6Q7D

Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with the NVP-BHG712 derivative ATDL13

• PDB DOI: https://doi.org/10.2210/pdb6Q7D/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2018-12-13 Released: 2020-01-15 
• Deposition Author(s): Kudlinzki, D., Troester, A., Witt, K., Linhard, V.L., Gande, S.L., Saxena, K., Schwalbe, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free: 0.207 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 

Starting Model: experimental

Literature

Effects of NVP-BHG712 chemical modifications on EPHA2 binding and affinity

Troester, A., Kudlinzki, D., Saxena, K., Gande, S., Schwalbe, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 35 kDa 
• Atom Count: 2,733 
• Modelled Residue Count: 275 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin type-A receptor 2	A	306	Homo sapiens	Mutation(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 GTEx:  ENSG00000142627

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HOT	B [auth A]	3-[[4-imidazol-1-yl-6-(4-oxidanylpiperidin-1-yl)-1,3,5-triazin-2-yl]amino]-4-methyl-~{N}-[3-(trifluoromethyl)phenyl]benzamide C26 H25 F3 N8 O2 ZHVJHWWEVILTJQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free: 0.207 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.725	α = 90
b = 107.16	β = 108.42
c = 40.463	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-15 
Deposition Author(s): Kudlinzki, D., Troester, A., Witt, K., Linhard, V.L., Gande, S.L., Saxena, K., Schwalbe, H.

Revision History  

• Version 1.0: 2020-01-15
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description