Ribothymidine (BioDeep_00000003091)

 

Secondary id: BioDeep_00000399621, BioDeep_00000405389, BioDeep_00000405731

human metabolite PANOMIX_OTCML-2023 Endogenous blood metabolite


代谢物信息卡片


1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione

化学式: C10H14N2O6 (258.0851824)
中文名称: 5-甲基尿苷, 阿糖胸苷
谱图信息: 最多检出来源 Homo sapiens(feces) 0.16%

分子结构信息

SMILES: CC1=CN(C(=O)NC1=O)C2C(C(C(O2)CO)O)O
InChI: InChI=1S/C10H14N2O6/c1-4-2-12(10(17)11-8(4)16)9-7(15)6(14)5(3-13)18-9/h2,5-7,9,13-15H,3H2,1H3,(H,11,16,17)/t5-,6-,7-,9-/m1/s1

描述信息

Ribothymidine is an endogenous methylated nucleoside found in human fluids; methylated purine bases are present in higher amounts in tumor-bearing patients compared to healthy controls.DNA hypermethylation is a common finding in malignant cells and has been explored as a therapeutic target for hypomethylating agents. When chemical bonds to DNA, the DNA becomes damaged and proper and complete replication cannot occur to make the normal intended cell. A DNA adduct is an abnormal piece of DNA covalently-bonded to a cancer-causing chemical. This has shown to be the start of a cancerous cell, or carcinogenesis. DNA adducts in scientific experiments are used as bio-markers and as such are themselves measured to reflect quantitatively, for comparison, the amount of cancer in the subject. (PMID: 3506820, 17044778, 17264127, 16799933) [HMDB]
Ribothymidine is an endogenous methylated nucleoside found in human fluids; methylated purine bases are present in higher amounts in tumor-bearing patients compared to healthy controls.DNA hypermethylation is a common finding in malignant cells and has been explored as a therapeutic target for hypomethylating agents. When chemical bonds to DNA, the DNA becomes damaged and proper and complete replication cannot occur to make the normal intended cell. A DNA adduct is an abnormal piece of DNA covalently-bonded to a cancer-causing chemical. This has shown to be the start of a cancerous cell, or carcinogenesis. DNA adducts in scientific experiments are used as bio-markers and as such are themselves measured to reflect quantitatively, for comparison, the amount of cancer in the subject. (PMID:3506820, 17044778, 17264127, 16799933).
5-Methyluridine is a is an endogenous methylated nucleoside found in human fluids.
5-Methyluridine is a is an endogenous methylated nucleoside found in human fluids.

同义名列表

27 个代谢物同义名

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione; 5-Methyl-1-beta-delta-ribofuranosyl-2,4(1H,3H)-pyrimidinedione; 5-Methyl-1-beta-D-ribofuranosyl-2,4(1H,3H)-pyrimidinedione; Thymine-1 beta-delta-ribofuranosylthymine; Thymine-1 beta-D-ribofuranosylthymine; beta-delta-Ribofuranoside thymine-1; 1-beta-delta-Ribofuranosylthymine; Thymine-beta-D-arabinofuranoside; 1-(beta-D-Ribofuranosyl)thymine; 1-(b-D-Ribofuranosyl)thymine; 1-(Β-D-ribofuranosyl)thymine; b-D-Ribofuranoside thymine-1; 1-b-D-Ribofuranosylthymine; beta-delta-Ribofuranoside; Thymine ribonucleoside; Thymine ribofuranoside; beta-D-Ribofuranoside; Ribosylthymidine; 5-Methyl-uridine; Thymine riboside; 5-Methyluridine; Spongothymidine; Ribosylthymine; Spongothymidin; Ribothymidine; Thymidin; T



数据库引用编号

19 个数据库交叉引用编号

分类词条

相关代谢途径

Reactome(0)

BioCyc(0)

PlantCyc(0)

代谢反应

0 个相关的代谢反应过程信息。

Reactome(0)

BioCyc(0)

WikiPathways(0)

Plant Reactome(0)

INOH(0)

PlantCyc(0)

COVID-19 Disease Map(0)

PathBank(0)

PharmGKB(0)

8 个相关的物种来源信息

在这里通过桑基图来展示出与当前的这个代谢物在我们的BioDeep知识库中具有相关联信息的其他代谢物。在这里进行关联的信息来源主要有：

  • PubMed: 来源于PubMed文献库中的文献信息，我们通过自然语言数据挖掘得到的在同一篇文献中被同时提及的相关代谢物列表，这个列表按照代谢物同时出现的文献数量降序排序，取前10个代谢物作为相关研究中关联性很高的代谢物集合展示在桑基图中。
  • NCBI Taxonomy: 通过文献数据挖掘，得到的代谢物物种来源信息关联。这个关联信息同样按照出现的次数降序排序，取前10个代谢物作为高关联度的代谢物集合展示在桑吉图上。
  • Chemical Taxonomy: 在物质分类上处于同一个分类集合中的其他代谢物
  • Chemical Reaction: 在化学反应过程中，存在为当前代谢物相关联的生化反应过程中的反应底物或者反应产物的关联代谢物信息。

