6XIB

PCSK9(deltaCRD) in complex with cyclic peptide 30

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Series of Novel and Highly Potent Cyclic Peptide PCSK9 Inhibitors Derived from an mRNA Display Screen and Optimized via Structure-Based Design.

Alleyne, C., Amin, R.P., Bhatt, B., Bianchi, E., Blain, J.C., Boyer, N., Branca, D., Embrey, M.W., Ha, S.N., Jette, K., Johns, D.G., Kerekes, A.D., Koeplinger, K.A., LaPlaca, D., Li, N., Murphy, B., Orth, P., Ricardo, A., Salowe, S., Seyb, K., Shahripour, A., Stringer, J.R., Sun, Y., Tracy, R., Wu, C., Xiong, Y., Youm, H., Zokian, H.J., Tucker, T.J.

(2020) J Med Chem 63: 13796-13824

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01084
  • Primary Citation of Related Structures:  
    6XIB, 6XIC, 6XID, 6XIE, 6XIF

  • PubMed Abstract: 

    • Proprotein convertase subtilisin-like/kexin type 9 (PCSK9) is a key regulator of plasma LDL-cholesterol (LDL-C) and a clinically validated target for the treatment of hypercholesterolemia and coronary artery disease. In this paper, we describe a series of novel cyclic peptides derived from an mRNA display screen which inhibit the protein-protein interaction between PCSK9 and LDLR ...

    Proprotein convertase subtilisin-like/kexin type 9 (PCSK9) is a key regulator of plasma LDL-cholesterol (LDL-C) and a clinically validated target for the treatment of hypercholesterolemia and coronary artery disease. In this paper, we describe a series of novel cyclic peptides derived from an mRNA display screen which inhibit the protein-protein interaction between PCSK9 and LDLR. Using a structure-based drug design approach, we were able to modify our original screening lead 2 to optimize the potency and metabolic stability and minimize the molecular weight to provide novel bicyclic next-generation PCSK9 inhibitor peptides such as 78 . These next-generation peptides serve as a critical foundation for continued exploration of potential oral, once-a-day PCSK9 therapeutics for the treatment of cardiovascular disease.

    Organizational Affiliation: 

    Departments of Medicinal Chemistry, Merck & Company, Inc., 770 Sumneytown Pike, P.O. Box 4, West Point, Pennsylvania 19486, United States.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proprotein convertase subtilisin/kexin type 9122Homo sapiensMutation(s): 0 
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
Proprotein convertase subtilisin/kexin type 9308Homo sapiensMutation(s): 0 
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: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide 30C [auth I]12Homo 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
GOL
Query on GOL
Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
3WX
Query on 3WX		C [auth I]PEPTIDE-LIKEC6 H11 N O2PRO
FTR
Query on FTR		C [auth I]L-PEPTIDE LINKINGC11 H11 F N2 O2TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.027α = 90
b = 71.027β = 90
c = 152.357γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2020-11-18 
    • Deposition Author(s): Orth, P.

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references