2X9F

ephB4 kinase domain inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb2X9F/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2010-03-17 Released: 2010-09-29 
• Deposition Author(s): Read, J., Brassington, C.A., Green, I., McCall, E.J., Valentine, A.L., Barratt, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.194 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 

Starting Model: experimental

Literature

Inhibitors of the Tyrosine Kinase Ephb4. Part 3: Identification of Non-Benzodioxole-Based Kinase Inhibitors.

Bardelle, C., Barlaam, B., Brooks, N., Coleman, T., Cross, D., Ducray, R., Green, I., Brempt, C.L., Olivier, A., Read, J.

(2010) Bioorg Med Chem Lett 20: 6242

• PubMed: 20850301 
• DOI: https://doi.org/10.1016/j.bmcl.2010.08.100
• Primary Citation of Related Structures:  
  2X9F


• PubMed Abstract: 
  

  Starting from the initial bis-anilinopyrimidine 1, good potency against EphB4 was retained when benzodioxole at C-4 was replaced by an indazole. The key interactions of the indazole with the protein were characterised by crystallographic studies. Further optimisation led to compound 20, a potent inhibitor of the EphB4 and Src kinases with good pharmacokinetics in various preclinical species and high fraction unbound in plasma. Compound 20 may be used as a tool for evaluating the potential of EphB4 kinase inhibitors in vivo.

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Organizational Affiliation: 

AstraZeneca, Mereside, Alderley Park, Macclesfield SK10 4TG, UK.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 34.36 kDa 
• Atom Count: 2,351 
• Modelled Residue Count: 265 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EPHRIN TYPE-B RECEPTOR 4	A	302	Homo sapiens	Mutation(s): 1  EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P54760 (Homo sapiens) Explore P54760  Go to UniProtKB:  P54760
GTEx:  ENSG00000196411

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X9F	B [auth A]	N^4^-1H-INDAZOL-4-YL-N^2^-[3-(METHYLSULFONYL)PHENYL]PYRIMIDINE-2,4-DIAMINE C18 H16 N6 O2 S FIWCLCRWDUELGO-UHFFFAOYSA-N
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
X9F	BindingDB:  2X9F	IC50: min: 61, max: 2530 (nM) from 2 assay(s)
	PDBBind:  2X9F	IC50: 61 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.194 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.12	α = 90
b = 52.479	β = 112.05
c = 61.369	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-29 
Deposition Author(s): Read, J., Brassington, C.A., Green, I., McCall, E.J., Valentine, A.L., Barratt, D.

Revision History  

• Version 1.0: 2010-09-29
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2019-04-03
  Changes: Data collection, Experimental preparation
• Version 1.5: 2019-04-24
  Changes: Data collection, Source and taxonomy
• Version 1.6: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.7: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description