Human DNMT1(729-1600) bound to zebularine-containing 12MER dsdna and inhibitor GSK3735967A

Structure

x-ray diffraction · 3 distinct chains · 24% helix, 25% strand (DSSP).

Ligands and binding sites

• I67 · N-{[4-({[3,5-dicyano-4-ethyl-6-(4-methyl-1,4-diazepan-1-yl)pyridin-2-yl]sulfanyl}methyl) phenyl]methyl}glycinamide · ligand · 3 copies · chains A, C, D
• ZN · Zinc ion · metal · 2 copies · chains A
• EDO · 1,2-ethanediol · additive · 19 copies · chains A
• GOL · Glycerol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–C · 678 Ų buried · 13 hydrogen bonds · protein-nucleic
• C–D · 525 Ų buried · 54 hydrogen bonds · nucleic-nucleic
• A–D · 510 Ų buried · 8 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

• 7SFC · Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3735967A · the same entry in another collection · chain A against A, TM-score 1.00
• P26358 · AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 1 (P26358) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P26358
• Elsewhere: RCSB PDB 7SFC · PDBe 7SFC · UniProt P26358