6U3X

PCSK9 in complex with compound 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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.

(2019) Cell Chem Biol --: --

  • DOI: 10.1016/j.chembiol.2019.10.002
  • Primary Citation of Related Structures:  

  • 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-prot ...

    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.,Cardio Metabolic Diseases, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA.,Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA; Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA. Electronic address: roman.erdmann@merck.com.,Computational and Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA.,Pharmacology, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA. Electronic address: gregory_adam@merck.com.,In Vitro Pharmacology, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA.,Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA.,Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA. Electronic address: whitney_petrilli@merck.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proprotein convertase subtilisin/kexin type 9
A, B
707Homo sapiensMutation(s): 2 
Gene Names: PCSK9 (NARC1)
EC: 3.4.21.-
Find proteins for Q8NBP7 (Homo sapiens)
Go to Gene View: PCSK9
Go to UniProtKB:  Q8NBP7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PVV
Query on PVV

Download SDF File 
Download CCD File 
B
2-[(1R)-6,7-dimethoxy-1-methyl-1,2,3,4-tetrahydroisoquinolin-1-yl]-N-(1,3-thiazol-2-yl)acetamide
C17 H21 N3 O3 S
GGTAOAOMAPVDLB-QGZVFWFLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.312α = 90.00
b = 70.417β = 90.00
c = 148.202γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACphasing
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-08-22 
  • Released Date: 2019-11-06 
  • Deposition Author(s): Lu, J., Soisson, S.

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release