Page last updated: 2024-12-07

5-hydroxymethyl-2'-deoxyuridine

Description Research Excerpts Clinical Trials Roles Classes Pathways Study Profile Bioassays Related Drugs Related Conditions Protein Interactions Research Growth Market Indicators

Description

5-hydroxymethyl-2'-deoxyuridine (5hmU) is a modified nucleoside found in DNA, specifically in the form of 5-hydroxymethylcytosine (5hmC). 5hmC is an intermediate in the active demethylation pathway of DNA, where it is converted from 5-methylcytosine (5mC) by the ten-eleven translocation (TET) enzymes. 5hmC is also a potential epigenetic mark in its own right, and its levels are altered in various diseases, including cancer. The synthesis of 5hmU can be achieved through chemical or enzymatic methods. Chemically, 5hmU can be synthesized by reacting 2'-deoxyuridine with formaldehyde. Enzymatically, 5hmU can be synthesized by the action of TET enzymes on 5mC. Studies have shown that 5hmU can have various effects on gene expression, depending on its genomic context. In some cases, 5hmU has been associated with increased gene expression, while in other cases, it has been associated with decreased gene expression. 5hmU is studied for its potential role in various biological processes, including DNA replication, repair, and gene regulation. It is also a potential therapeutic target for cancer and other diseases.'

5-hydroxymethyl-2'-deoxyuridine : A pyrimidine 2'-deoxyribonucleoside composed of 2'-deoxyuridine having a 5-hydroxymethyl substituent. [Chemical Entities of Biological Interest (ChEBI), Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C. (2016). ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res]

Cross-References

ID SourceID
PubMed CID44289445
SCHEMBL ID10178297
MeSH IDM0069301
PubMed CID91541
CHEMBL ID376876
CHEBI ID61288
SCHEMBL ID529456
MeSH IDM0069301

Synonyms (47)

Synonym
5-hydroxymethyl-2'-deoxyuridine
W-202927
SCHEMBL10178297
HY-129983
CS-0108972
PD193004
5homedu
5-hydroxymethyl-deoxyuridine
5-hydroxymethyl-durd
5ohme-du
1-[(2r,4s,5r)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-5-(hydroxymethyl)pyrimidine-2,4-dione
einecs 225-848-0
alpha-hydroxythymidine
2'-deoxy-5-(hydroxymethyl)uridine
5-hydroxymethyldeoxyuridine
uridine, 2'-deoxy-5-(hydroxymethyl)-
ccris 2347
thymidine, alpha-hydroxy-
CHEMBL376876
chebi:61288 ,
5116-24-5
alpha-hydroxy-thymidin
hmdu
1-((2r,4s,5r)-4-hydroxy-5-(hydroxymethyl)-tetrahydrofuran-2-yl)-5-(2-hydroxymethyl)pyrimidine-2,4(1h,3h)-dione
2'-DEOXY-5-HYDROXYMETHYLURIDINE ,
5-hmdu
A828469
ejz33w33jn ,
unii-ejz33w33jn
nsc 749425
AKOS016011210
EPITOPE ID:146101
BRD-K45801156-001-01-3
SCHEMBL529456
thymidine, .alpha.-hydroxy-
1-[(2r,4s,5r)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(hydroxymethyl)-1,2,3,4-tetrahydropyrimidine-2,4-dione
AS-60778
1-((2r,4s,5r)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-5-(hydroxymethyl)pyrimidine-2,4(1h,3h)-dione
Q27130988
1-(2-deoxypentofuranosyl)-4-hydroxy-5-(hydroxymethyl)pyrimidin-2(1h)-one
DTXSID70965430
F82496
2'-deoxy-5-hydroxymethyl-d-uridine
2'-desoxy-5-hydroxymethyluridine
.alpha.-hydroxythymidine
5-(hydroxymethyl)-2'-desoxyuridine
PD064172

Research Excerpts

Toxicity

A spontaneously arising clone, stably resistant to the toxic effects of the thymidine analog, 5-hydroxymethyl-2'-deoxyuridine (hmdU), was isolated from unmutagenized V79.

