2X9F

ephB4 kinase domain inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibitors of the Tyrosine Kinase Ephb4. Part 3: Identification of Non-Benzodioxole-Based Kinase Inhibitors.

Bardelle, C.Barlaam, B.Brooks, N.Coleman, T.Cross, D.Ducray, R.Green, I.Brempt, C.L.Olivier, A.Read, J.

(2010) Bioorg.Med.Chem.Lett. 20: 6242

  • DOI: 10.1016/j.bmcl.2010.08.100

  • PubMed Abstract: 
  • Starting from the initial bis-anilinopyrimidine 1, good potency against EphB4 was retained when benzodioxole at C-4 was replaced by an indazole. The key interactions of the indazole with the protein were characterised by crystallographic studies. Fur ...

    Starting from the initial bis-anilinopyrimidine 1, good potency against EphB4 was retained when benzodioxole at C-4 was replaced by an indazole. The key interactions of the indazole with the protein were characterised by crystallographic studies. Further optimisation led to compound 20, a potent inhibitor of the EphB4 and Src kinases with good pharmacokinetics in various preclinical species and high fraction unbound in plasma. Compound 20 may be used as a tool for evaluating the potential of EphB4 kinase inhibitors in vivo.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EPHRIN TYPE-B RECEPTOR 4
A
302Homo sapiensGene 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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
X9F
Query on X9F

Download SDF File 
Download CCD File 
A
N^4^-1H-INDAZOL-4-YL-N^2^-[3-(METHYLSULFONYL)PHENYL]PYRIMIDINE-2,4-DIAMINE
C18 H16 N6 O2 S
FIWCLCRWDUELGO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
X9FIC50: 61 - 2530 nM (99) BINDINGDB
X9FIC50: 61 nM BINDINGMOAD
X9FIC50: 61 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.120α = 90.00
b = 52.479β = 112.05
c = 61.369γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
AMoREphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-29
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance