Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32439.48 
• Atom Count: 2236 
• Residue Count: 279 
• Unique protein chains: 1

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

• DOI: 10.2210/pdb4K9Y/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni


• Deposited: 2013-04-21 Released: 2013-09-11 
• Deposition Author(s): Musil, D., Graedler, U., Lehmann, M., Heinrich, T., Dresing, V.

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Experimental Data Snapshot

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

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: 10.1016/j.bmcl.2013.07.050
• Primary Citation of Related Structures:  
  4KAO, 4KAB, 4K8A


• 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]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Focal adhesion kinase 1	A	279	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
K9Y	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
K9Y	Kd: 111 nM (100) BINDINGDB
K9Y	IC50: 266 - 750 nM (100) BINDINGDB
K9Y	Kd: 111 nM BINDINGMOAD
K9Y	Kd: 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 = 134.790	α = 90.00
b = 61.770	β = 100.50
c = 61.900	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
XDS	data reduction
BUSTER	refinement
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-04-21 
• Released Date: 2013-09-11 
• Deposition Author(s): Musil, D., Graedler, U., Lehmann, M., Heinrich, T., Dresing, V.

Revision History 

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