Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 4a

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1002/cmdc.201700217
  • Primary Citation of Related Structures:  
    5NJZ, 5NK0, 5NK1, 5NK2, 5NK3, 5NK4, 5NK5, 5NK6, 5NK7, 5NK8, 5NK9, 5NKA, 5NKB, 5NKC, 5NKD, 5NKE, 5NKF, 5NKG, 5NKH, 5NKI

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ephrin type-A receptor 2306Homo sapiensMutation(s): 0 
Gene Names: EPHA2ECK
UniProt & NIH Common Fund Data Resources
Find proteins for P29317 (Homo sapiens)
Explore P29317 
Go to UniProtKB:  P29317
PHAROS:  P29317
GTEx:  ENSG00000142627 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29317
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 8ZT

Download Ideal Coordinates CCD File 
B [auth A]~{N}-(2-chloranyl-6-methyl-phenyl)-2-[(3,5-dimorpholin-4-ylphenyl)amino]-1,3-thiazole-5-carboxamide
C25 H28 Cl N5 O3 S
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
C2 H6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
8ZT Binding MOAD:  5NKB Kd: 0.76 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.816α = 90
b = 107.688β = 108.85
c = 40.515γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references
  • Version 1.2: 2019-06-12
    Changes: Data collection, Structure summary
  • Version 1.3: 2019-08-14
    Changes: Data collection
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Refinement description