Crystal structure of DOT1L in complex with inhibitor CPD7 [N-(3-(((R)- 1-(7H-PYRROLO[2,3-D]PYRIMIDIN-4-YL)PIPERIDIN-3-YL)(METHYL)AMINO) propyl)-2-(3-(2-chloro-3-(2-methylpyridin-3-YL)BENZO[B]THIOPHEN-5- YL)UREIDO)ACETAMIDE]

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).

Ligands and binding sites

• 5JU · N~2~-{[2-chloro-3-(2-methylpyridin-3-yl)-1-benzothiophen-5-yl]carbamoyl}-N-(3-{methyl[(3R)-1-(5H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl]amino}propyl)glycinamide · ligand · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · 4 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1138 Ų buried · 12 hydrogen bonds · protein-protein

Compared structures

• 5MW4 · Crystal structure of Dot1L in complex with inhibitor CPD7… · the same entry in another collection · chain A against A, TM-score 1.00
• Q8TEK3 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase, H3 lysine-79… · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q8TEK3
• Elsewhere: RCSB PDB 5MW4 · PDBe 5MW4 · UniProt Q8TEK3