5-Ethynyl-2'-deoxyuridine(EdU) - ≥98% , CAS No.61135-33-9

CAS: 61135-33-9 Cat. No.: E131265 Molecular Weight: 252.22 EC Number: 804-162-0

GRADE & PURITY ≥98%

Synonyms

5-Ethynyl-2'-deoxyuridine, (EdU), AldrichCPR | AC-32360 | 5-ethynyl-1-((2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)pyrimidine-2,4(1H,3H)-dione | 5-Ethynyl-2'-deoxyuridine | 5-ethynyl-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2

Storage

Protected from light,Store at -20°C

Shipped In

Ice chest + Ice pads

Overview

5-Ethynyl-2'-deoxyuridine(EdU) is an extensively used nucleoside analog used as a probe for DNA synthesis. 5-Ethynyl-2’-deoxyuridine is known as an toxic anti-metabolite, which potentially causes DNA instabiliy, necrosis and cell-cycle arrest, therefore it is often used for short-term DNA synthesis in tissue culture and living organisms where prolonged cell survival is not required.
An extensively used nucleoside analog

Specifications

Synonyms

5-Ethynyl-2'-deoxyuridine, (EdU), AldrichCPR | AC-32360 | 5-ethynyl-1-((2R, 4S, 5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)pyrimidine-2, 4(1H, 3H)-dione | 5-Ethynyl-2'-deoxyuridine | 5-ethynyl-1-[(2R, 4S, 5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1, 2

Specifications & Purity

≥98%

Storage

Protected from light, Store at -20°C

Shipped In

Ice chest + Ice pads

This product requires cold chain shipping. Ground and other economy services are not available.

Purity

≥98%

Names and Identifiers

• Pubchem Sid: 504758929
• Pubchem Sid Url: https://pubchem.ncbi.nlm.nih.gov/substance/504758929
• Canonical Smiles: C#CC1=CN(C(=O)NC1=O)C2CC(C(O2)CO)O
• IUPAC Name: 5-ethynyl-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4-dione
• InChIKey: CDEURGJCGCHYFH-DJLDLDEBSA-N
• INCHI: 1S/C11H12N2O5/c1-2-6-4-13(11(17)12-10(6)16)9-3-7(15)8(5-14)18-9/h1,4,7-9,14-15H,3,5H2,(H,12,16,17)/t7-,8+,9+/m0/s1
• Isomeric SMILES: C#CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O
• WGK Germany: 3
• Molecular Weight: 252.22
• Reaxy-Rn: 24708468
• Reaxys-RN_link_address: https://www.reaxys.com/reaxys/secured/hopinto.do?context=S&query=IDE.XRN=24708468&ln=

Taxonomic Classification

Taxonomy Tree

• Kingdom Organic compounds
  • Superclass Nucleosides, nucleotides, and analogues
    • Class Pyrimidine nucleosides
      • Subclass Pyrimidine 2'-deoxyribonucleosides

• Kingdom: Organic compounds
• Superclass: Nucleosides, nucleotides, and analogues
• Class: Pyrimidine nucleosides
• Subclass: Pyrimidine 2'-deoxyribonucleosides
• Intermediate Tree Nodes: Not available
• Direct Parent: Pyrimidine 2'-deoxyribonucleosides
• Alternative Parents: Pyrimidones Hydropyrimidines Vinylogous amides Heteroaromatic compounds Tetrahydrofurans Ureas Secondary alcohols Lactams Acetylides Azacyclic compounds Oxacyclic compounds Organonitrogen compounds Organic oxides Hydrocarbon derivatives Organopnictogen compounds Primary alcohols
• Molecular Framework: Aromatic heteromonocyclic compounds
• Substituents: Pyrimidine 2'-deoxyribonucleoside - Pyrimidone - Hydropyrimidine - Pyrimidine - Heteroaromatic compound - Vinylogous amide - Tetrahydrofuran - Lactam - Urea - Secondary alcohol - Acetylide - Oxacycle - Azacycle - Organoheterocyclic compound - Alcohol - Hydrocarbon derivative - Organic oxide - Organopnictogen compound - Primary alcohol - Organooxygen compound - Organonitrogen compound - Organic oxygen compound - Organic nitrogen compound - Aromatic heteromonocyclic compound
• Description: This compound belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. These are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.
• External Descriptors: Not available

Data sources

1. Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS. ClassyFire: Automated Chemical Classification With A Comprehensive, Computable Taxonomy. Journal of Cheminformatics, 2016, 8:61.

