6MJU | pdb_00006mju

human cGAS catalytic domain bound with the inhibitor G108


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.256 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted JUMClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Development of human cGAS-specific small-molecule inhibitors for repression of dsDNA-triggered interferon expression.

Lama, L.Adura, C.Xie, W.Tomita, D.Kamei, T.Kuryavyi, V.Gogakos, T.Steinberg, J.I.Miller, M.Ramos-Espiritu, L.Asano, Y.Hashizume, S.Aida, J.Imaeda, T.Okamoto, R.Jennings, A.J.Michino, M.Kuroita, T.Stamford, A.Gao, P.Meinke, P.Glickman, J.F.Patel, D.J.Tuschl, T.

(2019) Nat Commun 10: 2261-2261

  • DOI: https://doi.org/10.1038/s41467-019-08620-4
  • Primary Citation of Related Structures:  
    6MJU, 6MJW, 6MJX

  • PubMed Abstract: 

    Cyclic GMP-AMP synthase (cGAS) is the primary sensor for aberrant intracellular dsDNA producing the cyclic dinucleotide cGAMP, a second messenger initiating cytokine production in subsets of myeloid lineage cell types. Therefore, inhibition of the enzyme cGAS may act anti-inflammatory. Here we report the discovery of human-cGAS-specific small-molecule inhibitors by high-throughput screening and the targeted medicinal chemistry optimization for two molecular scaffolds. Lead compounds from one scaffold co-crystallize with human cGAS and occupy the ATP- and GTP-binding active site. The specificity and potency of these drug candidates is further documented in human myeloid cells including primary macrophages. These novel cGAS inhibitors with cell-based activity will serve as probes into cGAS-dependent innate immune pathways and warrant future pharmacological studies for treatment of cGAS-dependent inflammatory diseases.


  • Organizational Affiliation

    Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, NY, 10065, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic GMP-AMP synthase372Homo 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
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JUM (Subject of Investigation/LOI)
Query on JUM

Download Ideal Coordinates CCD File 
B [auth A]1-[6,7-dichloro-9-(1H-pyrazol-4-yl)-1,3,4,5-tetrahydro-2H-pyrido[4,3-b]indol-2-yl]-2-hydroxyethan-1-one
C16 H14 Cl2 N4 O2
UUDFSTGSYHGEEV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
JUM BindingDB:  6MJU IC50: min: 27, max: 2950 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.989α = 90
b = 116.989β = 90
c = 59.957γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted JUMClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-06-05
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references