点击图上的相关代谢物的名称，可以跳转到相关代谢物的信息页面。



文献列表

  • Yingshan Ji, Jianqiang Sun, Jingxuan Xie, Wei Wu, Stella C Shuai, Qi Zhao, Wei Chen. m5UMCB: Prediction of RNA 5-methyluridine sites using multi-scale convolutional neural network with BiLSTM. Computers in biology and medicine. 2024 01; 168(?):107793. doi: 10.1016/j.compbiomed.2023.107793. [PMID: 38048661]
  • Shangyu Gao, Yu Sun, Xiaoguang Chen, Changhua Zhu, Xiaoye Liu, Wenlei Wang, Lijun Gan, Yanwu Lu, Frank Schaarschmidt, Marco Herde, Claus-Peter Witte, Mingjia Chen. Pyrimidine catabolism is required to prevent the accumulation of 5-methyluridine in RNA. Nucleic acids research. 2023 Jun; ?(?):. doi: 10.1093/nar/gkad529. [PMID: 37334828]
  • Pengmian Feng, Wei Chen. iRNA-m5U: A sequence based predictor for identifying 5-methyluridine modification sites in Saccharomyces cerevisiae. Methods (San Diego, Calif.). 2022 07; 203(?):28-31. doi: 10.1016/j.ymeth.2021.04.013. [PMID: 33882361]
  • Hong Lin, Binghai Lou, Jonathan M Glynn, Harshavardhan Doddapaneni, Edwin L Civerolo, Chuanwu Chen, Yongping Duan, Lijuan Zhou, Cheryl M Vahling. The complete genome sequence of 'Candidatus Liberibacter solanacearum', the bacterium associated with potato zebra chip disease. PloS one. 2011 Apr; 6(4):e19135. doi: 10.1371/journal.pone.0019135. [PMID: 21552483]
  • Ofelia A Olivero, Irma L Vazquez, Catherine C Cooch, Jessica Ming, Emily Keller, Mia Yu, Jennifer P Borojerdi, Hannan M Braun, Edward McKee, Miriam C Poirier. Long-term AZT exposure alters the metabolic capacity of cultured human lymphoblastoid cells. Toxicological sciences : an official journal of the Society of Toxicology. 2010 May; 115(1):109-17. doi: 10.1093/toxsci/kfq023. [PMID: 20106944]
  • Feng-Ling Cui, Ying-Hua Yan, Qiang-Zhai Zhang, Gui-Rong Qu, Juan Du, Xiao-Jun Yao. A study on the interaction between 5-Methyluridine and human serum albumin using fluorescence quenching method and molecular modeling. Journal of molecular modeling. 2010 Feb; 16(2):255-62. doi: 10.1007/s00894-009-0548-4. [PMID: 19588173]
  • Feng-ling Cui, Ying-hua Yan, Qiang-zhai Zhang, Gui-rong Qu, Yan Lu. [Determination of protein in biological samples by synchronous fluorescence]. Guang pu xue yu guang pu fen xi = Guang pu. 2009 Sep; 29(9):2531-4. doi: NULL. [PMID: 19950668]
  • Damien Jégourel, Raphaël Delépée, Florent Breton, Antoine Rolland, Richard Vidal, Luigi A Agrofoglio. Molecularly imprinted polymer of 5-methyluridine for solid-phase extraction of pyrimidine nucleoside cancer markers in urine. Bioorganic & medicinal chemistry. 2008 Oct; 16(19):8932-9. doi: 10.1016/j.bmc.2008.08.063. [PMID: 18789867]
  • Xinyu Zheng, Mathias Lundberg, Anna Karlsson, Magnus Johansson. Lipid-mediated protein delivery of suicide nucleoside kinases. Cancer research. 2003 Oct; 63(20):6909-13. doi: . [PMID: 14583490]
  • H F Becker, Y Motorin, C Florentz, R Giegé, H Grosjean. Pseudouridine and ribothymidine formation in the tRNA-like domain of turnip yellow mosaic virus RNA. Nucleic acids research. 1998 Sep; 26(17):3991-7. doi: 10.1093/nar/26.17.3991. [PMID: 9705510]
  • G A Gentry, N Lawrence, W Lushbaugh. Isolation and differentiation of herpes simplex virus and Trichomonas vaginalis in cell culture. Journal of clinical microbiology. 1985 Aug; 22(2):199-204. doi: 10.1128/jcm.22.2.199-204.1985. [PMID: 2993349]
  • R H Weisbart, G Chan, A Kacena, R E Saxton. Characterization of mouse and human monoclonal antibodies cross-reactive with SLE serum antibodies to guanosine. Journal of immunology (Baltimore, Md. : 1950). 1984 Jun; 132(6):2909-12. doi: NULL. [PMID: 6725946]
  • H Machida, S Sakata, M Morozumi, T Kiyanagi, A Kuninaka, H Yoshino. Comparison of the in vitro and in vivo anti-herpes activities of 1-beta-D-arabinofuranosylthymine and its 5'-monophosphate. Antiviral research. 1982 Sep; 2(4):217-26. doi: 10.1016/0166-3542(82)90044-4. [PMID: 6293376]
  • D Falke, H Moser, D Link, W E Müller. The effects of alpha- and beta-D-arabinosyladenosine and beta-D-arabinosylthymine on the synthesis of HSV types 1- and 2-infected cells. Advances in ophthalmology = Fortschritte der Augenheilkunde = Progres en ophtalmologie. 1979; 38(?):197-203. doi: NULL. [PMID: 230716]
  • A S Delk, J M Romeo, D P Nagle, J C Rabinowitz. Biosynthesis of ribothymidine in the transfer RNA of Streptococcus faecalis and Bacillus subtilis. A methylation of RNA involving 5,10-methylenetetrahydrofolate. The Journal of biological chemistry. 1976 Dec; 251(23):7649-56. doi: 10.1016/s0021-9258(17)32901-0. [PMID: 826533]