4RRV: Crystal structure of PDK1 in complex with ATP and PIFtide

There is great interest in developing selective protein kinase inhibitors by targeting allosteric sites, but these sites often involve protein-protein or protein-peptide interfaces that are very challenging to target with small molecules. Here we present a systematic approach to targeting a functionally conserved allosteric site on the protein kinase PDK1 called the PDK1-interacting fragment (PIF)tide-binding site, or PIF pocket. More than two dozen prosurvival and progrowth kinases dock a conserved peptide tail into this binding site, which recruits them to PDK1 to become activated. Using a site-directed chemical screen, we identified and chemically optimized ligand-efficient, selective, and cell-penetrant small molecules (molecular weight approximately 380 Da) that compete with the peptide docking motif for binding to PDK1. We solved the first high-resolution structure of a peptide docking motif (PIFtide) bound to PDK1 and mapped binding energy hot spots using mutational analysis. We then solved structures of PDK1 bound to the allosteric small molecules, which revealed a binding mode that remarkably mimics three of five hot-spot residues in PIFtide. These allosteric small molecules are substrate-selective PDK1 inhibitors when used as single agents, but when combined with an ATP-competitive inhibitor, they completely suppress the activation of the downstream kinases. This work provides a promising new scaffold for the development of high-affinity PIF pocket ligands, which may be used to enhance the anticancer activity of existing PDK1 inhibitors. Moreover, our results provide further impetus for exploring the helix alphaC patches of other protein kinases as potential therapeutic targets even though they involve protein-protein interfaces.
PDB ID: 4RRVDownload
MMDB ID: 125658
PDB Deposition Date: 2014/11/6
Updated in MMDB: 2017/12
Experimental Method:
x-ray diffraction
Resolution: 1.412  Å
Source Organism:
Homo sapiens
Similar Structures:
Biological Unit for 4RRV: dimeric; determined by author and by software (PISA)
Molecular Components in 4RRV
Label Count Molecule
Proteins (2 molecules)
3-phosphoinositide-dependent Protein Kinase 1(Gene symbol: PDPK1)
Molecule annotation
Serine/threonine-protein Kinase N2(Gene symbol: PKN2)
Molecule annotation
Chemicals (3 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB