9ELX | pdb_00009elx

Crystal Structure of human cyclic GMP-AMP synthase (cGAS) in complex with compound 5; 3-((2-((3-chloro-4-fluorophenyl)amino)-2-oxoethyl)carbamoyl)picolinic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 
    0.200 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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Literature

Discovery of Potent and Orally Bioavailable Pyrimidine Amide cGAS Inhibitors via Structure-Guided Hybridization.

Cyr, P.Fader, L.D.Burch, J.D.Pike, K.A.Sietsema, D.V.Boily, M.O.Ciblat, S.Sgarioto, N.Skeldon, A.M.Gaudreault, S.Le Gros, P.Dumais, V.McKay, D.J.J.Abraham, N.S.Seliniotakis, R.Beveridge, R.E.

(2024) ACS Med Chem Lett 15: 2201-2209

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00471
  • Primary Citation of Related Structures:  
    9ELX, 9MDC, 9MDD

  • PubMed Abstract: 

    Using a high-throughput screening (HTS) approach, a new GTP-site binding pyridine-carboxylate series of cGAS inhibitors was discovered. The biochemical potency of this new pyridine carboxylate series was improved 166-fold from the original hit to double-digit nanomolar levels using structure-based design insights, but the series was found to suffer from low permeability and low bioavailability. A structure-based hybridization of the metal-binding motifs of the pyridine carboxylate series and our previously disclosed tetrahydrocarboline GTP-site ligand 23 identified pyrimidine amide compound 36 . Compound 36 is potent against both human and mouse cGAS isoforms and has a favorable pharmacokinetic (PK) profile in mice. Additionally, compound 36 displayed a dose-dependent reduction in cGAMP production in a ConA pharmacodynamic mouse model of acute liver injury, demonstrating potential utility as an in vivo tool compound for further investigation of the cGAS pathway.


  • Organizational Affiliation

    Ventus Therapeutics, 4800 rue Lévy #110, Saint-Laurent H4R 2P1, Quebec, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic GMP-AMP synthase366Homo 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
A1BJH (Subject of Investigation/LOI)
Query on A1BJH

Download Ideal Coordinates CCD File 
C [auth A]3-{[2-(3-chloro-4-fluoroanilino)-2-oxoethyl]carbamoyl}pyridine-2-carboxylic acid
C15 H11 Cl F N3 O4
SEYIPRFGSMAHNV-UHFFFAOYSA-N
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free:  0.200 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.246α = 90
b = 51.233β = 90
c = 59.953γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-01
    Type: Initial release