SNAP-annotated 5mC-DNA-protein interactions: PDB entry 9v5p

PDB-id

9v5p; DSSR-derived features in text and JSON formats; DNAproDB

Class

transferase

Method

cryo-EM (2.85 Å)

Summary

Human dnmt1 (aa 698-1616) in complex with hemimethylated dsDNA and inhibitor dmt207

Reference

Shen Y, Wei J, Tang S, Wu D, Zong L, Ma S, Xiong Q, Gong R, Xu S, Peng C, Feng Q, Liu S, Liu Q, Ye Y, Zhao Q, Luo C, Huang P, Li Z, Kong X, Lan X (2026): "Discovery of a Novel DNMT1 Inhibitor with Improved Efficacy in Treating beta-Thalassemia." Adv Sci, 13, e13469. doi: 10.1002/advs.202513469.

Abstract

 

• The contacts include paired nucleotides (mostly a G in Watson-Crick G-C pairing) and amino-acids within a 4.5-Å distance cutoff to base atoms of 5mC.
• The structure is oriented in the base reference frame of 5mC, allowing for easy comparison and direct superimposition between entries.
• The black sphere (•) denotes the 5-methyl carbon atom in 5mC.