4K8A

Fragment-based discovery of Focal Adhesion Kinase Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb4K8A/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2013-04-18 Released: 2013-09-11 
• Deposition Author(s): Graedler, U., Bomke, J., Musil, D., Dresing, V., Lehmann, M., Hoelzemann, G., Esdar, C., Krier, M., Heinrich, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 
  0.224 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Fragment-based discovery of focal adhesion kinase inhibitors.

Gradler, U., Bomke, J., Musil, D., Dresing, V., Lehmann, M., Holzemann, G., Greiner, H., Esdar, C., Krier, M., Heinrich, T.

(2013) Bioorg Med Chem Lett 23: 5401-5409

• PubMed: 23973211 
• DOI: https://doi.org/10.1016/j.bmcl.2013.07.050
• Primary Citation of Related Structures:  
  4K8A, 4K9Y, 4KAB, 4KAO


• PubMed Abstract: 
  

  Chemically diverse fragment hits of focal adhesion kinase (FAK) were discovered by surface plasmon resonance (SPR) screening of our in-house fragment library. Site specific binding of the primary hits was confirmed in a competition setup using a high-affinity ATP-site inhibitor of FAK. Protein crystallography revealed the binding mode of 41 out of 48 selected fragment hits within the ATP-site. Structural comparison of the fragment binding modes with a DFG-out inhibitor of FAK initiated first synthetic follow-up optimization leading to improved binding affinity.

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Organizational Affiliation: 

Merck KGaA, Merck Serono Research, Darmstadt, Germany. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.37 kDa 
• Atom Count: 4,140 
• Modelled Residue Count: 509 
• Deposited Residue Count: 558 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Focal adhesion kinase 1	A, B	279	Homo sapiens	Mutation(s): 0  Gene Names: FAK, FAK1, PTK2 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q05397 (Homo sapiens) Explore Q05397  Go to UniProtKB:  Q05397
PHAROS:  Q05397 GTEx:  ENSG00000169398

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K8A	C [auth A], D [auth B]	3-bromo-5-(2H-tetrazol-5-yl)pyridine C6 H4 Br N5 XJGDASCALCDOQH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free:  0.224 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.07	α = 90
b = 88.559	β = 90
c = 137.087	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
MOLREP	phasing
BUSTER	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-11 
Deposition Author(s): Graedler, U., Bomke, J., Musil, D., Dresing, V., Lehmann, M., Hoelzemann, G., Esdar, C., Krier, M., Heinrich, T.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2013-10-09
  Changes: Database references
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-10-30
  Changes: Structure summary