ExcerptReferenceRelevance
" HeLa cells, known to be resistant to the toxic effects of HmdUrd, do not incorporate HmdUrd into their DNA."( Effects of 5-hydroxymethyluracil and 3-aminobenzamide on the repair and toxicity of 5-hydroxymethyl-2'-deoxyuridine in mammalian cells.
Boorstein, RJ; Teebor, GW, 1989
)
0.28
"Cellular and biochemical analyses of the toxic effects of the thymidine analog, 5-hydroxymethyl-2'-deoxyuridine (hmdUrd), were carried out using V79."( Biochemical analysis of toxic effects of 5-hydroxymethyl-2'-deoxyuridine in mammalian cells.
Kaufman, ER, 1986
)
0.27
"A spontaneously arising clone, stably resistant to the toxic effects of the thymidine analog, 5-hydroxymethyl-2'-deoxyuridine (hmdU), was isolated from unmutagenized V79."( Resistance to toxic effects of 5-hydroxymethyl-2'-deoxyuridine in mammalian cells.
Kaufman, ER, 1987
)
0.27

Dosage Studied

ExcerptRelevanceReference
" 1,6-Dinitropyrene dosing did not affect the levels of 8-hydroxy-2'-deoxyguanosine in these two tissues."( Formation of DNA adducts and oxidative DNA damage in rats treated with 1,6-dinitropyrene.
Beland, FA; Culp, SJ; Djurić, Z; Luongo, DA; Potter, DW, 1993
)
0.29
" We evaluated the dose-response relationship of ODD level to breast cancer risk, using quartiles of ODD."( Recruitment for a pilot case control study of oxidative DNA damage and breast cancer risk.
Djuric, Z; Heilbrun, LK; Lababidi, S; Simon, MS; Stephens, D, 2000
)
0.31
" Also, the patterns of urinary nucleosides in three dosage groups (control, BPA1, BPA2) were significantly different."( Metabolic significance of bisphenol A-induced oxidative stress in rat urine measured by liquid chromatography-mass spectrometry.
Cho, SH; Choi, MH; Chung, BC; Kwon, OS; Lee, WY, 2009
)
0.35
[information is derived through text-mining from research data collected from National Library of Medicine (NLM), extracted Dec-2023]

Drug Classes (1)

ClassDescription
pyrimidine 2'-deoxyribonucleoside
[compound class information is derived from Chemical Entities of Biological Interest (ChEBI), Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C. (2016). ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res]

Protein Targets (2)

Other Measurements

ProteinTaxonomyMeasurementAverageMin (ref.)Avg (ref.)Max (ref.)Bioassay(s)
Thymidylate synthaseMus musculus (house mouse)ID501,000.00000.03500.03500.0350AID212649
Thymidine phosphorylaseHomo sapiens (human)Km577.00000.16000.16000.1600AID211066
[prepared from compound, protein, and bioassay information from National Library of Medicine (NLM), extracted Dec-2023]

Biological Processes (11)

Processvia Protein(s)Taxonomy
mitochondrial genome maintenanceThymidine phosphorylaseHomo sapiens (human)
angiogenesisThymidine phosphorylaseHomo sapiens (human)
pyrimidine nucleobase metabolic processThymidine phosphorylaseHomo sapiens (human)
pyrimidine nucleoside metabolic processThymidine phosphorylaseHomo sapiens (human)
chemotaxisThymidine phosphorylaseHomo sapiens (human)
signal transductionThymidine phosphorylaseHomo sapiens (human)
cell differentiationThymidine phosphorylaseHomo sapiens (human)
regulation of myelinationThymidine phosphorylaseHomo sapiens (human)
dTMP catabolic processThymidine phosphorylaseHomo sapiens (human)
regulation of transmission of nerve impulseThymidine phosphorylaseHomo sapiens (human)
regulation of gastric motilityThymidine phosphorylaseHomo sapiens (human)
[Information is prepared from geneontology information from the June-17-2024 release]

