4JOA

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

• PDB DOI: https://doi.org/10.2210/pdb4JOA/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2013-03-18 Released: 2013-07-17 
• Deposition Author(s): Hosahalli, S., Krishnamurthy, N.R., Lakshminarasimhan, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.290 
• R-Value Work: 0.251 
• R-Value Observed: 0.253 

Starting Model: experimental

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

• PubMed: 23880539 
• DOI: https://doi.org/10.1016/j.bmcl.2013.06.071
• Primary Citation of Related Structures:  
  4JOA


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 39.03 kDa 
• Atom Count: 2,001 
• Modelled Residue Count: 251 
• Deposited Residue Count: 344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALK tyrosine kinase receptor	A	344	Homo sapiens	Mutation(s): 1  Gene Names: ALK EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UM73 (Homo sapiens) Explore Q9UM73  Go to UniProtKB:  Q9UM73
PHAROS:  Q9UM73 GTEx:  ENSG00000171094

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3DK	B [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
3DK	PDBBind:  4JOA	IC50: 29 (nM) from 1 assay(s)
	BindingDB:  4JOA	IC50: min: 29, max: 1592 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.290 
• R-Value Work: 0.251 
• R-Value Observed: 0.253 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.794	α = 90
b = 56.503	β = 90
c = 104.536	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-17 
Deposition Author(s): Hosahalli, S., Krishnamurthy, N.R., Lakshminarasimhan, A.

Revision History  

• Version 1.0: 2013-07-17
  Type: Initial release
  
• Version 1.1: 2014-04-23
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description