Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 34.44 kDa 
• Atom Count: 2390 
• Residue Count: 280 
• Unique protein chains: 1

2VV9

CDK2 in complex with an imidazole piperazine

• DOI: 10.2210/pdb2VV9/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2008-06-04 Released: 2008-08-05 
• Deposition Author(s): Acton, D.G., Anderson, M., Andrews, D.M., Barker, A.J., Brassington, C.A., Finlay, M.R., Fisher, E., Gerhardt, S., Graham, M.A., Green, C.P., Heaton, D.W., Loddick, S.A., Morgentin, R., Read, J., Roberts, A., Stanway, J., Tucker, J.A., Weir, H.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.228 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

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

• PubMed: 18617397 
• DOI: 10.1016/j.bmcl.2008.06.027
• Structures With Same Primary Citation


• 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 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.

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Organizational Affiliation: 

Cancer and Infection Research Area, AstraZeneca Pharmaceuticals, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CELL DIVISION PROTEIN KINASE 2	A	299	Homo sapiens	Mutation(s): 0  Gene Names: CDK2, CDKN2 EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens) Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS  P24941 GTEx  ENSG00000123374

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IM9	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
IM9	IC50:  17   nM  BindingDB
IM9	IC50 :  17   nM  PDBBind
IM9	IC50:  17   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.228 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.252	α = 90
b = 71.153	β = 90
c = 71.933	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
TRUNCATE	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-06-04 
• Released Date: 2008-08-05 
Deposition Author(s): Acton, D.G., Anderson, M., Andrews, D.M., Barker, A.J., Brassington, C.A., Finlay, M.R., Fisher, E., Gerhardt, S., Graham, M.A., Green, C.P., Heaton, D.W., Loddick, S.A., Morgentin, R., Read, J., Roberts, A., Stanway, J., Tucker, J.A., Weir, H.M.

Revision History 

• Version 1.0: 2008-08-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2019-04-24
  Changes: Data collection, Derived calculations, Other, Source and taxonomy