9C8T | pdb_00009c8t

Crystal Structure of human cyclic GMP-AMP synthase in complex with AMPPNP and compound 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 
    0.212 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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Literature

Structural insight into the cGAS active site explains differences between therapeutically relevant species.

Skeldon, A.M.Wang, L.Sgarioto, N.Beveridge, R.E.Chan, S.Dorich, S.Dumais, V.Fradet, N.Gaudreault, S.LeGros, P.McKay, D.Seliniotakis, R.Sietsema, D.V.Zhang, L.Boily, M.O.Burch, J.D.Caron, A.Fader, L.D.Lama, L.Xie, W.Patel, D.J.Tuschl, T.Crackower, M.A.Pike, K.A.

(2025) Commun Chem 8: 88-88

  • DOI: https://doi.org/10.1038/s42004-025-01481-7
  • Primary Citation of Related Structures:  
    9C8N, 9C8T

  • PubMed Abstract: 

    Cyclic GMP-AMP synthase (cGAS) is an intracellular sensor of double-stranded DNA that triggers a pro-inflammatory response upon binding. The interest in cGAS as a drug discovery target has increased substantially over the past decade due to growing evidence linking its activation to numerous peripheral and neurological diseases. Here, we report the binding mode of previously described cGAS inhibitors while also uncovering the structural basis for the interspecies potency shifts within this chemotype. A single threonine to isoleucine substitution between human and mouse cGAS drives compound activity, as demonstrated by biochemical, cellular, and in vivo studies. Finally, we utilize a structurally enabled design approach to engineer a novel chemical inhibitor with excellent potency for both human and mouse enzymes by targeting key interactions within the enzyme active site. Overall, this work provides the framework for rational optimization of cGAS inhibitors and potential preclinical translational strategies.


  • Organizational Affiliation

    Ventus Therapeutics, Saint-Laurent, QC, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic GMP-AMP synthase367Homo sapiensMutation(s): 1 
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
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
E [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
JUJ (Subject of Investigation/LOI)
Query on JUJ

Download Ideal Coordinates CCD File 
G [auth A]1-[9-(6-aminopyridin-3-yl)-6,7-dichloro-1,3,4,5-tetrahydro-2H-pyrido[4,3-b]indol-2-yl]-2-hydroxyethan-1-one
C18 H16 Cl2 N4 O2
VVUOUIPXYFIWLE-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free:  0.212 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.426α = 90
b = 51.972β = 90
c = 59.777γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited StatesVentus therapeutics

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-02
    Type: Initial release