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 7KEV | pdb_00007kev

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 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.226 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7KEV

This is version 1.2 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.

(2022) Cell Chem Biol 29: 249

  • DOI: https://doi.org/10.1016/j.chembiol.2021.08.012
  • Primary Citation 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. 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.


  • Organizational Affiliation: 
    • Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA. Electronic address: margaret.brousseau@novartis.com.

Macromolecule Content 

  • Total Structure Weight: 74.06 kDa 
  • Atom Count: 4,387 
  • Modeled Residue Count: 577 
  • Deposited Residue Count: 684 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proprotein convertase subtilisin/kexin type 9 Propeptide124Homo 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
GTEx:  ENSG00000169174 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NBP7
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Proprotein convertase subtilisin/kexin type 9546Homo 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
GTEx:  ENSG00000169174 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NBP7
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
cyclic peptide LDLR disruptor14synthetic constructMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Non-standard Monomers  2 Unique
IDChains TypeFormula2D Diagram
ALO
Query on ALO
L-PEPTIDE LINKINGC4 H9 N O3
WCM
Query on WCM
PEPTIDE LINKINGC19 H22 N2 O3

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.280 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.226 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
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
  • Version 1.1: 2022-03-02
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description