5XZG

Mouse cGAS bound to the inhibitor RU521


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Small molecule inhibition of cGAS reduces interferon expression in primary macrophages from autoimmune mice.

Vincent, J.Adura, C.Gao, P.Luz, A.Lama, L.Asano, Y.Okamoto, R.Imaeda, T.Aida, J.Rothamel, K.Gogakos, T.Steinberg, J.Reasoner, S.Aso, K.Tuschl, T.Patel, D.J.Glickman, J.F.Ascano, M.

(2017) Nat Commun 8: 750-750

  • DOI: https://doi.org/10.1038/s41467-017-00833-9
  • Primary Citation of Related Structures:  
    5XZB, 5XZE, 5XZG

  • PubMed Abstract: 

    Cyclic GMP-AMP synthase is essential for innate immunity against infection and cellular damage, serving as a sensor of DNA from pathogens or mislocalized self-DNA. Upon binding double-stranded DNA, cyclic GMP-AMP synthase synthesizes a cyclic dinucleotide that initiates an inflammatory cellular response. Mouse studies that recapitulate causative mutations in the autoimmune disease Aicardi-Goutières syndrome demonstrate that ablating the cyclic GMP-AMP synthase gene abolishes the deleterious phenotype. Here, we report the discovery of a class of cyclic GMP-AMP synthase inhibitors identified by a high-throughput screen. These compounds possess defined structure-activity relationships and we present crystal structures of cyclic GMP-AMP synthase, double-stranded DNA, and inhibitors within the enzymatic active site. We find that a chemically improved member, RU.521, is active and selective in cellular assays of cyclic GMP-AMP synthase-mediated signaling and reduces constitutive expression of interferon in macrophages from a mouse model of Aicardi-Goutières syndrome. RU.521 will be useful toward understanding the biological roles of cyclic GMP-AMP synthase and can serve as a molecular scaffold for development of future autoimmune therapies.Upon DNA binding cyclic GMP-AMP synthase (cGAS) produces a cyclic dinucleotide, which leads to the upregulation of inflammatory genes. Here the authors develop small molecule cGAS inhibitors, functionally characterize them and present the inhibitor and DNA bound cGAS crystal structures, which will facilitate drug development.


  • Organizational Affiliation

    Vanderbilt University School of Medicine, Nashville, TN, 37027, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic GMP-AMP synthase362Mus musculusMutation(s): 0 
Gene Names: Mb21d1
EC: 2.7.7.86
UniProt & NIH Common Fund Data Resources
Find proteins for Q8C6L5 (Mus musculus)
Explore Q8C6L5 
Go to UniProtKB:  Q8C6L5
IMPC:  MGI:2442261
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8C6L5
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*AP*AP*TP*TP*GP*CP*CP*GP*AP*AP*GP*AP*CP*G)-3')B [auth E]15Mus musculus
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*GP*TP*CP*TP*TP*CP*GP*GP*CP*AP*AP*TP*T)-3')C [auth F]14Mus musculus
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AEV
Query on AEV

Download Ideal Coordinates CCD File 
E [auth A]2-(4,5-dichloro-1H-benzimidazol-2-yl)-5-methyl-4-[(1R)-3-oxo-1,3-dihydro-2-benzofuran-1-yl]-1,2-dihydro-3H-pyrazol-3-one
C19 H12 Cl2 N4 O3
IAWZUQAOMURCLV-MRXNPFEDSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.562α = 90
b = 98.43β = 90
c = 130.372γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)ChinaNSFC31670903
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM104962

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references