FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH N-{3-[(5-Cyano-2-phenyl-1H-pyrrolo[2,3-b]pyridin-4-ylamino)- methyl]-pyridin-2-yl}-N-methyl-methanesulfonamide

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

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Fragment-based discovery of new highly substituted 1H-pyrrolo[2,3-b]- and 3H-imidazolo[4,5-b]-pyridines as focal adhesion kinase inhibitors.

Heinrich, T.Seenisamy, J.Emmanuvel, L.Kulkarni, S.S.Bomke, J.Rohdich, F.Greiner, H.Esdar, C.Krier, M.Gradler, U.Musil, D.

(2013) J Med Chem 56: 1160-1170

  • DOI: https://doi.org/10.1021/jm3016014
  • Primary Citation of Related Structures:  
    4GU6, 4GU9

  • PubMed Abstract: 

    Focal adhesion kinase (FAK) is considered as an attractive target for oncology, and small-molecule inhibitors are reported to be in clinical testing. In a surface plasmon resonance (SPR)-mediated fragment screening campaign, we discovered bicyclic scaffolds like 1H-pyrazolo[3,4-d]pyrimidines binding to the hinge region of FAK. By an accelerated knowledge-based fragment growing approach, essential pharmacophores were added. The establishment of highly substituted unprecedented 1H-pyrrolo[2,3-b]pyridine derivatizations provided compounds with submicromolar cellular FAK inhibition potential. The combination of substituents on the bicyclic templates and the nature of the core structure itself have a significant impact on the compounds FAK selectivity. Structural analysis revealed that the appropriately substituted pyrrolo[2,3-b]pyridine induced a rare helical DFG-loop conformation. The discovered synthetic route to introduce three different substituents independently paves the way for versatile applications of the 7-azaindole core.

  • Organizational Affiliation

    Merck Serono Research, Merck KGaA , 64271 Darmstadt, Germany. timo.heinrich@merckgroup.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Focal adhesion kinase 1
A, B
282Homo 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 10N

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C22 H20 N6 O2 S
Binding Affinity Annotations 
IDSourceBinding Affinity
10N BindingDB:  4GU6 Kd: 44 (nM) from 1 assay(s)
IC50: min: 195, max: 1100 (nM) from 2 assay(s)
Binding MOAD:  4GU6 Kd: 44 (nM) from 1 assay(s)
PDBBind:  4GU6 Kd: 44 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.378α = 90
b = 55.698β = 90
c = 192.881γ = 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: 2013-09-04
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description