5IA2

Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with compound 66


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.619 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

  • 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 appropri ...

    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.


    Organizational Affiliation

    Chair of Proteomics and Bioanalytics, Technical University of Munich , 85354 Freising, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ephrin type-A receptor 2
A
306Homo sapiensMutation(s): 0 
Gene 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
L66
Query on L66

Download SDF File 
Download CCD File 
A
7-(5-hydroxy-2-methylphenyl)-8-(2-methoxyphenyl)-1-methyl-1H-imidazo[2,1-f]purine-2,4(3H,8H)-dione
C22 H19 N5 O4
JTWMOWRMSZZHDR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.619 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.163 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 32.864α = 90.00
b = 107.517β = 108.84
c = 40.731γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
SCALAdata scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DKTKGermanyL590

Revision History 

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2016-12-28
    Type: Database references