6GCW | pdb_00006gcw

Focal Adhesion Kinase catalytic domain in complex with irreversible inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6GCW/pdb

• Classification: CELL ADHESION
• Organism(s): Gallus gallus
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2018-04-19 Released: 2019-05-01 
• Deposition Author(s): Yen-Pon, E., Li, B., Acebron-Garcia-de-Eulate, M., Tomkiewicz-Raulet, C., Dawson, J., Lietha, D., Frame, M.C., Coumoul, X., Garbay, C., Etheve-Quelquejeu, M., Chen, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.274 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

Structure-Based Design, Synthesis, and Characterization of the First Irreversible Inhibitor of Focal Adhesion Kinase.

Yen-Pon, E., Li, B., Acebron-Garcia-de-Eulate, M., Tomkiewicz-Raulet, C., Dawson, J., Lietha, D., Frame, M.C., Coumoul, X., Garbay, C., Etheve-Quelquejeu, M., Chen, H.

(2018) ACS Chem Biol 13: 2067-2073

• PubMed: 29897729 
• DOI: https://doi.org/10.1021/acschembio.8b00250
• Primary Citation Related Structures: 
  6GCR, 6GCW, 6GCX


• PubMed Abstract: 
  

  Focal Adhesion Kinase signaling pathway and its functions have been involved in the development and aggressiveness of tumor malignancy, it then presents a promising cancer therapeutic target. Several reversible FAK inhibitors have been developed and are being conducted in clinical trials. On the other hand, irreversible covalent inhibitors would bring many desirable pharmacological features including high potency and increased duration of action. Herein we report the structure-guided development of the first highly potent and irreversible inhibitor of the FAK kinase. This inhibitor showed a very potent decrease of autophosphorylation of FAK in squamous cell carcinoma. A cocrystal structure of the FAK kinase domain in complex with this compound revealed the inhibitor binding mode within the ATP binding site and confirmed the covalent linkage between the targeted Cys427 of the protein and the inhibitor.

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Organizational Affiliation: 
• Chemistry of RNA, Nucleosides, Peptides and Heterocycles, CNRS UMR8601 , Université Paris Descartes, PRES Sorbonne Paris Cité, UFR Biomédicale , 45 rue des Saints-Pères , 75270 Paris Cedex 06 , France.
Cell Signalling and Adhesion Group, Structural Biology Programme , Spanish National Cancer Research Centre (CNIO) , Calle Melchor Fernández Almagro 3 , Madrid 28029 , Spain.
Toxicologie, Pharmacologie et Signalisation Cellulaire, INSERM, UMR S 1124 , Université Paris Descartes, PRES Sorbonne Paris Cité, UFR Biomédicale , 45 rue des Saints-Pères , 75270 Paris Cedex 06 , France.
Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine , University of Edinburgh , Edinburgh EH4 2XR , United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 64.69 kDa 
• Atom Count: 4,518 
• Modeled Residue Count: 513 
• Deposited Residue Count: 552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Focal adhesion kinase 1	A, B	276	Gallus gallus	Mutation(s): 0  Gene Names: PTK2, FAK, FAK1 EC: 2.7.10.2
UniProt
Find proteins for Q00944 (Gallus gallus) Explore Q00944  Go to UniProtKB:  Q00944

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EUQ	C [auth A], E [auth B]	2-[[5-chloranyl-2-[[4-[[[1-[2-(propanoylamino)ethyl]-1,2,3-triazol-4-yl]methylamino]methyl]phenyl]amino]pyrimidin-4-yl]amino]-~{N}-methyl-benzamide C27 H31 Cl N10 O2 NQZYJQAUOJXIDJ-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.274 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.916	α = 90
b = 119.798	β = 90.56
c = 52.81	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-01 
Deposition Author(s): Yen-Pon, E., Li, B., Acebron-Garcia-de-Eulate, M., Tomkiewicz-Raulet, C., Dawson, J., Lietha, D., Frame, M.C., Coumoul, X., Garbay, C., Etheve-Quelquejeu, M., Chen, H.

Revision History  

• Version 1.0: 2019-05-01
  Type: Initial release
  
• Version 1.1: 2019-10-02
  Changes: Data collection, Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references