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
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9C3G

Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

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 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.

Macromolecule Content 

  • Total Structure Weight: 43.94 kDa 
  • Atom Count: 2,904 
  • Modeled Residue Count: 350 
  • Deposited Residue Count: 373 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
Expand
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

View Full Validation Report



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