7S5G | pdb_00007s5g

PCSK9 in complex with compound 19


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 
    0.286 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7S5G

Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history

Literature

A Series of Novel, Highly Potent, and Orally Bioavailable Next-Generation Tricyclic Peptide PCSK9 Inhibitors.

Tucker, T.J.Embrey, M.W.Alleyne, C.Amin, R.P.Bass, A.Bhatt, B.Bianchi, E.Branca, D.Bueters, T.Buist, N.Ha, S.N.Hafey, M.He, H.Higgins, J.Johns, D.G.Kerekes, A.D.Koeplinger, K.A.Kuethe, J.T.Li, N.Murphy, B.Orth, P.Salowe, S.Shahripour, A.Tracy, R.Wang, W.Wu, C.Xiong, Y.Zokian, H.J.Wood, H.B.Walji, A.

(2021) J Med Chem 64: 16770-16800

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01599
  • Primary Citation Related Structures: 
    7S5G, 7S5H

  • 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. Starting from second-generation lead structures such as 2 , we were able to refine these structures to obtain extremely potent bi- and tricyclic PCSK9 inhibitor peptides. Optimized molecules such as 44 demonstrated sufficient oral bioavailability to maintain therapeutic levels in rats and cynomolgus monkeys after dosing with an enabled formulation. We demonstrated target engagement and LDL lowering in cynomolgus monkeys essentially identical to those observed with the clinically approved, parenterally dosed antibodies. These molecules represent the first report of highly potent and orally bioavailable macrocyclic peptide PCSK9 inhibitors with overall profiles favorable for potential development as once-daily oral lipid-lowering agents. In this manuscript, we detail the design criteria and multiparameter optimization of this novel series of PCSK9 inhibitors.


  • Organizational Affiliation
    • Department of Medicinal Chemistry, Merck & Co., Inc., 770 Sumneytown Pike, P.O. Box 4, West Point, Pennsylvania 19486 United States.

Macromolecule Content 

  • Total Structure Weight: 48.07 kDa 
  • Atom Count: 3,066 
  • Modeled Residue Count: 388 
  • Deposited Residue Count: 439 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Propeptide of Proprotein convertase subtilisin/kexin type 9122Homo 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
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 9308Homo 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
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
Z9J-ALA-DAL-PHE-FTR-PRO-THR-0A1-3WX9synthetic constructMutation(s): 0 

Small Molecules

Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
0A1
Query on 0A1
C
L-PEPTIDE LINKINGC10 H13 N O3TYR
3WX
Query on 3WX
C
PEPTIDE-LIKEC6 H11 N O2PRO
DAL
Query on DAL
C
D-PEPTIDE LINKINGC3 H7 N O2

--

FTR
Query on FTR
C
L-PEPTIDE LINKINGC11 H11 F N2 O2TRP
Z9J
Query on Z9J
C
PEPTIDE LINKINGC13 H19 N O2 S2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free:  0.286 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.027α = 90
b = 71.027β = 90
c = 153.606γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2021-11-03 
  • Deposition Author(s): Orth, P.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 1.1: 2021-12-08
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection, Derived calculations
  • Version 2.0: 2024-04-24
    Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary