5IA3

Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with PD173955

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

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Ligand Structure Quality Assessment 


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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: https://doi.org/10.1021/acschembio.6b00709
  • Primary Citation of Related Structures:  
    5I9U, 5I9V, 5I9W, 5I9X, 5I9Y, 5I9Z, 5IA0, 5IA1, 5IA2, 5IA3, 5IA4, 5IA5

  • 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 inhibitors and structural information ...

    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: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ephrin type-A receptor 2A306Homo sapiensMutation(s): 0 
Gene Names: EPHA2, ECK
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29317 (Homo sapiens)
Explore P29317 
Go to UniProtKB:  P29317
PHAROS:  P29317
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29317
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P17
Query on P17
Download Ideal Coordinates CCD File 
B [auth A]6-(2,6-DICHLORO-PHENYL)-8-METHYL-2-(3-METHYLSULFANYL-PHENYLAMINO)-8H-PYRIDO[2,3-D]PYRIMIDIN-7-ONE
C21 H16 Cl2 N4 O S
VAARYSWULJUGST-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
P17 BindingDB:  5IA3 Kd: min: 3.8, max: 46 (nM) from 2 assay(s)
IC50: 7.9 (nM) from 1 assay(s)
Binding MOAD:  5IA3 Kd: 46 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.766α = 90
b = 107.543β = 108.68
c = 40.534γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement
Cootmodel building
AutoPROCdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
DKTKGermanyL590

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Database references
  • Version 1.2: 2019-04-03
    Changes: Data collection, Source and taxonomy
  • Version 1.3: 2019-06-12
    Changes: Data collection, Structure summary