2W17

CDK2 in complex with the imidazole pyrimidine amide, compound (S)-8b

• PDB DOI: https://doi.org/10.2210/pdb2W17/pdb

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


• Deposited: 2008-10-15 Released: 2008-11-04 
• Deposition Author(s): Jones, C.D., Andrews, D.M., Barker, A.J., Blades, K., Daunt, P., East, S., Geh, C., Graham, M.A., Johnson, K.M., Loddick, S.A., McFarland, H.M., McGregor, A., Moss, L., Rudge, D.A., Simpson, P.B., Swain, M.L., Tam, K.Y., Tucker, J.A., Walker, M., Brassington, C., Haye, H., McCall, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.300 
• R-Value Work: 0.242 
• R-Value Observed: 0.244 

Starting Model: other

Literature

The Discovery of Azd5597, a Potent Imidazole Pyrimidine Amide Cdk Inhibitor Suitable for Intravenous Dosing.

Jones, C.D., Andrews, D.M., Barker, A.J., Blades, K., Daunt, P., East, S., Geh, C., Graham, M.A., Johnson, K.M., Loddick, S.A., Mcfarland, H.M., Mcgregor, A., Moss, L., Rudge, D.A., Simpson, P.B., Swain, M.L., Tam, K.Y., Tucker, J.A., Walker, M.

(2008) Bioorg Med Chem Lett 18: 6369

• PubMed: 18996007 
• DOI: https://doi.org/10.1016/j.bmcl.2008.10.102
• Primary Citation of Related Structures:  
  2W17


• PubMed Abstract: 
  

  The development of a novel series of imidazole pyrimidine amides as cyclin-dependent kinase (CDK) inhibitors is described. Optimisation of inhibitory potency against multiple CDK's (1, 2 and 9) resulted in imidazole pyrimidine amides with potent in vitro anti-proliferative effects against a range of cancer cell lines. Excellent physiochemical properties and large margins against inhibition of CYP isoforms and the hERG ion channel were achieved by modification of lipophilicity and amine basicity. A candidate with disease model activity in human cancer cell line xenografts and with suitable physiochemical and pharmacokinetic profiles for intravenous (i.v.) dosing was selected for further development as AZD5597.

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Organizational Affiliation: 

Cancer and Infection Research, 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: 34.51 kDa 
• Atom Count: 2,404 
• Modelled Residue Count: 279 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I19	C [auth A]	N-(4-{[(3S)-3-(dimethylamino)pyrrolidin-1-yl]carbonyl}phenyl)-5-fluoro-4-[2-methyl-1-(1-methylethyl)-1H-imidazol-5-yl]pyrimidin-2-amine C24 H30 F N7 O BACSZMCLZIDTIO-IBGZPJMESA-N
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
I19	PDBBind:  2W17	IC50: 2 (nM) from 1 assay(s)
	BindingDB:  2W17	IC50: 2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.300 
• R-Value Work: 0.242 
• R-Value Observed: 0.244 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.542	α = 90
b = 71.824	β = 90
c = 71.771	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-04 
Deposition Author(s): Jones, C.D., Andrews, D.M., Barker, A.J., Blades, K., Daunt, P., East, S., Geh, C., Graham, M.A., Johnson, K.M., Loddick, S.A., McFarland, H.M., McGregor, A., Moss, L., Rudge, D.A., Simpson, P.B., Swain, M.L., Tam, K.Y., Tucker, J.A., Walker, M., Brassington, C., Haye, H., McCall, E.

Revision History  

• Version 1.0: 2008-11-04
  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, Derived calculations, Other, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary