Crystal structure of human phosphoinositide-dependent protein kinase 1 (PDK1) 3-{5-[2-oxo-5-ureido-1,2-dihydro-indol-(3Z)-ylidenemethyl]-1H- pyrrol-3-yl}-N-(2-piperidin-1-yl-ethyl)-benzamide complex

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).

Ligands and binding sites

• 464 · 3-[5-({5-[(aminocarbonyl)amino]-2-oxo-2H-indol-3-yl}methyl)-1H-pyrrol-3-yl]-N-(2-piperidin-1-ylethyl)benzamide · ligand · chains A
• SO4 · Sulfate ion · ion · 3 copies · chains A
• GOL · Glycerol · additive · 8 copies · chains A

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

Pockets

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

Modifications

Observed in the structure: 1 modified (phosphorylation).

Compared structures

• 2PE2 · CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (PDK1)… · the same entry in another collection · chain A against A, TM-score 1.00
• O15530 · AlphaFold monomer V2.0 prediction for 3-phosphoinositide-dependent protein kinase 1… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 O15530
• Elsewhere: RCSB PDB 2PE2 · PDBe 2PE2 · UniProt O15530