2XVD | pdb_00002xvd

ephB4 kinase domain inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb2XVD/pdb

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


• Deposited: 2010-10-25 Released: 2011-06-08 
• Deposition Author(s): Read, J., Brassington, C.A., Green, I., McCall, E.J., Valentine, A.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.209 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Inhibitors of the Tyrosine Kinase Ephb4. Part 4: Discovery and Optimization of a Benzylic Alcohol Series.

Barlaam, B., Ducray, R., Lambert-Van Der Brempt, C., Ple, P., Bardelle, C., Brooks, N., Coleman, T., Cross, D., Kettle, J.G., Read, J.

(2011) Bioorg Med Chem Lett 21: 2207

• PubMed: 21441027 
• DOI: https://doi.org/10.1016/j.bmcl.2011.03.009
• Primary Citation Related Structures: 
  2XVD


• PubMed Abstract: 
  

  Optimization of our bis-anilino-pyrimidine series of EphB4 kinase inhibitors led to the discovery of compound 12 which incorporates a key m-hydroxymethylene group on the C4 aniline. 12 displays a good kinase selectivity profile, good physical properties and pharmacokinetic parameters, suggesting it is a suitable candidate to investigate the therapeutic potential of EphB4 kinase inhibitors.

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Organizational Affiliation: 
• AstraZeneca, Centre de Recherches, Z.I. la Pompelle, BP1050, 51689 Reims, Cedex 2, France.

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: 34.52 kDa 
• Atom Count: 2,334 
• Modeled Residue Count: 270 
• 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
PHAROS:  P54760 GTEx:  ENSG00000196411

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AS6	B [auth A]	{4-METHYL-3-[(1-METHYLETHYL)(2-{[3-(METHYLSULFONYL)-5-MORPHOLIN-4-YLPHENYL]AMINO}PYRIMIDIN-4-YL)AMINO]PHENYL}METHANOL C26 H33 N5 O4 S AAXNCGQOXAXDOW-UHFFFAOYSA-N
MG	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AS6	BindingDB:  2XVD	IC50: min: 2, max: 7 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.209 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.708	α = 90
b = 53.315	β = 111.75
c = 61.33	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-08 
Deposition Author(s): Read, J., Brassington, C.A., Green, I., McCall, E.J., Valentine, A.L.

Revision History  

• Version 1.0: 2011-06-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-06-28
  Changes: Data collection
• Version 1.3: 2019-04-24
  Changes: Data collection, Source and taxonomy
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description