Molecular Functions (5)

Processvia Protein(s)Taxonomy
1,4-alpha-oligoglucan phosphorylase activityThymidine phosphorylaseHomo sapiens (human)
protein bindingThymidine phosphorylaseHomo sapiens (human)
growth factor activityThymidine phosphorylaseHomo sapiens (human)
thymidine phosphorylase activityThymidine phosphorylaseHomo sapiens (human)
protein homodimerization activityThymidine phosphorylaseHomo sapiens (human)
[Information is prepared from geneontology information from the June-17-2024 release]

Ceullar Components (1)

Processvia Protein(s)Taxonomy
cytosolThymidine phosphorylaseHomo sapiens (human)
cytosolThymidine phosphorylaseHomo sapiens (human)
[Information is prepared from geneontology information from the June-17-2024 release]

Bioassays (16)

Assay IDTitleYearJournalArticle
AID211066Michaelis-Menten constant (Km) against horse liver thymidine phosphorylase1980Journal of medicinal chemistry, Aug, Volume: 23, Issue:8
Thymidine phosphorylase. Substrate specificity for 5-substituted 2'-deoxyuridines.
AID85425Antiviral activity against herpes simplex virus type I was measured at 200 uM concentration.1980Journal of medicinal chemistry, Feb, Volume: 23, Issue:2
Synthesis and biological activities of 5-(hydroxymethyl, azidomethyl, or aminomethyl)-2'-deoxyuridine and related 5'-substituted analogues.
AID458878Antiviral activity against HIV1 LAI in human CEM-SS cells assessed as RT activity after 4 serial passages with uninfected cells by serial passage experiment2010Journal of medicinal chemistry, Feb-25, Volume: 53, Issue:4
5-Modified-2'-dU and 2'-dC as mutagenic anti HIV-1 proliferation agents: synthesis and activity.
AID162825Kinetic inhibition constant against herpes simplex virus type I pyrimidine deoxyribonucleoside kinase was measured1980Journal of medicinal chemistry, Feb, Volume: 23, Issue:2
Synthesis and biological activities of 5-(hydroxymethyl, azidomethyl, or aminomethyl)-2'-deoxyuridine and related 5'-substituted analogues.
AID280941Cytotoxicity against mouse L1210/0 cells after 48 hrs2007Journal of medicinal chemistry, Apr-05, Volume: 50, Issue:7
Probing the anticancer activity of nucleoside analogues: a QSAR model approach using an internally consistent training set.
AID232840Ratio of Vmax to that of dThd (Vmax = 0.14)1980Journal of medicinal chemistry, Aug, Volume: 23, Issue:8
Thymidine phosphorylase. Substrate specificity for 5-substituted 2'-deoxyuridines.
AID458877Cytotoxicity against human MT4 cells by MTT assay2010Journal of medicinal chemistry, Feb-25, Volume: 53, Issue:4
5-Modified-2'-dU and 2'-dC as mutagenic anti HIV-1 proliferation agents: synthesis and activity.
AID458880Antiviral activity against HIV1 LAI in human CEM-SS cells assessed as RT activity after 8 serial passages with uninfected cells by serial passage experiment2010Journal of medicinal chemistry, Feb-25, Volume: 53, Issue:4
5-Modified-2'-dU and 2'-dC as mutagenic anti HIV-1 proliferation agents: synthesis and activity.
AID458875Cytotoxicity against human CEM-SS cells by MTT assay2010Journal of medicinal chemistry, Feb-25, Volume: 53, Issue:4
5-Modified-2'-dU and 2'-dC as mutagenic anti HIV-1 proliferation agents: synthesis and activity.
AID99530In vitro growth inhibition of L5178Y-Parental murine leukemia cells2000Journal of medicinal chemistry, Nov-30, Volume: 43, Issue:24
5-Substituted N(4)-hydroxy-2'-deoxycytidines and their 5'-monophosphates: synthesis, conformation, interaction with tumor thymidylate synthase, and in vitro antitumor activity.
AID99532In vitro growth inhibition of L5178Y-Parental murine leukemia cells by incorporation of [14C]-Thd.2000Journal of medicinal chemistry, Nov-30, Volume: 43, Issue:24
5-Substituted N(4)-hydroxy-2'-deoxycytidines and their 5'-monophosphates: synthesis, conformation, interaction with tumor thymidylate synthase, and in vitro antitumor activity.
AID99533In vitro growth inhibition of FdUrd resistant L5178Y-Resistant murine leukemia cells2000Journal of medicinal chemistry, Nov-30, Volume: 43, Issue:24
5-Substituted N(4)-hydroxy-2'-deoxycytidines and their 5'-monophosphates: synthesis, conformation, interaction with tumor thymidylate synthase, and in vitro antitumor activity.
AID458874Antiviral activity against HIV1 LAI in human CEM-SS cells assessed as RT activity after 5 days by single passage assay2010Journal of medicinal chemistry, Feb-25, Volume: 53, Issue:4
5-Modified-2'-dU and 2'-dC as mutagenic anti HIV-1 proliferation agents: synthesis and activity.
AID458876Antiviral activity against HIV1 3B in human MT4 cells assessed as RT activity after 5 days by single passage assay2010Journal of medicinal chemistry, Feb-25, Volume: 53, Issue:4
5-Modified-2'-dU and 2'-dC as mutagenic anti HIV-1 proliferation agents: synthesis and activity.
AID458879Antiviral activity against HIV1 LAI in human CEM-SS cells assessed as RT activity after 4 to 8 serial passages with uninfected cells by serial passage experiment2010Journal of medicinal chemistry, Feb-25, Volume: 53, Issue:4
5-Modified-2'-dU and 2'-dC as mutagenic anti HIV-1 proliferation agents: synthesis and activity.
AID212649The compound was tested for inhibition of thymidylate synthase (TS) in L1210 cells1988Journal of medicinal chemistry, Aug, Volume: 31, Issue:8
Nucleosides. 150. Synthesis and some biological properties of 5-monofluoromethyl, 5-difluoromethyl, and 5-trifluoromethyl derivatives of 2'-deoxyuridine and 2'-deoxy-2'-fluoro-beta-D-arabinofuranosyluracil.
[information is prepared from bioassay data collected from National Library of Medicine (NLM), extracted Dec-2023]

