6MJW | pdb_00006mjw

human cGAS catalytic domain bound with the inhibitor G150

• PDB DOI: https://doi.org/10.2210/pdb6MJW/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-09-23 Released: 2019-05-29 
• Deposition Author(s): 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., Michinom, M., Kuroita, T., Stamford, A., Gao, P., Meinke, P., Glickman, J.F., Patel, D.J., Tuschl, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.257 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

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

• PubMed: 31113940 
• DOI: https://doi.org/10.1038/s41467-019-08620-4
• Primary Citation 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.

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Organizational Affiliation: 
• Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, NY, 10065, USA.
High-Throughput and Spectroscopy Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.
Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street 16th Floor, New York, NY, 10021, USA.
Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
High-Throughput and Spectroscopy Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA. [e-mail].
Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA. [e-mail].
Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, NY, 10065, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 43.94 kDa 
• Atom Count: 2,775 
• Modeled Residue Count: 328 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic GMP-AMP synthase	A	372	Homo sapiens	Mutation(s): 2  Gene Names: CGAS, C6orf150, MB21D1 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JUJ (Subject of Investigation/LOI)	C [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
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.257 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.531	α = 90
b = 116.531	β = 90
c = 60.037	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-29 
Deposition Author(s): 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., Michinom, M., Kuroita, T., Stamford, A., Gao, P., Meinke, P., Glickman, J.F., Patel, D.J., Tuschl, T.

Revision History  

• 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