2W06 | pdb_00002w06

Structure of CDK2 in complex with an imidazolyl pyrimidine, compound 5c

• PDB DOI: https://doi.org/10.2210/pdb2W06/pdb

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


• Deposited: 2008-08-08 Released: 2008-09-23 
• Deposition Author(s): Anderson, M., Andrews, D.M., Barker, A.J., Brassington, C.A., Byth, K.F., Culshaw, J.D., Finlay, M.R.V., Fisher, E., Mcmiken, H.H.J., Green, C.P., Heaton, D.W., Nash, I.A., Newcombe, N.J., Oakes, S.E., Roberts, A., Stanway, J.J., Thomas, A.P., Tucker, J.A., Weir, H.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.234 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.207 (DCC) 

Starting Model: other

Literature

Imidazoles: Sar and Development of a Potent Class of Cyclin-Dependent Kinase Inhibitors

Anderson, M., Andrews, D.M., Barker, A.J., Brassington, C.A., Breed, J., Byth, K.F., Culshaw, J.D., Finlay, M.R.V., Fisher, E., Mcmiken, H.H.J., Green, C.P., Heaton, D.W., Nash, I.A., Newcombe, N.J., Oakes, S.E., Pauptit, R.A., Roberts, A., Stanway, J.J., Thomas, A.P., Tucker, J.A., Walker, M., Weir, H.M.

(2008) Bioorg Med Chem Lett 18: 5487

• PubMed: 18815031 
• DOI: https://doi.org/10.1016/j.bmcl.2008.09.024
• Primary Citation Related Structures: 
  2W05, 2W06


• PubMed Abstract: 
  

  An imidazole series of cyclin-dependent kinase (CDK) inhibitors has been developed. Protein inhibitor structure determination has provided an understanding of the emerging structure activity trends for the imidazole series. The introduction of a methyl sulfone at the aniline terminus led to a more orally bioavailable CDK inhibitor that was progressed into clinical development.

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Organizational Affiliation: 
• AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK.

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: 34.39 kDa 
• Atom Count: 2,375 
• Modeled Residue Count: 283 
• 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
FRV	B [auth A]	4-{[4-(1-CYCLOPROPYL-2-METHYL-1H-IMIDAZOL-5-YL)PYRIMIDIN-2-YL]AMINO}-N-METHYLBENZENESULFONAMIDE C18 H20 N6 O2 S MZWCVBFANHIPTJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.234 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.207 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.643	α = 90
b = 72.62	β = 90
c = 71.947	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-23 
Deposition Author(s): Anderson, M., Andrews, D.M., Barker, A.J., Brassington, C.A., Byth, K.F., Culshaw, J.D., Finlay, M.R.V., Fisher, E., Mcmiken, H.H.J., Green, C.P., Heaton, D.W., Nash, I.A., Newcombe, N.J., Oakes, S.E., Roberts, A., Stanway, J.J., Thomas, A.P., Tucker, J.A., Weir, H.M.

Revision History  

• Version 1.0: 2008-09-23
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2017-07-05
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2019-04-24
  Changes: Data collection, Source and taxonomy
• Version 2.2: 2024-05-01
  Changes: Data collection, Database references, Other, Refinement description
• Version 2.3: 2024-11-13
  Changes: Structure summary