6U2P image
Entry Detail
PDB ID:
6U2P
Keywords:
Title:
PCSK9 in complex with compound 5
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2019-08-20
Release Date:
2019-11-06
Method Details:
Experimental Method:
Resolution:
2.04 Å
R-Value Free:
0.21
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Proprotein convertase subtilisin/kexin type 9
Mutations:V474I, G670E
Chain IDs:A, B
Chain Length:707
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation

Abstact

Proprotein convertase substilisin-like/kexin type 9 (PCSK9) is a serine protease involved in a protein-protein interaction with the low-density lipoprotein (LDL) receptor that has both human genetic and clinical validation. Blocking this protein-protein interaction prevents LDL receptor degradation and thereby decreases LDL cholesterol levels. Our pursuit of small-molecule direct binders for this difficult to drug PPI target utilized affinity selection/mass spectrometry, which identified one confirmed hit compound. An X-ray crystal structure revealed that this compound was binding in an unprecedented allosteric pocket located between the catalytic and C-terminal domain. Optimization of this initial hit, using two distinct strategies, led to compounds with high binding affinity to PCSK9. Direct target engagement was demonstrated in the cell lysate with a cellular thermal shift assay. Finally, ligand-induced protein degradation was shown with a proteasome recruiting tag attached to the high-affinity allosteric ligand for PCSK9.

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Primary Citation of related structures