Structure of Focal Adhesion Kinase catalytic domain in complex with novel allosteric inhibitor

Experimental Data Snapshot

  • Resolution: 2.65 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.186 

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This is version 1.3 of the entry. See complete history


Discovery and characterization of novel allosteric FAK inhibitors.

Iwatani, M.Iwata, H.Okabe, A.Skene, R.J.Tomita, N.Hayashi, Y.Aramaki, Y.Hosfield, D.J.Hori, A.Baba, A.Miki, H.

(2013) Eur J Med Chem 61: 49-60

  • DOI: https://doi.org/10.1016/j.ejmech.2012.06.035
  • Primary Citation of Related Structures:  
    4EBV, 4EBW

  • PubMed Abstract: 

    Focal adhesion kinase (FAK) regulates cell survival and proliferation pathways. Here we report the discovery of a highly selective series of 1,5-dihydropyrazolo[4,3-c][2,1]benzothiazines that demonstrate a novel mode of allosteric inhibition of FAK. These compounds showed slow dissociation from unphosphorylated FAK and were noncompetitive with ATP after long preincubation. Co-crystal structural analysis revealed that the compounds target a novel allosteric site within the C-lobe of the kinase domain, which induces disruption of ATP pocket formation leading to the inhibition of kinase activity. The potency of allosteric inhibition was reduced by phosphorylation of FAK. Coupled SAR analysis revealed that N-substitution of the fused pyrazole is critical to achieve allosteric binding and high selectivity among kinases.

  • Organizational Affiliation

    Pharmaceutical Research Division, Takeda Pharmaceutical Company, Ltd., 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Focal adhesion kinase 1304Homo sapiensMutation(s): 0 
Gene Names: PTK2FAKFAK1
UniProt & NIH Common Fund Data Resources
Find proteins for Q05397 (Homo sapiens)
Explore Q05397 
Go to UniProtKB:  Q05397
GTEx:  ENSG00000169398 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05397
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0PF

Download Ideal Coordinates CCD File 
B [auth A]1-ethyl-8-(4-ethylphenyl)-5-methyl-1,5-dihydropyrazolo[4,3-c][2,1]benzothiazine 4,4-dioxide
C20 H21 N3 O2 S
Binding Affinity Annotations 
IDSourceBinding Affinity
0PF PDBBind:  4EBW IC50: 8700 (nM) from 1 assay(s)
BindingDB:  4EBW IC50: min: 1000, max: 3.00e+4 (nM) from 9 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.65 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.3α = 90
b = 47.86β = 118.39
c = 83.667γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references
  • Version 1.2: 2013-01-16
    Changes: Database references
  • Version 1.3: 2013-03-27
    Changes: Database references