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 PISA (software)

Macromolecule Content

• Total Structure Weight: 34.41 kDa 
• Atom Count: 2717 
• Residue Count: 295 
• Unique protein chains: 1

2XMY

Discovery and Characterisation of 2-Anilino-4-(thiazol-5-yl) pyrimidine Transcriptional CDK Inhibitors as Anticancer Agents

• DOI: 10.2210/pdb2XMY/pdb

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


• Deposited: 2010-07-29 Released: 2010-11-10 
• Deposition Author(s): Wang, S., Griffiths, G., Midgley, C.A., Barnett, A.L., Cooper, M., Grabarek, J., Ingram, L., Jackson, W., Kontopidis, G., McClue, S.J., McInnes, C., McLachlan, J., Meades, C., Mezna, M., Stuart, I., Thomas, M.P., Zheleva, D.I., Lane, D.P., Jackson, R.C., Glover, D.M., Blake, D.G., Fischer, P.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.271 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 

Literature

Discovery and Characterisation of 2-Anilino-4-(Thiazol-5-Yl)Pyrimidine Transcriptional Cdk Inhibitors as Anticancer Agents

Wang, S., Griffiths, G., Midgley, C.A., Barnett, A.L., Cooper, M., Grabarek, J., Ingram, L., Jackson, W., Kontopidis, G., Mcclue, S.J., Mcinnes, C., Mclachlan, J., Meades, C., Mezna, M., Stuart, I., Thomas, M.P., Zheleva, D.I., Lane, D.P., Jackson, R.C., Glover, D.M., Blake, D.G., Fischer, P.M.

(2010) Chem Biol 17: 1111

• PubMed: 21035734 
• DOI: 10.1016/j.chembiol.2010.07.016
• Primary Citation of Related Structures:  
  2XNB, 2XMY


• PubMed Abstract: 
  

The main difficulty in the development of ATP antagonist kinase inhibitors is target specificity, since the ATP-binding motif is present in many proteins. We introduce a strategy that has allowed us to identify compounds from a kinase inhibitor library that block the cyclin-dependent kinases responsible for regulating transcription, i.e., CDK7 and especially CDK9. The screening cascade employs cellular phenotypic assays based on mitotic index and nuclear p53 protein accumulation. This permitted us to classify compounds into transcriptional, cell cycle, and mitotic inhibitor groups. We describe the characterization of the transcriptional inhibitor class in terms of kinase inhibition profile, cellular mode of action, and selectivity for transformed cells. A structural selectivity rationale was used to optimize potency and biopharmaceutical properties and led to the development of a transcriptional inhibitor, 3,4-dimethyl-5-[2-(4-piperazin-1-yl-phenylamino)-pyrimidin-4-yl]-3H-thiazol-2-one, with anticancer activity in animal models.

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Organizational Affiliation: 

Cyclacel Limited, Dundee DD15JJ, Scotland, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELL DIVISION PROTEIN KINASE 2	A	298	Homo sapiens	Mutation(s): 0  Gene Names: CDK2, CDKN2 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (PDB Primary Data)
Find proteins for P24941 (Homo sapiens) Explore P24941  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
CDK	A	4-[4-(3,4-DIMETHYL-2-OXO-2,3-DIHYDRO-THIAZOL-5-YL)-PYRIMIDIN-2-YLAMINO]-N-(2-METHOXY-ETHYL)-BENZENESULFONAMIDE C18 H21 N5 O4 S2 WQZVTNFUNLTGDW-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
CDK	Ki :  0.10999999940395355   nM  PDBBind
CDK	Ki:  0.10999999940395355   nM  BindingDB
CDK	Ki:  0.10999999940395355   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.271 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.118	α = 90
b = 71.498	β = 90
c = 71.642	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-07-29 
• Released Date: 2010-11-10 
Deposition Author(s): Wang, S., Griffiths, G., Midgley, C.A., Barnett, A.L., Cooper, M., Grabarek, J., Ingram, L., Jackson, W., Kontopidis, G., McClue, S.J., McInnes, C., McLachlan, J., Meades, C., Mezna, M., Stuart, I., Thomas, M.P., Zheleva, D.I., Lane, D.P., Jackson, R.C., Glover, D.M., Blake, D.G., Fischer, P.M.

Revision History 

• Version 1.0: 2010-11-10
  Type: Initial release
  
• Version 1.1: 2012-03-28
  Changes: Database references, Other, Refinement description, Source and taxonomy, Version format compliance