2VV9

CDK2 in complex with an imidazole piperazine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Imidazole Piperazines: Sar and Development of a Potent Class of Cyclin-Dependent Kinase Inhibitors with a Novel Binding Mode.

Finlay, M.R.Acton, D.G.Andrews, D.M.Barker, A.J.Dennis, M.Fisher, E.Graham, M.A.Green, C.P.Heaton, D.W.Karoutchi, G.Loddick, S.A.Morgentin, R.Roberts, A.Tucker, J.A.Weir, H.M.

(2008) Bioorg.Med.Chem.Lett. 18: 4442

  • DOI: 10.1016/j.bmcl.2008.06.027

  • PubMed Abstract: 
  • A piperazine series of cyclin-dependent kinase (CDK) inhibitors have been identified. The compounds exhibit excellent physiochemical properties and a novel binding mode, whereby a bridging interaction via a water molecule with Asp 86 of CDK2, leads t ...

    A piperazine series of cyclin-dependent kinase (CDK) inhibitors have been identified. The compounds exhibit excellent physiochemical properties and a novel binding mode, whereby a bridging interaction via a water molecule with Asp 86 of CDK2, leads to selectivity for the CDK family of enzymes over other kinases. Piperazines 2e and 2i were subsequently shown to inhibit tumour growth when dosed orally in a nude mouse xenograft study. Additional chemical series that exploit this unexpected interaction with Asp 86 are also described.


    Organizational Affiliation

    Cancer and Infection Research Area, AstraZeneca Pharmaceuticals, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK. ray.finlay@astrazeneca.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CELL DIVISION PROTEIN KINASE 2
A
299Homo sapiensGene Names: CDK2 (CDKN2)
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Go to Gene View: CDK2
Go to UniProtKB:  P24941
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IM9
Query on IM9

Download SDF File 
Download CCD File 
A
2-{4-[4-({4-[2-methyl-1-(1-methylethyl)-1H-imidazol-5-yl]pyrimidin-2-yl}amino)phenyl]piperazin-1-yl}-2-oxoethanol
C23 H29 N7 O2
PVTKDXZNSUHUMO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IM9IC50: 17 nM (100) BINDINGDB
IM9IC50: 17 nM BINDINGMOAD
IM9IC50: 17 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.252α = 90.00
b = 71.153β = 90.00
c = 71.933γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
MOSFLMdata reduction
TRUNCATEdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance