5I9U

Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Chemical Proteomics and Structural Biology Define EPHA2 Inhibition by Clinical Kinase Drugs.

Heinzlmeir, S.Kudlinzki, D.Sreeramulu, S.Klaeger, S.Gande, S.L.Linhard, V.Wilhelm, M.Qiao, H.Helm, D.Ruprecht, B.Saxena, K.Medard, G.Schwalbe, H.Kuster, B.

(2016) ACS Chem Biol 11: 3400-3411

  • DOI: 10.1021/acschembio.6b00709
  • Primary Citation of Related Structures:  
    5I9V, 5I9U, 5I9X, 5I9W, 5I9Z, 5I9Y, 5IA5, 5IA0, 5IA2, 5IA1

  • PubMed Abstract: 
  • The receptor tyrosine kinase EPHA2 (Ephrin type-A receptor 2) plays important roles in oncogenesis, metastasis, and treatment resistance, yet therapeutic targeting, drug discovery, or investigation of EPHA2 biology is hampered by the lack of appropriate ...

    The receptor tyrosine kinase EPHA2 (Ephrin type-A receptor 2) plays important roles in oncogenesis, metastasis, and treatment resistance, yet therapeutic targeting, drug discovery, or investigation of EPHA2 biology is hampered by the lack of appropriate inhibitors and structural information. Here, we used chemical proteomics to survey 235 clinical kinase inhibitors for their kinase selectivity and identified 24 drugs with submicromolar affinities for EPHA2. NMR-based conformational dynamics together with nine new cocrystal structures delineated drug-EPHA2 interactions in full detail. The combination of selectivity profiling, structure determination, and kinome wide sequence alignment allowed the development of a classification system in which amino acids in the drug binding site of EPHA2 are categorized into key, scaffold, potency, and selectivity residues. This scheme should be generally applicable in kinase drug discovery, and we anticipate that the provided information will greatly facilitate the development of selective EPHA2 inhibitors in particular and the repurposing of clinical kinase inhibitors in general.


    Related Citations: 
    • Expression and Purification of EPHA2 Tyrosine Kinase Domain for Crystallographic and NMR Studies.
      Gande, S.L., Saxena, K., Sreeramulu, S., Linhard, V., Kudlinzki, D., Heinzlmeir, S., Reichert, A.J., Skerra, A., Kuster, B., Schwalbe, H.
      (2016) Chembiochem 17: 2257

    Organizational Affiliation

    Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich , 85354 Freising, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ephrin type-A receptor 2 A306Homo sapiensMutation(s): 0 
Gene Names: EPHA2ECK
EC: 2.7.10.1
Find proteins for P29317 (Homo sapiens)
Explore P29317 
Go to UniProtKB:  P29317
NIH Common Fund Data Resources
PHAROS:  P29317
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.715α = 90
b = 104.904β = 93.9
c = 39.681γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DKTKGermanyL590

Revision History 

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Database references
  • Version 1.2: 2016-12-28
    Changes: Database references
  • Version 1.3: 2019-06-12
    Changes: Data collection, Structure summary