Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 34451.88 
• Atom Count: 2203 
• Residue Count: 302 
• Unique protein chains: 1

2VWX

ephB4 kinase domain inhibitor complex

• DOI: 10.2210/pdb2VWX/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): 1 


• Deposited: 2008-06-27 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: 0.209 
• R-Value Work: 0.166 

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: 10.1016/j.bmcl.2008.09.087
• Primary Citation of Related Structures:  
  2VX1, 2VWZ, 2VWY
• Also Cited By: 2VX0


• 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.

---

Related Citations: 

• 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




---

Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
EPHRIN TYPE-B RECEPTOR 4	A	302	Homo sapiens	Mutation(s): 1  Gene Names: EPHB4 (HTK, MYK1, TYRO11) EC: 2.7.10.1
Find proteins for P54760 (Homo sapiens) Go to Gene View: EPHB4 Go to UniProtKB:  P54760

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
7X4	A	3-({4-[(5-chloro-1,3-benzodioxol-4-yl)amino]pyrimidin-2-yl}amino)benzenesulfonamide C17 H14 Cl N5 O4 S TZHCXOMEOHEZDX-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
7X4	IC50: 40 - 172 nM (99) BINDINGDB
7X4	IC50: 40 nM BINDINGMOAD
7X4	IC50: 40 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.209 
• R-Value Work: 0.166 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 45.777	α = 90.00
b = 53.451	β = 110.57
c = 61.347	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-06-27 
• 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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-06-28
  Type: Data collection
• Version 1.4: 2019-04-24
  Type: Data collection, Source and taxonomy
• Version 1.5: 2019-05-08
  Type: Data collection, Experimental preparation