2XNB

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

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

  • 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 ...

    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.


    Organizational Affiliation

    Cyclacel Limited, Dundee DD15JJ, Scotland, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CELL DIVISION PROTEIN KINASE 2A298Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Y8L (Subject of Investigation/LOI)
Query on Y8L

Download Ideal Coordinates CCD File 
B [auth A]3,4-DIMETHYL-5-(2-{[(1Z)-4-PIPERAZIN-1-YLCYCLOHEXA-2,4-DIEN-1-YLIDENE]AMINO}PYRIMIDIN-4-YL)-1,3-THIAZOL-2(3H)-ONE
C19 H22 N6 O S
SNCJEJRBHBIGKH-HYARGMPZSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
Y8L PDBBind:  2XNB Ki: 149 (nM) from 1 assay(s)
Binding MOAD:  2XNB Ki: 149 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.005α = 90
b = 71.108β = 90
c = 72.028γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

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