6U36

PCSK9 in complex with a Fab and compound 14


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 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.

(2020) Cell Chem Biol 27: 32-40.e3

  • DOI: 10.1016/j.chembiol.2019.10.002
  • Structures With Same Primary Citation

  • 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

    Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA.



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: PCSK9NARC1PSEC0052
EC: 3.4.21
Find proteins for Q8NBP7 (Homo sapiens)
Go to UniProtKB:  Q8NBP7
NIH Common Fund Data Resources
PHAROS  Q8NBP7

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab Light Chain
L
215Homo sapiensMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab Heavy Chain
H
246Homo sapiensMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PVM
Query on PVM

Download CCD File 
B
2-fluoro-4-{[(1R)-6-(2-{4-[1-(4-methoxyphenyl)-5-methyl-6-oxo-1,6-dihydropyridazin-3-yl]-1H-1,2,3-triazol-1-yl}ethoxy)-1-methyl-1-{2-oxo-2-[(1,3-thiazol-2-yl)amino]ethyl}-1,2,3,4-tetrahydroisoquinolin-7-yl]oxy}benzoic acid
C38 H35 F N8 O7 S
CKGQJOFAVYEVFG-KXQOOQHDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.605α = 90
b = 155.605β = 90
c = 152.451γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2019-08-21 
  • Released Date: 2019-11-06 
  • Deposition Author(s): Lu, J., Soisson, S.

Revision History 

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