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: 2,356 
• Modelled Residue Count: 273 
• Deposited Residue Count: 302 
• Unique protein chains: 1

 2VX0

ephB4 kinase domain inhibitor complex

• PDB DOI:  https://doi.org/10.2210/pdb2VX0/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.233 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 

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.

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Related Citations: 

• 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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EPHRIN TYPE-B RECEPTOR 4	A	302	Homo sapiens	Mutation(s): 1  Gene Names: EPHB4, HTK, MYK1, TYRO11 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7X7	B [auth A]	N'-(5-CHLORO-1,3-BENZODIOXOL-4-YL)-N-(3-MORPHOLIN-4-YLPHENYL)PYRIMIDINE-2,4-DIAMINE C21 H20 Cl N5 O3 PNEWIQAEGKQNCE-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
7X7	PDBBind:  2VX0	IC50: 580 (nM) from 1 assay(s)
	BindingDB:  2VX0	IC50: 580 (nM) from 1 assay(s)
	Binding MOAD:  2VX0	IC50: 580 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.233 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.123	α = 90
b = 53.492	β = 110.91
c = 61.265	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