2VWW | pdb_00002vww

ephB4 kinase domain inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb2VWW/pdb

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


• Deposited: 2008-06-27 Released: 2008-07-08 
• 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: 1.90 Å
• R-Value Free: 
  0.229 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Inhibitors of the Tyrosine Kinase Ephb4. Part 1: Structure-Based Design and Optimization of a Series of 2,4-Bis-Anilinopyrimidines

Bardelle, C., 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: 2776

• PubMed: 18434142 
• DOI: https://doi.org/10.1016/j.bmcl.2008.04.015
• Primary Citation of Related Structures:  
  2VWU, 2VWV, 2VWW, 2VX0


• PubMed Abstract: 
  

  A series of bis-anilinopyrimidines have been identified as potent inhibitors of the tyrosine kinase EphB4. Structural information from two alternative series identified from screening efforts was combined to identify the initial leads.

---

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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 34.37 kDa 
• Atom Count: 2,126 
• Modeled Residue Count: 253 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7X2	B [auth A]	N'-(5-CHLORO-1,3-BENZODIOXOL-4-YL)-N-(3,4,5- TRIMETHOXYPHENYL)PYRIMIDINE-2,4-DIAMINE C20 H19 Cl N4 O5 HMKLUOPMOJOUDZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
7X2	BindingDB:  2VWW	IC50: 240 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.229 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.462	α = 90
b = 53.414	β = 111.38
c = 61.644	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: 2008-07-08 
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: 2008-07-08
  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, Other, Refinement description