Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 37.40 kDa 
• Atom Count: 2166 
• Modelled Residue Count: 282 
• Deposited Residue Count: 329 
• Unique protein chains: 1

4BDJ

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

• PDB DOI: 10.2210/pdb4BDJ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-10-05 Released: 2013-06-26 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 0.215 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

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

• PubMed: 23776527 
• DOI: 10.1371/journal.pone.0065689
• Primary Citation of Related Structures:  
  4BDA, 4BDB, 4BDC, 4BDD, 4BDE, 4BDF, 4BDG, 4BDH, 4BDI, 4BDJ, 4BDK


• 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, 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHECKPOINT KINASE 2	A	329	Homo sapiens	Mutation(s): 0  Gene Names: CHEK2, CDS1, CHK2, RAD53 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O96017 (Homo sapiens) Explore O96017  Go to UniProtKB:  O96017
PHAROS:  O96017 GTEx:  ENSG00000183765

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Z2M	B [auth A]	3-cyclopropyl-4-(furan-2-yl)-1H-pyrazolo[3,4-b]pyridine C13 H11 N3 O CVODVHVJEVVKKB-UHFFFAOYSA-N
NO3	C [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
Z2M	PDBBind:  4BDJ	IC50: 7200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 0.215 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.93	α = 90
b = 90.93	β = 90
c = 92.13	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-05 
• Released Date: 2013-06-26 
Deposition Author(s): 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.

Revision History  

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