HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR [4-(2-Amino-4-methyl-thiazol-5-yl)-pyrimidin-2-yl]-(3-nitro-phenyl)-amine

Experimental Data Snapshot

  • Resolution: 1.96 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


2-Anilino-4-(thiazol-5-yl)pyrimidine CDK inhibitors: synthesis, SAR analysis, X-ray crystallography, and biological activity.

Wang, S.Meades, C.Wood, G.Osnowski, A.Anderson, S.Yuill, R.Thomas, M.Mezna, M.Jackson, W.Midgley, C.Griffiths, G.Fleming, I.Green, S.McNae, I.Wu, S.Y.McInnes, C.Zheleva, D.Walkinshaw, M.D.Fischer, P.M.

(2004) J Med Chem 47: 1662-1675

  • DOI: https://doi.org/10.1021/jm0309957
  • Primary Citation of Related Structures:  
    1PXM, 1PXN, 1PXO, 1PXP

  • PubMed Abstract: 

    Following the identification through virtual screening of 4-(2,4-dimethyl-thiazol-5-yl)pyrimidin-2-ylamines as moderately potent inhibitors of cyclin-dependent kinase-2 (CDK2), a CDK inhibitor analogue program was initiated. The first aims were to optimize potency and to evaluate the cellular mode of action of lead candidate molecules. Here the synthetic chemistry, the structure-guided design approach, and the structure-activity relationships (SARs) that led to the discovery of 2-anilino-4-(thiazol-5-yl)pyrimidine ATP-antagonistic CDK2 inhibitors, many with very low nM K(i)s against CDK2, are reported. Furthermore, X-ray crystal structures of four representative analogues from our chemical series in complex with CDK2 are presented, and these structures are used to rationalize the observed biochemical SARs. Finally results are reported that show, using the most potent CDK2 inhibitor compound from the current series, that the observed antiproliferative and proapoptotic effects are consistent with cellular CDK2 and CDK9 inhibition.

  • Organizational Affiliation

    Cyclacel Limited, James Lindsay Place, Dundee DD1 5JJ, 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 
Gene Names: CDK2
EC: 2.7.1
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 CK7

Download Ideal Coordinates CCD File 
C14 H12 N6 O2 S
Binding Affinity Annotations 
IDSourceBinding Affinity
CK7 Binding MOAD:  1PXO Ki: 2 (nM) from 1 assay(s)
BindingDB:  1PXO Ki: min: 2, max: 396 (nM) from 2 assay(s)
IC50: min: 10, max: 4400 (nM) from 2 assay(s)
PDBBind:  1PXO Ki: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.96 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.489α = 90
b = 71.987β = 90
c = 72.362γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description