7AEL

alpha 1-antitrypsin (C232S) complexed with GSK716


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.189 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Development of a small molecule that corrects misfolding and increases secretion of Z alpha 1 -antitrypsin.

Lomas, D.A.Irving, J.A.Arico-Muendel, C.Belyanskaya, S.Brewster, A.Brown, M.Chung, C.W.Dave, H.Denis, A.Dodic, N.Dossang, A.Eddershaw, P.Klimaszewska, D.Haq, I.Holmes, D.S.Hutchinson, J.P.Jagger, A.M.Jakhria, T.Jigorel, E.Liddle, J.Lind, K.Marciniak, S.J.Messer, J.Neu, M.Olszewski, A.Ordonez, A.Ronzoni, R.Rowedder, J.Rudiger, M.Skinner, S.Smith, K.J.Terry, R.Trottet, L.Uings, I.Wilson, S.Zhu, Z.Pearce, A.C.

(2021) EMBO Mol Med 13: e13167-e13167

  • DOI: https://doi.org/10.15252/emmm.202013167
  • Primary Citation of Related Structures:  
    7AEL

  • PubMed Abstract: 

    Severe α 1 -antitrypsin deficiency results from the Z allele (Glu342Lys) that causes the accumulation of homopolymers of mutant α 1 -antitrypsin within the endoplasmic reticulum of hepatocytes in association with liver disease. We have used a DNA-encoded chemical library to undertake a high-throughput screen to identify small molecules that bind to, and stabilise Z α 1 -antitrypsin. The lead compound blocks Z α 1 -antitrypsin polymerisation in vitro, reduces intracellular polymerisation and increases the secretion of Z α 1 -antitrypsin threefold in an iPSC model of disease. Crystallographic and biophysical analyses demonstrate that GSK716 and related molecules bind to a cryptic binding pocket, negate the local effects of the Z mutation and stabilise the bound state against progression along the polymerisation pathway. Oral dosing of transgenic mice at 100 mg/kg three times a day for 20 days increased the secretion of Z α 1 -antitrypsin into the plasma by sevenfold. There was no observable clearance of hepatic inclusions with respect to controls over the same time period. This study provides proof of principle that "mutation ameliorating" small molecules can block the aberrant polymerisation that underlies Z α 1 -antitrypsin deficiency.


  • Organizational Affiliation

    UCL Respiratory, Rayne Institute, University College London, London, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-1-antitrypsinA [auth AAA]404Homo sapiensMutation(s): 0 
Gene Names: SERPINA1AATPIPRO0684PRO2209
UniProt & NIH Common Fund Data Resources
Find proteins for P01009 (Homo sapiens)
Explore P01009 
Go to UniProtKB:  P01009
PHAROS:  P01009
GTEx:  ENSG00000197249 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01009
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R7Z
Query on R7Z

Download Ideal Coordinates CCD File 
B [auth AAA]~{N}-[(1~{S},2~{R})-1-(3-fluoranyl-2-methyl-phenyl)-1-oxidanyl-pentan-2-yl]-2-oxidanylidene-1,3-dihydroindole-4-carboxamide
C21 H23 F N2 O3
MSZBLPYPBQYDNI-QUCCMNQESA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth AAA]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.954α = 90
b = 39.592β = 104.961
c = 90.517γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-03-10 
  • Deposition Author(s): Chung, C.

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release
  • Version 1.1: 2021-03-17
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Refinement description