4BDI

Fragment-based screening identifies a new area for inhibitor binding to checkpoint kinase 2 (CHK2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation 3D Report Full Report



Literature

Fragment-Based Screening Maps Inhibitor Interactions in the ATP-Binding Site of Checkpoint Kinase 2.

Silva-Santisteban, M.C.Westwood, I.M.Boxall, K.Brown, N.Peacock, S.Mcandrew, C.Barrie, E.Richards, M.Mirza, A.Oliver, A.W.Burke, R.Hoelder, S.Jones, K.Aherne, G.W.Blagg, J.Collins, I.Garrett, M.D.Van Montfort, R.L.M.

(2013) PLoS One 8: 65689

  • DOI: 10.1371/journal.pone.0065689
  • Primary Citation of Related Structures:  
    4BDF, 4BDG, 4BDH, 4BDI, 4BDJ, 4BDK, 4BDA, 4BDB, 4BDC, 4BDD

  • PubMed Abstract: 
  • Checkpoint kinase 2 (CHK2) is an important serine/threonine kinase in the cellular response to DNA damage. A fragment-based screening campaign using a combination of a high-concentration AlphaScreen™ kinase assay and a biophysical thermal shift assay ...

    Checkpoint kinase 2 (CHK2) is an important serine/threonine kinase in the cellular response to DNA damage. A fragment-based screening campaign using a combination of a high-concentration AlphaScreen™ kinase assay and a biophysical thermal shift assay, followed by X-ray crystallography, identified a number of chemically different ligand-efficient CHK2 hinge-binding scaffolds that have not been exploited in known CHK2 inhibitors. In addition, it showed that the use of these orthogonal techniques allowed efficient discrimination between genuine hit matter and false positives from each individual assay technology. Furthermore, the CHK2 crystal structures with a quinoxaline-based fragment and its follow-up compound highlight a hydrophobic area above the hinge region not previously explored in rational CHK2 inhibitor design, but which might be exploited to enhance both potency and selectivity of CHK2 inhibitors.


    Organizational Affiliation

    Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, Haddow Laboratories, Sutton, Surrey, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE/THREONINE-PROTEIN KINASE CHK2A329Homo sapiensMutation(s): 0 
Gene Names: CHEK2CDS1CHK2RAD53
EC: 2.7.11.1
Find proteins for O96017 (Homo sapiens)
Explore O96017 
Go to UniProtKB:  O96017
NIH Common Fund Data Resources
PHAROS  O96017
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HAU
Query on HAU

Download CCD File 
A
1-acetyl-N-(5-methylpyridin-2-yl)piperidine-4-carboxamide
C14 H19 N3 O2
LDNVJBRMIHEEJK-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HAUIC50:  227700   nM  Binding MOAD
HAUIC50 :  227700   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.23α = 90
b = 90.23β = 90
c = 92.9γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2013-06-26
    Type: Initial release