Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 20

Structure

x-ray diffraction · 1 distinct chain · 57% helix, 15% strand (DSSP).

Ligands and binding sites

• 5ZP · (3~{S})-3-[5-(8-cyclopropyl-2-methyl-9~{H}-pyrido[2,3-b]indol-3-yl)-1,3,4-oxadiazol-2-yl]-4-methyl-~{N}-[(1~{R})-1-phenylethyl]pentanamide · ligand · chains A
• CL · Chloride ion · ion · chains A
• DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
• ACT · Acetate ion · additive · chains A

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Compared structures

• 7VBX · Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 20 · the same entry in another collection · chain A against A, TM-score 1.00
• Q15119 · AlphaFold monomer V2.0 prediction for [pyruvate dehydrogenase (acetyl-transferring)]… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q15119
• Elsewhere: RCSB PDB 7VBX · PDBe 7VBX · UniProt Q15119