HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR 4-(2,4-Dimethyl-thiazol-5-yl)-pyrimidin-2-ylamine

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

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This is version 1.3 of the entry. See complete history


Discovery of a novel family of CDK inhibitors with the program LIDAEUS: structural basis for ligand-induced disordering of the activation loop

Wu, S.Y.McNae, I.Kontopidis, G.McClue, S.J.McInnes, C.Stewart, K.J.Wang, S.Zheleva, D.I.Marriage, H.Lane, D.P.Taylor, P.Fischer, P.M.Walkinshaw, M.D.

(2003) Structure 11: 399-410

  • DOI: https://doi.org/10.1016/s0969-2126(03)00060-1
  • Primary Citation of Related Structures:  
    1PW2, 1PXI, 1PXJ, 1PXK, 1PXL

  • PubMed Abstract: 

    A family of 4-heteroaryl-2-amino-pyrimidine CDK2 inhibitor lead compounds was discovered with the new database-mining program LIDAEUS through in silico screening. Four compounds with IC(50) values ranging from 17 to 0.9 microM were selected for X-ray crystal analysis. Two distinct binding modes are observed, one of which resembles the hydrogen bonding pattern of bound ATP. In the second binding mode, the ligands trigger a conformational change in the activation T loop by inducing movement of Lys(33) and Asp(145) side chains. The family of molecules discovered provides an excellent starting point for the design and synthesis of tight binding inhibitors, which may lead to a new class of antiproliferative drugs.

  • Organizational Affiliation

    Structural Biochemistry Group, The University of Edinburgh, Michael Swann Building, King's Buildings, EH9 3JR, Edinburgh, United Kingdom.

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 CK2

Download Ideal Coordinates CCD File 
C9 H10 N4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
CK2 BindingDB:  1PXJ Ki: min: 396, max: 6500 (nM) from 2 assay(s)
Kd: 3.03e+4 (nM) from 1 assay(s)
IC50: min: 6457, max: 6500 (nM) from 2 assay(s)
PDBBind:  1PXJ IC50: 1.30e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.736α = 90
b = 71.704β = 90
c = 72.199γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-09
    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