DNAmod: 5-(2-aminoethyl)-2'-deoxyuridine

Description

A pyrimidine 2'-deoxyribonucleoside that is 2'-deoxyuridine in which the hydrogen at position 5 has been replaced by a 2-aminoethyl group. It is a thymidine hypermodification replacing 30% of thymidine in the DNA of the Pseudomonas phage M6.

Chemical properties

Chemical formula	Net charge	Average mass
C11H17N3O5	0	271.270

Recommended notation

Name	5-(2-aminoethyl)uridine
Abbreviation	5-NedU

Nomenclature

IUPAC	SMILES	InChI	InChIKey	Synonyms
5-(2-aminoethyl)-2'-deoxyuridine	N1(C(NC(C(=C1)CCN)=O)=O)[C@H]2C[C@@H]([C@H](O2)CO)O	InChI=1S/C11H17N3O5/c12-2-1-6-4-14(11(18)13-10(6)17)9-3-7(16)8(5-15)19-9/h4,7-9,15-16H,1-3,5,12H2,(H,13,17,18)/t7-,8+,9+/m0/s1	WTDDCUXJNCBBKI-DJLDLDEBSA-N	5-(2-aminoethyl)-1-[(2r,4s,5r)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4-dione 5-(2-aminoethyl)-1-[(2r,4s,5r)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]pyrimidine-2,4(1h,3h)-dione 5-nedu

Nature

Origin	Function	Functional detail	Organisms	References
natural	hypermodified nucleobase		bacteriophage M6	Lee, YJ, et al. 2018. Identification and biosynthesis of thymidine hypermodifications in the genomic DNA of widespread bacterial viruses. Proceedings of the National Academy of Sciences of the United States of America. 115(14).

Database references:

CHEBI:142166

Citations

Lee, YJ, et al. 2018. Identification and biosynthesis of thymidine hypermodifications in the genomic DNA of widespread bacterial viruses. Proceedings of the National Academy of Sciences of the United States of America. 115(14).