Trypanosoma brucei CLK1 kinase domain in complex with a covalent aminobenzimidazole inhibitor AB1

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 15% strand (DSSP).

Ligands and binding sites

• 5XH · ~{N}-[1-[(3~{R})-1-[4-(dimethylamino)but-2-enoyl]azepan-3-yl]-7-methyl-benzimidazol-2-yl]-2-methyl-pyridine-4-carboxamide · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
• SO4 · Sulfate ion · ion · 33 copies · chains A, B, G, C, H, D, E, P, F, O, I, M, J, N, K, L

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Interfaces

25 interfaces between chains.

• B–E · 849 Ų buried · 7 hydrogen bonds · protein-protein
• J–K · 788 Ų buried · 8 hydrogen bonds · protein-protein
• C–F · 777 Ų buried · 8 hydrogen bonds · protein-protein
• A–B · 697 Ų buried · 7 hydrogen bonds · protein-protein
• I–M · 693 Ų buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 covalent (covalent ligand).

Compared structures

• 6Q2A · Trypanosoma brucei CLK1 kinase domain in complex with a covalent aminobenzimidazole… · the same entry in another collection · chain E against E, TM-score 1.00

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 Q382U0
• Elsewhere: RCSB PDB 6Q2A · PDBe 6Q2A · UniProt Q382U0