Page last updated: 2024-12-07

5-hydroxymethyluracil

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

5-hydroxymethyluracil (5hmU) is a modified base found in DNA that arises from the oxidation of 5-methylcytosine (5mC). It plays a crucial role in epigenetic regulation, acting as an intermediate in the demethylation pathway. 5hmU is generated by the ten-eleven translocation (TET) family of dioxygenases, which catalyze the oxidation of 5mC to 5hmU. 5hmU is further oxidized by TET enzymes to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), which are then removed from DNA by the thymine DNA glycosylase (TDG) enzyme. The presence of 5hmU in DNA has been associated with various biological processes, including development, gene expression, and cancer. It is also being investigated as a potential biomarker for disease diagnosis and prognosis. The ability of 5hmU to serve as a substrate for TET enzymes, enabling its conversion to 5fC and 5caC, highlights its importance in the dynamic regulation of DNA methylation. 5hmU is therefore a key player in epigenetic reprogramming and its study provides insights into the intricate mechanisms that govern gene expression and cellular function.'

Cross-References

ID SourceID
PubMed CID78168
CHEBI ID16964
SCHEMBL ID44459
SCHEMBL ID5744433
MeSH IDM0051594

Synonyms (72)

Synonym
ccris 8815
590tq3gl34 ,
unii-590tq3gl34
5-(hydroxymethyl)-2,4(1h,3h)-pyrimidinedione
5-(hydroxymethyl)pyrimidine-2,4(1h,3h)-dione
5-hydroxymethyl uracil
CHEBI:16964 ,
nsc20901
nsc-20901
2,3h)-pyrimidinedione, 5-(hydroxymethyl)-
5-oxymethyluracil
5-(hydroxymethyl)uracil
uracil, 5-(hydroxymethyl)-
thymine, .alpha.-hydroxy-
4433-40-3
5-hydroxymethyluracil ,
C03088
HMU ,
5-(hydroxymethyl)uracil, 97%
thymine, alpha-hydroxy-
4-methyl-5-oxyuracil
ai3-62720
2,4(1h,3h)-pyrimidinedione, 5-(hydroxymethyl)-, hemihydrate
2,4(1h,3h)-pyrimidinedione, 5-(hydroxymethyl)-
nsc 20901
einecs 224-636-5
HMS1619D05
2,4-dihydroxy-5-hydroxymethylpyrimidine
AKOS002270843
5-(hydroxymethyl)-1h-pyrimidine-2,4-dione
A18783
5-(hydroxymethyl)pyrimidine-2,4(1h,3h)-dione;5-(hydroxymethyl)uracil
5-(hydroxymethyl)pyrimidine-2,4-diol
5-hydroxymethyl-1h-pyrimidine-2,4-dione
5-(hydroxymethyl)-1,3-dihydropyrimidine-2,4-dione
FT-0619713
F3096-1963
S6127
AKOS022634000
SCHEMBL44459
SCHEMBL5744433
5-hydroxymethyl-2,4(1h,3h)-pyrimidinedione
5-(hydroxymethyl)-1,2,3,4-tetrahydropyrimidine-2,4-dione
HD-0707
DTXSID9063455
5-(hydroxymethyl)-2,4-pyrimidinediol #
W-106201
oxymethyluracil, 5-
HMS3649O14
STL453062
hydroxymethyl uracil, aldrichcpr
mfcd00056024
CS-W004924
AC-8387
alpha-hydroxythymine
a-hydroxythymine
HY-W004924
STL519355
'5-(hydroxymethyl)pyrimidine-2,4(1h,3h)-dione'
BCP03534
Q27102155
SR-01000946630-1
sr-01000946630
BBL100110
AMY9301
P16594
5-(hydroxymethyl)pyrimidine-2,4-dione
SB57726
hydroxymethyl uracil
SY075692
EN300-1601108
Z276550478

Research Excerpts

Toxicity

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
)
0.67

Compound-Compound Interactions

ExcerptReferenceRelevance
" This approach presents as main advantages the ability to easily collect and store urine samples for further processing and the high sensitivity, reproducibility, and robustness of eVol(®)MEPS combined with UHPLC analysis, thus retrieving a fast and reliable assessment of oxidatively damaged DNA."( A micro-extraction technique using a new digitally controlled syringe combined with UHPLC for assessment of urinary biomarkers of oxidatively damaged DNA.
Aveiro, F; Câmara, JS; Mendes, B; Pereira, J; Silva, P, 2013
)
0.39

Dosage Studied

ExcerptRelevanceReference
" Dose-response curves for its formation in [3H]thymidine-labeled DNA were constructed by exposing the DNA to increasing amounts of gamma-radiation and measuring the HMUra content."( Quantitative determination of the 5-(hydroxymethyl)uracil moiety in the DNA of gamma-irradiated cells.
Cadet, J; Cummings, A; Frenkel, K; Solomon, J; Steinberg, JJ; Teebor, GW, 1985
)
0.27
[information is derived through text-mining from research data collected from National Library of Medicine (NLM), extracted Dec-2023]

