8BOM

Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 14


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Optimization of the Lead Compound NVP-BHG712 as a Colorectal Cancer Inhibitor.

Troster, A.DiPrima, M.Jores, N.Kudlinzki, D.Sreeramulu, S.Gande, S.L.Linhard, V.Ludig, D.Schug, A.Saxena, K.Reinecke, M.Heinzlmeir, S.Leisegang, M.S.Wollenhaupt, J.Lennartz, F.Weiss, M.S.Kuster, B.Tosato, G.Schwalbe, H.

(2023) Chemistry 29: e202203967-e202203967

  • DOI: https://doi.org/10.1002/chem.202203967
  • Primary Citation of Related Structures:  
    8BOC, 8BOD, 8BOF, 8BOG, 8BOH, 8BOI, 8BOK, 8BOM

  • PubMed Abstract: 

    The ephrin type-A receptor 2 (EPHA2) kinase belongs to the largest family of receptor tyrosine kinases. There are several indications of an involvement of EPHA2 in the development of infectious diseases and cancer. Despite pharmacological potential, EPHA2 is an under-examined target protein. In this study, we synthesized a series of derivatives of the inhibitor NVP-BHG712 and triazine-based compounds. These compounds were evaluated to determine their potential as kinase inhibitors of EPHA2, including elucidation of their binding mode (X-ray crystallography), affinity (microscale thermophoresis), and selectivity (Kinobeads assay). Eight inhibitors showed affinities in the low-nanomolar regime (K D <10 nM). Testing in up to seven colon cancer cell lines that express EPHA2 reveals that several derivatives feature promising effects for the control of human colon carcinoma. Thus, we have developed a set of powerful tool compounds for fundamental new research on the interplay of EPH receptors in a cellular context.


  • Organizational Affiliation

    Center for Biomolecular Magnetic Resonance Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany.


Macromolecules
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
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
GTEx:  ENSG00000142627 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29317
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QU6 (Subject of Investigation/LOI)
Query on QU6

Download Ideal Coordinates CCD File 
B [auth A]~{N}-(3-methoxyphenyl)-4-methyl-3-[(1-methyl-6-pyridin-3-yl-pyrazolo[3,4-d]pyrimidin-4-yl)amino]benzamide
C26 H23 N7 O2
AWTFDMFFAXABDI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.56α = 90
b = 107β = 108.56
c = 40.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release
  • Version 1.1: 2023-03-15
    Changes: Database references
  • Version 1.2: 2023-03-22
    Changes: Database references
  • Version 1.3: 2023-04-05
    Changes: Database references
  • Version 1.4: 2023-05-03
    Changes: Database references
  • Version 1.5: 2024-02-07
    Changes: Data collection, Refinement description