4K9Y

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1016/j.bmcl.2013.07.050
  • Primary Citation of Related Structures:  

  • 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 ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Focal adhesion kinase 1
A
279Homo sapiensMutation(s): 0 
Gene Names: PTK2 (FAK, FAK1)
EC: 2.7.10.2
Find proteins for Q05397 (Homo sapiens)
Go to Gene View: PTK2
Go to UniProtKB:  Q05397
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K9Y
Query on K9Y

Download SDF File 
Download CCD File 
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
INQBVHWEOAKYED-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
K9YKd: 111 nM (100) BINDINGDB
K9YIC50: 266 - 750 nM (100) BINDINGDB
K9YKd: 111 nM BINDINGMOAD
K9YKd: 111 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.163 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 134.790α = 90.00
b = 61.770β = 100.50
c = 61.900γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
BUSTERrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-11
    Type: Initial release
  • Version 1.1: 2013-10-09
    Type: Database references