4JOA

Crystal Structure of Human Anaplastic Lymphoma Kinase in complex with 7-azaindole based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of 7-azaindole based anaplastic lymphoma kinase (ALK) inhibitors: wild type and mutant (L1196M) active compounds with unique binding mode

Gummadi, V.R.Rajagopalan, S.Looi, C.Y.Paydar, M.Renukappa, G.A.Ainan, B.R.Krishnamurthy, N.R.Panigrahi, S.K.Mahasweta, K.Raghuramachandran, S.Rajappa, M.Ramanathan, A.Lakshminarasimhan, A.Ramachandra, M.Wong, P.F.Mustafa, M.R.Nanduri, S.Hosahalli, S.

(2013) Bioorg.Med.Chem.Lett. 23: 4911-4918

  • DOI: 10.1016/j.bmcl.2013.06.071

  • PubMed Abstract: 
  • We have identified a novel 7-azaindole series of anaplastic lymphoma kinase (ALK) inhibitors. Compounds 7b, 7 m and 7 n demonstrate excellent potencies in biochemical and cellular assays. X-ray crystal structure of one of the compounds (7 k) revealed ...

    We have identified a novel 7-azaindole series of anaplastic lymphoma kinase (ALK) inhibitors. Compounds 7b, 7 m and 7 n demonstrate excellent potencies in biochemical and cellular assays. X-ray crystal structure of one of the compounds (7 k) revealed a unique binding mode with the benzyl group occupying the back pocket, explaining its potency towards ALK and selectivity over tested kinases particularly Aurora-A. This binding mode is in contrast to that of known ALK inhibitors such as Crizotinib and NVP-TAE684 which occupy the ribose binding pocket, close to DFG motif.


    Organizational Affiliation

    Aurigene Discovery Technologies Ltd, #39/40, KIADB Industrial Area, Hosur Road, Electronic City Phase-II, Bangalore 560100, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALK tyrosine kinase receptor
A
344Homo sapiensGene Names: ALK
EC: 2.7.10.1
Find proteins for Q9UM73 (Homo sapiens)
Go to Gene View: ALK
Go to UniProtKB:  Q9UM73
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3DK
Query on 3DK

Download SDF File 
Download CCD File 
A
3-[1-(2,5-difluorobenzyl)-1H-pyrazol-4-yl]-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridine
C21 H16 F2 N6
SDWMCZUOCJDBOJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3DKIC50: 29 - 1592 nM (99) BINDINGDB
3DKIC50: 29 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.251 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.794α = 90.00
b = 56.503β = 90.00
c = 104.536γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CrystalCleardata collection
REFMACrefinement
DENZOdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2014-04-23
    Type: Database references