DOI: 10.1186/s13321-016-0174-y

Associated Targets(Human)

MCF7 (126967 Activities)

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OST (42 Activities)

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E6SM (1586 Activities)

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HEL (6614 Activities)

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MDA-MB-231 (73002 Activities)

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Associated Targets(non-human)

Human alphaherpesvirus 2 (4932 Activities)

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Human respirovirus 3 (1674 Activities)

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Human alphaherpesvirus 3 (4092 Activities)

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Human betaherpesvirus 5 (5122 Activities)

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Vaccinia virus (4609 Activities)

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Human alphaherpesvirus 1 (11089 Activities)

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Sindbis virus (1599 Activities)

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Vesicular stomatitis virus (4460 Activities)

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Punta Toro virus (1491 Activities)

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Coxsackievirus B4 (2249 Activities)

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Respiratory syncytial virus (3434 Activities)

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FM3A (1296 Activities)

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L1210 (27553 Activities)

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Mechanisms of Action

Chemical and Physical Properties

• Solubility: Soluble in methanol, DMSO, water (slightly), DMF, and chloroform
• Sensitivity: Heat and light sensitive
• Specific Rotation[α]: [α]D：23° (C=0.7,MeOH)
• Melt Point(°C): 199 °C
• Molecular Weight: 252.220 g/mol
• XLogP3: -1.300
• Hydrogen Bond Donor Count: 3
• Hydrogen Bond Acceptor Count: 5
• Rotatable Bond Count: 3
• Exact Mass: 252.075 Da
• Monoisotopic Mass: 252.075 Da
• Topological Polar Surface Area: 99.100 Ų
• Heavy Atom Count: 18
• Formal Charge: 0
• Complexity: 463.000
• Isotope Atom Count: 0
• Defined Atom Stereocenter Count: 3
• Undefined Atom Stereocenter Count: 0
• Defined Bond Stereocenter Count: 0
• Undefined Bond Stereocenter Count: 0
• The total count of all stereochemical bonds: 0
• Covalently-Bonded Unit Count: 1

References

1. Xianke Zhou, Yadie Xiang, Dier Li, Menghua Zhong, Xue Hong, Yuan Gui, Wenjian Min, Yudan Chen, Xi Zeng, Haili Zhu, Youhua Liu, Shijia Liu, Peng Yang, Fanfan Hou, Dong Zhou, Haiyan Fu.  (2023)  Limonin, a natural ERK2 agonist, protects against ischemic acute kidney injury.  International Journal of Biological Sciences,      [PMID:37324945] [10.7150/ijbs.82417]

2. Zhang Jing, Liang Lijia, Guan Xin, Deng Rong, Qu Huixin, Huang Dianshuai, Xu Shuping, Liang Chongyang, Xu Weiqing.  (2017)  In situ, accurate, surface-enhanced Raman scattering detection of cancer cell nucleus with synchronous location by an alkyne-labeled biomolecular probe.  ANALYTICAL AND BIOANALYTICAL CHEMISTRY,  410  (2): (585-594).  [PMID:29214531] [10.1007/s00216-017-0761-4]

3. Xiao Gongyi, Li Xiangwei, Yang Huiping, Zhang Ruobin, Huang Junlan, Tian Yu, Nie Mao, Sun Xianding.  (2024)  mTOR mutation disrupts larval zebrafish tail fin regeneration via regulating proliferation of blastema cells and mitochondrial functions.  Journal of Orthopaedic Surgery and Research,  19  (1): (1-15).  [PMID:38812038] [10.1186/s13018-024-04802-z]

4. Muhammad Zubair Saleem, Ruyi Huang, Yingying Huang, Xin Guo, Yang Liu, Miao Gao, Yinjuan Fan, Zhe-Sheng Chen, Zun-Fu Ke, Shengnan Ye, Jianhua Xu.  (2025)  Targeting TRAP1-dependent metabolic reprogramming to overcome doxorubicin resistance in quiescent breast cancer.  DRUG RESISTANCE UPDATES,      [PMID:40086176] [10.1016/j.drup.2025.101226]

5. Jun-Song Wen, Zi-Wei Pan, Xue-Dan Yao, Yan-Qing Liu, Yao-Dong Zhu.  (2026)  Pristimerin ameliorates spasmolytic polypeptide-expressing metaplasia by modulating Cdkn1c (p57)-mediated glycolytic reprogramming.  WORLD JOURNAL OF GASTROENTEROLOGY,  32  (10): (113771).  [PMID:41809458] [10.3748/wjg.v32.i10.113771]