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

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 

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This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1016/j.bmcl.2013.03.100
  • Primary Citation of Related Structures:  

  • 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.

  • Organizational Affiliation

    Merck Research Laboratories, 320 Bent Street, Cambridge, MA 02141, USA. zhaoyang.meng@merck.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase Chk1273Homo sapiensMutation(s): 0 
Gene Names: CHEK1CHK1
UniProt & NIH Common Fund Data Resources
Find proteins for O14757 (Homo sapiens)
Explore O14757 
Go to UniProtKB:  O14757
PHAROS:  O14757
GTEx:  ENSG00000149554 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14757
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1KO

Download Ideal Coordinates CCD File 
B [auth A]2-(4-chlorophenyl)-8-[(3S)-piperidin-3-ylamino]imidazo[1,2-c]pyrimidine-5-carboxamide
C18 H19 Cl N6 O
Binding Affinity Annotations 
IDSourceBinding Affinity
1KO Binding MOAD:  4JIK IC50: 18 (nM) from 1 assay(s)
PDBBind:  4JIK IC50: 18 (nM) from 1 assay(s)
BindingDB:  4JIK IC50: 18 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.11α = 90
b = 65.9β = 102.74
c = 54.76γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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