5NKE

Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 3a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Chemoproteomics-Aided Medicinal Chemistry for the Discovery of EPHA2 Inhibitors.

Heinzlmeir, S.Lohse, J.Treiber, T.Kudlinzki, D.Linhard, V.Gande, S.L.Sreeramulu, S.Saxena, K.Liu, X.Wilhelm, M.Schwalbe, H.Kuster, B.Medard, G.

(2017) ChemMedChem 12: 999-1011

  • DOI: 10.1002/cmdc.201700217
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The receptor tyrosine kinase EPHA2 has gained attention as a therapeutic drug target for cancer and infectious diseases. However, EPHA2 research and EPHA2-based therapies have been hampered by the lack of selective small-molecule inhibitors. Herein w ...

    The receptor tyrosine kinase EPHA2 has gained attention as a therapeutic drug target for cancer and infectious diseases. However, EPHA2 research and EPHA2-based therapies have been hampered by the lack of selective small-molecule inhibitors. Herein we report the synthesis and evaluation of dedicated EPHA2 inhibitors based on the clinical BCR-ABL/SRC inhibitor dasatinib as a lead structure. We designed hybrid structures of dasatinib and the previously known EPHA2 binders CHEMBL249097, PD-173955, and a known EPHB4 inhibitor in order to exploit both the ATP pocket entrance as well as the ribose pocket as binding epitopes in the kinase EPHA2. Medicinal chemistry and inhibitor design were guided by a chemical proteomics approach, allowing early selectivity profiling of the newly synthesized inhibitor candidates. Concomitant protein crystallography of 17 inhibitor co-crystals delivered detailed insight into the atomic interactions that underlie the structure-affinity relationship. Finally, the anti-proliferative effect of the inhibitor candidates was confirmed in the glioblastoma cell line SF-268. In this work, we thus discovered a novel EPHA2 inhibitor candidate that features an improved selectivity profile while maintaining potency against EPHA2 and anticancer activity in SF-268 cells.


    Organizational Affiliation

    Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer-Forum 5, 85354, Freising, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ephrin type-A receptor 2
A
306Homo sapiensGene Names: EPHA2 (ECK)
EC: 2.7.10.1
Find proteins for P29317 (Homo sapiens)
Go to Gene View: EPHA2
Go to UniProtKB:  P29317
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
90B
Query on 90B

Download SDF File 
Download CCD File 
A
2-[[3-bromanyl-5-(piperidin-4-ylcarbamoyl)phenyl]amino]-~{N}-(2-chloranyl-6-methyl-phenyl)-1,3-thiazole-5-carboxamide
C23 H23 Br Cl N5 O2 S
QPHLKSOMHMCVPZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 32.520α = 90.00
b = 106.562β = 94.96
c = 39.430γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
DKTKGermanyL590

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-06-28
    Type: Database references