2VWY | pdb_00002vwy

ephB4 kinase domain inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb2VWY/pdb

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


• Deposited: 2008-06-30 Released: 2008-10-28 
• Deposition Author(s): Read, J., Brassington, C.A., Green, I., McCall, E.J., Valentine, A.L., Barratt, D., Leach, A.G., Kettle, J.G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.238 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Inhibitors of the Tyrosine Kinase Ephb4. Part 2: Structure-Based Discovery and Optimisation of 3,5-Bis Substituted Anilinopyrimidines.

Bardelle, C., Coleman, T., Cross, D., Davenport, S., Kettle, J.G., Ko, E.J., Leach, A.G., Mortlock, A., Read, J., Roberts, N.J., Robins, P., Williams, E.J.

(2008) Bioorg Med Chem Lett 18: 5717

• PubMed: 18851911 
• DOI: https://doi.org/10.1016/j.bmcl.2008.09.087
• Primary Citation Related Structures: 
  2VWX, 2VWY, 2VWZ, 2VX1


• PubMed Abstract: 
  

  Crystallographic studies of a range of 3-substituted anilinopyrimidine inhibitors of EphB4 have highlighted two alternative C-2 aniline conformations and this discovery has been exploited in the design of a highly potent series of 3,5-disubstituted anilinopyrimidines. The observed range of cellular activities has been rationalised on the basis of physicochemical and structural characteristics.

---

Organizational Affiliation: 
• AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire 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: 34.43 kDa 
• Atom Count: 2,439 
• Modeled Residue Count: 274 
• 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
7X5	B [auth A]	N'-(5-chloro-1,3-benzodioxol-4-yl)-N-(3-methylsulfonylphenyl)pyrimidine-2,4-diamine C18 H15 Cl N4 O4 S QTFCKBFCXDAZIU-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
7X5	BindingDB:  2VWY	IC50: min: 25, max: 190 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.238 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.073	α = 90
b = 53.479	β = 110.9
c = 61.517	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-28 
Deposition Author(s): Read, J., Brassington, C.A., Green, I., McCall, E.J., Valentine, A.L., Barratt, D., Leach, A.G., Kettle, J.G.

Revision History  

• Version 1.0: 2008-10-28
  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: 2017-06-28
  Changes: Data collection
• Version 1.4: 2019-04-24
  Changes: Data collection, Source and taxonomy
• Version 1.5: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.6: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description