Research

Studies (86)

TimeframeStudies, This Drug (%)All Drugs %
pre-199024 (27.91)18.7374
1990's23 (26.74)18.2507
2000's17 (19.77)29.6817
2010's17 (19.77)24.3611
2020's5 (5.81)2.80
[information is prepared from research data collected from National Library of Medicine (NLM), extracted Dec-2023]

Market Indicators

Research Demand Index: 20.11

According to the monthly volume, diversity, and competition of internet searches for this compound, as well the volume and growth of publications, there is estimated to be moderate demand-to-supply ratio for research on this compound.

MetricThis Compound (vs All)
Research Demand Index20.11 (24.57)
Research Supply Index1.95 (2.92)
Research Growth Index4.42 (4.65)
Search Engine Demand Index15.26 (26.88)
Search Engine Supply Index2.00 (0.95)

This Compound (20.11)

All Compounds (24.57)

Study Types

Publication TypeThis drug (%)All Drugs (%)
Trials4 (4.71%)5.53%
Trials0 (0.00%)5.53%
Reviews1 (1.18%)6.00%
Reviews0 (0.00%)6.00%
Case Studies0 (0.00%)4.05%
Case Studies0 (0.00%)4.05%
Observational0 (0.00%)0.25%
Observational0 (0.00%)0.25%
Other80 (94.12%)84.16%
Other6 (100.00%)84.16%
[information is prepared from research data collected from National Library of Medicine (NLM), extracted Dec-2023]