4KAB

FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH 3-Methyl-1,4-dihydro-pyrazolo[4,5-c]pyrazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

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:  
    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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Focal adhesion kinase 1AB279Homo sapiensMutation(s): 0 
Gene Names: PTK2FAKFAK1
EC: 2.7.10.2
Find proteins for Q05397 (Homo sapiens)
Explore Q05397 
Go to UniProtKB:  Q05397
NIH Common Fund Data Resources
PHAROS  Q05397
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4KA
Query on 4KA

Download CCD File 
A, B
3-methyl-1,5-dihydropyrazolo[4,3-c]pyrazole
C5 H6 N4
KRAKREBEXWCQMF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4KAKd :  93000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.96α = 90
b = 88.59β = 90
c = 136.89γ = 90
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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