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 

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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: 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proprotein convertase subtilisin/kexin type 9A, B707Homo sapiensMutation(s): 2 
Gene Names: PCSK9, NARC1, PSEC0052
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBP7 (Homo sapiens)
Explore Q8NBP7 
Go to UniProtKB:  Q8NBP7
PHAROS:  Q8NBP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NBP7
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab Heavy ChainC [auth H]246Homo sapiensMutation(s): 0 
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Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab Light ChainD [auth L]215Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PVM (Subject of Investigation/LOI)
Query on PVM
Download Ideal Coordinates CCD File 
E [auth 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

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Ligand Structure Quality Assessment 


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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