Roles (1)

RoleDescription
human metaboliteAny mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens).
[role 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]

Drug Classes (2)

ClassDescription
primary alcoholA primary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has either three hydrogen atoms attached to it or only one other carbon atom and two hydrogen atoms attached to it.
pyrimidoneA pyrimidine carrying one or more oxo substituents.
[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]

Pathways (1)

PathwayProteinsCompounds
Biomarkers for pyrimidine metabolism disorders1432

Protein Targets (1)

Inhibition Measurements

ProteinTaxonomyMeasurementAverageMin (ref.)Avg (ref.)Max (ref.)Bioassay(s)
Carbonic anhydrase 1Homo sapiens (human)Ki49.51000.00001.372610.0000AID1238072
[prepared from compound, protein, and bioassay information from National Library of Medicine (NLM), extracted Dec-2023]

Biological Processes (1)

Processvia Protein(s)Taxonomy
one-carbon metabolic processCarbonic anhydrase 1Homo sapiens (human)
[Information is prepared from geneontology information from the June-17-2024 release]

Molecular Functions (6)

Processvia Protein(s)Taxonomy
arylesterase activityCarbonic anhydrase 1Homo sapiens (human)
carbonate dehydratase activityCarbonic anhydrase 1Homo sapiens (human)
protein bindingCarbonic anhydrase 1Homo sapiens (human)
zinc ion bindingCarbonic anhydrase 1Homo sapiens (human)
hydro-lyase activityCarbonic anhydrase 1Homo sapiens (human)
cyanamide hydratase activityCarbonic anhydrase 1Homo sapiens (human)
[Information is prepared from geneontology information from the June-17-2024 release]

Ceullar Components (2)

Processvia Protein(s)Taxonomy
cytosolCarbonic anhydrase 1Homo sapiens (human)
extracellular exosomeCarbonic anhydrase 1Homo sapiens (human)
[Information is prepared from geneontology information from the June-17-2024 release]

Bioassays (5)

Assay IDTitleYearJournalArticle
AID1238073Inhibition of human erythrocytes CA2 using 4-nitrophenylacetate as substrate by esterase assay2015Bioorganic & medicinal chemistry letters, Aug-15, Volume: 25, Issue:16
Synthesis and carbonic anhydrase inhibitory properties of novel uracil derivatives.
AID1238074Competitive inhibition of human erythrocytes CA1 using 4-nitrophenylacetate as substrate by Lineweaver-Burk plot analysis2015Bioorganic & medicinal chemistry letters, Aug-15, Volume: 25, Issue:16
Synthesis and carbonic anhydrase inhibitory properties of novel uracil derivatives.
AID1238072Inhibition of human erythrocytes CA1 using 4-nitrophenylacetate as substrate by esterase assay2015Bioorganic & medicinal chemistry letters, Aug-15, Volume: 25, Issue:16
Synthesis and carbonic anhydrase inhibitory properties of novel uracil derivatives.
AID540299A screen for compounds that inhibit the MenB enzyme of Mycobacterium tuberculosis2010Bioorganic & medicinal chemistry letters, Nov-01, Volume: 20, Issue:21
Synthesis and SAR studies of 1,4-benzoxazine MenB inhibitors: novel antibacterial agents against Mycobacterium tuberculosis.
AID588519A screen for compounds that inhibit viral RNA polymerase binding and polymerization activities2011Antiviral research, Sep, Volume: 91, Issue:3
High-throughput screening identification of poliovirus RNA-dependent RNA polymerase inhibitors.
[information is prepared from bioassay data collected from National Library of Medicine (NLM), extracted Dec-2023]

Research

Studies (133)

TimeframeStudies, This Drug (%)All Drugs %
pre-199025 (18.80)18.7374
1990's40 (30.08)18.2507
2000's20 (15.04)29.6817
2010's41 (30.83)24.3611
2020's7 (5.26)2.80
[information is prepared from research data collected from National Library of Medicine (NLM), extracted Dec-2023]

Market Indicators

Research Demand Index: 25.75

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 Index25.75 (24.57)
Research Supply Index5.00 (2.92)
Research Growth Index4.80 (4.65)
Search Engine Demand Index26.69 (26.88)
Search Engine Supply Index2.00 (0.95)

This Compound (25.75)

All Compounds (24.57)

Study Types

Publication TypeThis drug (%)All Drugs (%)
Trials4 (2.80%)5.53%
Reviews6 (4.20%)6.00%
Case Studies2 (1.40%)4.05%
Observational0 (0.00%)0.25%
Other131 (91.61%)84.16%
[information is prepared from research data collected from National Library of Medicine (NLM), extracted Dec-2023]