7KEV

PCSK9 in complex with a cyclic peptide LDLR disruptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Identification of a PCSK9-LDLR disruptor peptide with in vivo function.

Brousseau, M.E.Clairmont, K.B.Spraggon, G.Flyer, A.N.Golosov, A.A.Grosche, P.Amin, J.Andre, J.Burdick, D.Caplan, S.Chen, G.Chopra, R.Ames, L.Dubiel, D.Fan, L.Gattlen, R.Kelly-Sullivan, D.Koch, A.W.Lewis, I.Li, J.Liu, E.Lubicka, D.Marzinzik, A.Nakajima, K.Nettleton, D.Ottl, J.Pan, M.Patel, T.Perry, L.Pickett, S.Poirier, J.Reid, P.C.Pelle, X.Seepersaud, M.Subramanian, V.Vera, V.Xu, M.Yang, L.Yang, Q.Yu, J.Zhu, G.Monovich, L.G.

(2021) Cell Chem Biol 

  • DOI: 10.1016/j.chembiol.2021.08.012
  • Primary Citation of Related Structures:  
    7KEV, 7KFA

  • PubMed Abstract: 
  • Proprotein convertase subtilisin/kexin type 9 (PCSK9) regulates plasma low-density lipoprotein cholesterol (LDL-C) levels by promoting hepatic LDL receptor (LDLR) degradation. Therapeutic antibodies that disrupt PCSK9-LDLR binding reduce LDL-C concentrations and cardiovascular disease risk ...

    Proprotein convertase subtilisin/kexin type 9 (PCSK9) regulates plasma low-density lipoprotein cholesterol (LDL-C) levels by promoting hepatic LDL receptor (LDLR) degradation. Therapeutic antibodies that disrupt PCSK9-LDLR binding reduce LDL-C concentrations and cardiovascular disease risk. The epidermal growth factor precursor homology domain A (EGF-A) of the LDLR serves as a primary contact with PCSK9 via a flat interface, presenting a challenge for identifying small molecule PCSK9-LDLR disruptors. We employ an affinity-based screen of 10 13 in vitro-translated macrocyclic peptides to identify high-affinity PCSK9 ligands that utilize a unique, induced-fit pocket and partially disrupt the PCSK9-LDLR interaction. Structure-based design led to molecules with enhanced function and pharmacokinetic properties (e.g., 13 PCSK9i). In mice, 13 PCSK9i reduces plasma cholesterol levels and increases hepatic LDLR density in a dose-dependent manner. 13 PCSK9i functions by a unique, allosteric mechanism and is the smallest molecule identified to date with in vivo PCSK9-LDLR disruptor function.


    Related Citations: 
    • The self-inhibited structure of full-length PCSK9 at 1.9 A reveals structural homology with resistin within the C-terminal domain.
      Hampton, E.N., Knuth, M.W., Li, J., Harris, J.L., Lesley, S.A., Spraggon, G.
      (2007) Proc Natl Acad Sci U S A 104: 14604

    Organizational Affiliation

    Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proprotein convertase subtilisin/kexin type 9 PropeptideA124Homo sapiensMutation(s): 0 
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
Proprotein convertase subtilisin/kexin type 9B546Homo 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
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
cyclic peptide LDLR disruptorC14synthetic constructMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
D [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALO
Query on ALO
CL-PEPTIDE LINKINGC4 H9 N O3THR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.225α = 90
b = 70.441β = 90
c = 149.257γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release