4GU6

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.194 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 10NClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

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


Macromolecules
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
EC: 2.7.10.2
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
10N
Query on 10N

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
N-(3-{[(5-cyano-2-phenyl-1H-pyrrolo[2,3-b]pyridin-4-yl)amino]methyl}pyridin-2-yl)-N-methylmethanesulfonamide
C22 H20 N6 O2 S
IFWXGGDEGREJOB-UHFFFAOYSA-N
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)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.194 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
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
MOLREPphasing
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 10NClick on this verticalbar to view details

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
  • Version 1.2: 2024-10-16
    Changes: Structure summary