PCSK9 in complex with compound 5

Experimental Data Snapshot

  • Resolution: 2.04 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


From Screening to Targeted Degradation: Strategies for the Discovery and Optimization of Small Molecule Ligands for PCSK9.

Petrilli, W.L.Adam, G.C.Erdmann, R.S.Abeywickrema, P.Agnani, V.Ai, X.Baysarowich, J.Byrne, N.Caldwell, J.P.Chang, W.DiNunzio, E.Feng, Z.Ford, R.Ha, S.Huang, Y.Hubbard, B.Johnston, J.M.Kavana, M.Lisnock, J.M.Liang, R.Lu, J.Lu, Z.Meng, J.Orth, P.Palyha, O.Parthasarathy, G.Salowe, S.P.Sharma, S.Shipman, J.Soisson, S.M.Strack, A.M.Youm, H.Zhao, K.Zink, D.L.Zokian, H.Addona, G.H.Akinsanya, K.Tata, J.R.Xiong, Y.Imbriglio, J.E.

(2020) Cell Chem Biol 27: 32-40.e3

  • DOI: https://doi.org/10.1016/j.chembiol.2019.10.002
  • Primary Citation of Related Structures:  
    6U26, 6U2N, 6U2P, 6U36, 6U38, 6U3X

  • PubMed Abstract: 

    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.

  • Organizational Affiliation

    Computational and Structural Chemistry, Merck & Co. Inc., 770 Sumneytown Pike, West Point, PA 19486, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proprotein convertase subtilisin/kexin type 9
A, B
707Homo sapiensMutation(s): 2 
Gene Names: PCSK9NARC1PSEC0052
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBP7 (Homo sapiens)
Explore Q8NBP7 
Go to UniProtKB:  Q8NBP7
GTEx:  ENSG00000169174 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NBP7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.04 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.851α = 90
b = 70.647β = 90
c = 149.345γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Database references