Discovery and Characterisation of 2-Anilino-4-(thiazol-5-yl) pyrimidine Transcriptional CDK Inhibitors as Anticancer Agents

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

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Discovery and Characterisation of 2-Anilino-4-(Thiazol-5-Yl)Pyrimidine Transcriptional Cdk Inhibitors as Anticancer Agents

Wang, S.Griffiths, G.Midgley, C.A.Barnett, A.L.Cooper, M.Grabarek, J.Ingram, L.Jackson, W.Kontopidis, G.Mcclue, S.J.Mcinnes, C.Mclachlan, J.Meades, C.Mezna, M.Stuart, I.Thomas, M.P.Zheleva, D.I.Lane, D.P.Jackson, R.C.Glover, D.M.Blake, D.G.Fischer, P.M.

(2010) Chem Biol 17: 1111

  • DOI: https://doi.org/10.1016/j.chembiol.2010.07.016
  • Primary Citation of Related Structures:  
    2XMY, 2XNB

  • PubMed Abstract: 

    The main difficulty in the development of ATP antagonist kinase inhibitors is target specificity, since the ATP-binding motif is present in many proteins. We introduce a strategy that has allowed us to identify compounds from a kinase inhibitor library that block the cyclin-dependent kinases responsible for regulating transcription, i.e., CDK7 and especially CDK9. The screening cascade employs cellular phenotypic assays based on mitotic index and nuclear p53 protein accumulation. This permitted us to classify compounds into transcriptional, cell cycle, and mitotic inhibitor groups. We describe the characterization of the transcriptional inhibitor class in terms of kinase inhibition profile, cellular mode of action, and selectivity for transformed cells. A structural selectivity rationale was used to optimize potency and biopharmaceutical properties and led to the development of a transcriptional inhibitor, 3,4-dimethyl-5-[2-(4-piperazin-1-yl-phenylamino)-pyrimidin-4-yl]-3H-thiazol-2-one, with anticancer activity in animal models.

  • Organizational Affiliation

    Cyclacel Limited, Dundee DD15JJ, Scotland, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CELL DIVISION PROTEIN KINASE 2298Homo sapiensMutation(s): 0 
EC: (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
PHAROS:  P24941
GTEx:  ENSG00000123374 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24941
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CDK

Download Ideal Coordinates CCD File 
C18 H21 N5 O4 S2
Binding Affinity Annotations 
IDSourceBinding Affinity
CDK BindingDB:  2XMY Ki: 0.11 (nM) from 1 assay(s)
Binding MOAD:  2XMY Ki: 0.11 (nM) from 1 assay(s)
PDBBind:  2XMY Ki: 0.11 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.118α = 90
b = 71.498β = 90
c = 71.642γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2012-03-28
    Changes: Database references, Other, Refinement description, Source and taxonomy, Version format compliance
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description