FOCAL ADHESION KINASE Catalytic domain in complex with 1-[4-(6-Amino-purin-9-yl)-phenyl]-3-(5-tert-butyl-2-p-tolyl-2H-pyrazol-3-yl)-urea

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

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This is version 1.1 of the entry. See complete history


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

  • 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.

  • Organizational Affiliation

    Merck KGaA, Merck Serono Research, Darmstadt, Germany. ulrich.graedler@merckgroup.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Focal adhesion kinase 1279Homo sapiensMutation(s): 0 
Gene Names: PTK2FAKFAK1
UniProt & NIH Common Fund Data Resources
Find proteins for Q05397 (Homo sapiens)
Explore Q05397 
Go to UniProtKB:  Q05397
PHAROS:  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 K9Y

Download Ideal Coordinates CCD File 
B [auth A]1-[4-(6-amino-9H-purin-9-yl)phenyl]-3-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]urea
C26 H27 N9 O
Binding Affinity Annotations 
IDSourceBinding Affinity
K9Y BindingDB:  4K9Y Kd: 111 (nM) from 1 assay(s)
IC50: min: 266, max: 750 (nM) from 2 assay(s)
PDBBind:  4K9Y Kd: 111 (nM) from 1 assay(s)
Binding MOAD:  4K9Y Kd: 111 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.79α = 90
b = 61.77β = 100.5
c = 61.9γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata 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: 2013-09-11
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Database references