum torvum
• Stenocereus thurberi
• Tanacetum sinaicum
• Tillandsia usneoides
• Trifolium alexandrinum
• Trifolium pratense
• Typha angustifolia
• Typha orientalis
• Vincetoxicum indicum var. glabrum
• Vitex negundo
• Wunderlichia mirabilis
• Zilla spinosa
• Ziziphus jujuba

Cross-Links

• PubChem: 5789
• NPASS: NPC71339
• ChEMBL: CHEMBL52609
• LOTUS: LTS0162810
• wikiData: Q422464