2XEZ | pdb_00002xez

Crystal structure of checkpoint kinase 1 (Chk1) in complex with inhibitors

• PDB DOI: https://doi.org/10.2210/pdb2XEZ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2010-05-19 Released: 2010-07-07 
• Deposition Author(s): Matthews, T.P., McHardy, T., Klair, S., Boxall, K., Fisher, M., Cherry, M., Allen, C.E., Addison, G.J., Ellard, J., Aherne, G.W., Westwood, I.M., vanMontfort, R., Garrett, M.D., Reader, J.C., Collins, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.237 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Design and Evaluation of 3,6-Di(Hetero)Aryl Imidazo[1,2-A]Pyrazines as Inhibitors of Checkpoint and Other Kinases.

Matthews, T.P., Mchardy, T., Klair, S., Boxall, K., Fisher, M., Cherry, M., Allen, C.E., Addison, G.J., Ellard, J., Aherne, G.W., Westwood, I.M., Montfort, R.V., Garrett, M.D., Reader, J.C., Collins, I.

(2010) Bioorg Med Chem Lett 20: 4045

• PubMed: 20561787 
• DOI: https://doi.org/10.1016/j.bmcl.2010.05.096
• Primary Citation Related Structures: 
  2XEY, 2XEZ, 2XF0


• PubMed Abstract: 
  

  A range of 3,6-di(hetero)arylimidazo[1,2-a]pyrazine ATP-competitive inhibitors of CHK1 were developed by scaffold hopping from a weakly active screening hit. Efficient synthetic routes for parallel synthesis were developed to prepare analogues with improved potency and ligand efficiency against CHK1. Kinase profiling showed that the imidazo[1,2-a]pyrazines could inhibit other kinases, including CHK2 and ABL, with equivalent or better potency depending on the pendant substitution. These 3,6-di(hetero)aryl imidazo[1,2-a]pyrazines appear to represent a general kinase inhibitor scaffold.

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Organizational Affiliation: 
• Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, United Kingdom. [e-mail]

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: 33.67 kDa 
• Atom Count: 2,149 
• Modeled Residue Count: 249 
• Deposited Residue Count: 289 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE CHK1	A	289	Homo sapiens	Mutation(s): 0  EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14757 (Homo sapiens) Explore O14757  Go to UniProtKB:  O14757
PHAROS:  O14757 GTEx:  ENSG00000149554

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XEZ	B [auth A]	6-(1H-PYRAZOL-3-YL)-3-(1H-PYRAZOL-4-YL)IMIDAZO[1,2-A]PYRAZINE C12 H9 N7 ALMSMDKNGFZAEU-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.237 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.84	α = 90
b = 65.6	β = 95.11
c = 57.45	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-07 
Deposition Author(s): Matthews, T.P., McHardy, T., Klair, S., Boxall, K., Fisher, M., Cherry, M., Allen, C.E., Addison, G.J., Ellard, J., Aherne, G.W., Westwood, I.M., vanMontfort, R., Garrett, M.D., Reader, J.C., Collins, I.

Revision History  

• Version 1.0: 2010-07-07
  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: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description