Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with NVP-BHG712

Experimental Data Snapshot

  • Resolution: 1.56 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.234 

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NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family.

Troster, A.Heinzlmeir, S.Berger, B.T.Gande, S.L.Saxena, K.Sreeramulu, S.Linhard, V.Nasiri, A.H.Bolte, M.Muller, S.Kuster, B.Medard, G.Kudlinzki, D.Schwalbe, H.

(2018) ChemMedChem 13: 1629-1633

  • DOI: https://doi.org/10.1002/cmdc.201800398
  • Primary Citation of Related Structures:  
    6FNF, 6FNG, 6FNH, 6FNI, 6FNJ, 6FNK, 6FNL, 6FNM

  • PubMed Abstract: 

    Erythropoietin-producing hepatocellular (EPH) receptors are transmembrane receptor tyrosine kinases. Their extracellular domains bind specifically to ephrin A/B ligands, and this binding modulates intracellular kinase activity. EPHs are key players in bidirectional intercellular signaling, controlling cell morphology, adhesion, and migration. They are increasingly recognized as cancer drug targets. We analyzed the binding of NVP-BHG712 (NVP) to EPHA2 and EPHB4. Unexpectedly, all tested commercially available NVP samples turned out to be a regioisomer (NVPiso) of the inhibitor, initially described in a Novartis patent application. They only differ by the localization of a single methyl group on either one of two adjacent nitrogen atoms. The two compounds of identical mass revealed different binding modes. Furthermore, both in vitro and in vivo experiments showed that the isomers differ in their kinase affinity and selectivity.

  • Organizational Affiliation

    Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DXH

Download Ideal Coordinates CCD File 
B [auth A]4-methyl-3-[(1-methyl-6-pyridin-3-yl-pyrazolo[3,4-d]pyrimidin-4-yl)amino]-~{N}-[3-(trifluoromethyl)phenyl]benzamide
C26 H20 F3 N7 O
Binding Affinity Annotations 
IDSourceBinding Affinity
DXH Binding MOAD:  6FNF Kd: 13 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.56 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.23α = 90
b = 104.796β = 108.31
c = 39.957γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description