6U38

PCSK9 in complex with a Fab and compound 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
  • 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proprotein convertase subtilisin/kexin type 9A, B707Homo 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
PHAROS:  Q8NBP7
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab Heavy ChainC [auth H]246Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab Light ChainD [auth L]215Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PVJ (Subject of Investigation/LOI)
Query on PVJ

Download Ideal Coordinates CCD File 
E [auth B]2-fluoro-4-{[(1R)-1-methyl-6-{[(2S)-oxan-2-yl]methoxy}-1-{2-oxo-2-[(1,3-thiazol-2-yl)amino]ethyl}-1,2,3,4-tetrahydroisoquinolin-7-yl]oxy}benzoic acid
C28 H30 F N3 O6 S
VYXFBZAJVWTJQP-HMILPKGGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.033α = 90
b = 155.033β = 90
c = 151.919γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

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