Crystal structure of the human CDK2 complexed with the triazolopyrimidine inhibitor

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.189 

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This is version 1.4 of the entry. See complete history


Triazolo[1,5-A]Pyrimidines as Novel Cdk2 Inhibitors: Protein Structure-Guided Design and Sar.

Richardson, C.M.Williamson, D.S.Parratt, M.J.Borgognoni, J.Cansfield, A.D.Dokurno, P.Francis, G.L.Howes, R.Moore, J.D.Murray, J.B.Robertson, A.Surgenor, A.E.Torrance, C.J.

(2006) Bioorg Med Chem Lett 16: 1353

  • DOI: https://doi.org/10.1016/j.bmcl.2005.11.048
  • Primary Citation of Related Structures:  
    2C68, 2C69, 2C6I, 2C6K, 2C6L, 2C6M, 2C6O, 2C6T

  • PubMed Abstract: 

    Crystallographic and modelling data, in conjunction with a medicinal chemistry template-hopping approach, led to the identification of a series of novel and potent inhibitors of human cyclin-dependent kinase 2 (CDK2), with selectivity over glycogen synthase kinase-3beta (GSK-3beta). One example had a CDK2 IC(50) of 120 nM and showed selectivity over GSK-3beta of 167-fold.

  • Organizational Affiliation

    Vernalis (R&D) Ltd, Granta Park, Great Abington, Cambridge CB1 6GB, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CELL DIVISION PROTEIN KINASE 2298Homo sapiensMutation(s): 0 
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 DT2

Download Ideal Coordinates CCD File 
C17 H21 N7 O2 S
Binding Affinity Annotations 
IDSourceBinding Affinity
DT2 Binding MOAD:  2C6K IC50: 730 (nM) from 1 assay(s)
PDBBind:  2C6K IC50: 730 (nM) from 1 assay(s)
BindingDB:  2C6K IC50: 730 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.55α = 90
b = 71.633β = 90
c = 72.262γ = 90
Software Package:
Software NamePurpose
CrystalCleardata reduction
d*TREKdata 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: 2005-12-07
    Type: Initial release
  • Version 1.1: 2015-10-14
    Changes: Derived calculations, Non-polymer description, Other, Source and taxonomy, Version format compliance
  • Version 1.2: 2019-01-30
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-04-24
    Changes: Data collection, Source and taxonomy
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description