6NAO

Discovery of a high affinity inhibitor of cGAS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of PF-06928215 as a high affinity inhibitor of cGAS enabled by a novel fluorescence polarization assay.

Hall, J.Brault, A.Vincent, F.Weng, S.Wang, H.Dumlao, D.Aulabaugh, A.Aivazian, D.Castro, D.Chen, M.Culp, J.Dower, K.Gardner, J.Hawrylik, S.Golenbock, D.Hepworth, D.Horn, M.Jones, L.Jones, P.Latz, E.Li, J.Lin, L.L.Lin, W.Lin, D.Lovering, F.Niljanskul, N.Nistler, R.Pierce, B.Plotnikova, O.Schmitt, D.Shanker, S.Smith, J.Snyder, W.Subashi, T.Trujillo, J.Tyminski, E.Wang, G.Wong, J.Lefker, B.Dakin, L.Leach, K.

(2017) PLoS One 12: e0184843

  • DOI: https://doi.org/10.1371/journal.pone.0184843
  • Primary Citation of Related Structures:  
    5V8O, 6NAO

  • PubMed Abstract: 

    Cyclic GMP-AMP synthase (cGAS) initiates the innate immune system in response to cytosolic dsDNA. After binding and activation from dsDNA, cGAS uses ATP and GTP to synthesize 2', 3' -cGAMP (cGAMP), a cyclic dinucleotide second messenger with mixed 2'-5' and 3'-5' phosphodiester bonds. Inappropriate stimulation of cGAS has been implicated in autoimmune disease such as systemic lupus erythematosus, thus inhibition of cGAS may be of therapeutic benefit in some diseases; however, the size and polarity of the cGAS active site makes it a challenging target for the development of conventional substrate-competitive inhibitors. We report here the development of a high affinity (KD = 200 nM) inhibitor from a low affinity fragment hit with supporting biochemical and structural data showing these molecules bind to the cGAS active site. We also report a new high throughput cGAS fluorescence polarization (FP)-based assay to enable the rapid identification and optimization of cGAS inhibitors. This FP assay uses Cy5-labelled cGAMP in combination with a novel high affinity monoclonal antibody that specifically recognizes cGAMP with no cross reactivity to cAMP, cGMP, ATP, or GTP. Given its role in the innate immune response, cGAS is a promising therapeutic target for autoinflammatory disease. Our results demonstrate its druggability, provide a high affinity tool compound, and establish a high throughput assay for the identification of next generation cGAS inhibitors.


  • Organizational Affiliation

    Medicine Design, Pfizer, Groton, Connecticut, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYCLIC GMP-AMP SYNTHASE
A, B
362Homo sapiensMutation(s): 0 
Gene Names: CGASC6orf150MB21D1
EC: 2.7.7.86
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N884 (Homo sapiens)
Explore Q8N884 
Go to UniProtKB:  Q8N884
PHAROS:  Q8N884
GTEx:  ENSG00000164430 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N884
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
KHM BindingDB:  6NAO Kd: 200 (nM) from 1 assay(s)
IC50: min: 2000, max: 4900 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 219.99α = 90
b = 45.946β = 111.46
c = 90.105γ = 90
Software Package:
Software NamePurpose
Aimlessdata reduction
SCALAdata scaling
REFMACphasing
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2018-12-19 
  • Deposition Author(s): Hall, J.
  • This entry supersedes: 5V8N

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Data collection, Database references