Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 34438.05 
• Atom Count: 2238 
• Residue Count: 299 
• 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


• 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: 1.9 Å
• R-Value Free: 0.228 
• R-Value Work: 0.189 

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


• 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

Find similar proteins by: Sequence  |  Structure

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 Gene View: CDK2 Go to UniProtKB:  P24941

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ACE	A	NON-POLYMER	C2 H4 O		--

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
IM9	IC50: 17 nM (100) BINDINGDB
IM9	IC50: 17 nM BINDINGMOAD
IM9	IC50: 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 = 53.252	α = 90.00
b = 71.153	β = 90.00
c = 71.933	γ = 90.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
TRUNCATE	data scaling
REFMAC	refinement
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
  Type: Advisory, Version format compliance
• Version 1.2: 2019-04-24
  Type: Data collection, Derived calculations, Other, Source and taxonomy