2VV9 | pdb_00002vv9

CDK2 in complex with an imidazole piperazine

• PDB DOI: https://doi.org/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 (Depositor) 
• R-Value Work: 
  0.189 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: other

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: https://doi.org/10.1016/j.bmcl.2008.06.027
• Primary Citation Related Structures: 
  2VV9


• 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]

Biological Assembly 1  

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: 2,390 
• Modeled Residue Count: 280 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.228 (Depositor) 
• R-Value Work:  0.189 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

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

• 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
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary