9C3G | pdb_00009c3g

human cGAS core domain (K427E/K428E) bound to Cladophorol A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.258 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Cladophorol-A is an inhibitor of cyclic GMP-AMP synthase.

Kissai, M.Chin, E.N.Martinez-Pena, F.Sulpizio, A.Stout, E.P.Usui, I.Barmare, F.Sanchez, B.Esquenazi, E.Stanfield, R.L.Wilson, I.A.Lairson, L.L.

(2025) Bioorg Med Chem Lett 115: 130007-130007

  • DOI: https://doi.org/10.1016/j.bmcl.2024.130007
  • Primary Citation of Related Structures:  
    9C3G

  • PubMed Abstract: 

    Cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) synthase (cGAS) is an enzyme sensor of double-stranded DNA (dsDNA) that serves to trigger activation of the cGAS-stimulator of interferon genes (STING) pathway. Excessive activation of this pathway has been demonstrated to contribute to various forms of inflammatory disease. As such, cGAS has arisen as a potential therapeutic target with broad potential applications. Using a pathway-targeted cell-based screening approach, we identified the natural product Cladophorol-A as a new class of non-cytotoxic cGAS inhibitor (cell-based IC 50  = 370 nM). An X-ray co-crystal structure at 2.75 Å resolution revealed that Cladophorol-A inhibits cGAS by binding to its active site within the conserved adenosine nucleobase binding site.


  • Organizational Affiliation
    • Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic GMP-AMP synthase373Homo sapiensMutation(s): 2 
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.258 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.597α = 90
b = 115.597β = 90
c = 60.378γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release