4JIK | pdb_00004jik

X-RAY Crystal structure of compound 22a (R)-2-(4-chlorophenyl)-8-(piperidin-3-ylamino)imidazo[1,2-c]pyrimidine-5-carboxamide bound to human chk1 kinase domain

• PDB DOI: https://doi.org/10.2210/pdb4JIK/pdb

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


• Deposited: 2013-03-06 Released: 2013-04-17 
• Deposition Author(s): Fischmann, T.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.237 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Potency switch between CHK1 and MK2: discovery of imidazo[1,2-a]pyrazine- and imidazo[1,2-c]pyrimidine-based kinase inhibitors.

Meng, Z., Ciavarri, J.P., McRiner, A., Zhao, Y., Zhao, L., Reddy, P.A., Zhang, X., Fischmann, T.O., Whitehurst, C., Arshad Siddiqui, M.

(2013) Bioorg Med Chem Lett 23: 2863-2867

• PubMed: 23587425 
• DOI: https://doi.org/10.1016/j.bmcl.2013.03.100
• Primary Citation Related Structures: 
  4JIK


• PubMed Abstract: 
  

  Chemistry has been developed to access both imidazo[1,2-a]pyrazines and imidazo[1,2-c]pyrimidines. Small structural modifications in both series led to a switch of potency between two kinases involved in mediating cell cycle checkpoint control, CHK1 and MK2.

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Organizational Affiliation: 
• Merck Research Laboratories, 320 Bent Street, Cambridge, MA 02141, USA. [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: 31.83 kDa 
• Atom Count: 2,256 
• Modeled Residue Count: 256 
• Deposited Residue Count: 273 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase Chk1	A	273	Homo sapiens	Mutation(s): 0  Gene Names: CHEK1, CHK1 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1KO	B [auth A]	2-(4-chlorophenyl)-8-[(3S)-piperidin-3-ylamino]imidazo[1,2-c]pyrimidine-5-carboxamide C18 H19 Cl N6 O VUQDZGWRLHHYTB-ZDUSSCGKSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1KO	BindingDB:  4JIK	IC50: 18 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.237 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.11	α = 90
b = 65.9	β = 102.74
c = 54.76	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-17 
Deposition Author(s): Fischmann, T.O.

Revision History  

• Version 1.0: 2013-04-17
  Type: Initial release
  
• Version 1.1: 2013-07-10
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations