5MHQ

CCT068127 in complex with CDK2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular profiling and combinatorial activity of CCT068127: a potent CDK2 and CDK9 inhibitor.

Whittaker, S.R.Barlow, C.Martin, M.P.Mancusi, C.Wagner, S.Self, A.Barrie, E.Te Poele, R.Sharp, S.Brown, N.Wilson, S.Jackson, W.Fischer, P.M.Clarke, P.A.Walton, M.I.McDonald, E.Blagg, J.Noble, M.Garrett, M.D.Workman, P.

(2018) Mol Oncol 12: 287-304

  • DOI: 10.1002/1878-0261.12148

  • PubMed Abstract: 
  • Deregulation of the cyclin-dependent kinases (CDKs) has been implicated in the pathogenesis of multiple cancer types. Consequently, CDKs have garnered intense interest as therapeutic targets for the treatment of cancer. We describe herein the molecul ...

    Deregulation of the cyclin-dependent kinases (CDKs) has been implicated in the pathogenesis of multiple cancer types. Consequently, CDKs have garnered intense interest as therapeutic targets for the treatment of cancer. We describe herein the molecular and cellular effects of CCT068127, a novel inhibitor of CDK2 and CDK9. Optimized from the purine template of seliciclib, CCT068127 exhibits greater potency and selectivity against purified CDK2 and CDK9 and superior antiproliferative activity against human colon cancer and melanoma cell lines. X-ray crystallography studies reveal that hydrogen bonding with the DFG motif of CDK2 is the likely mechanism of greater enzymatic potency. Commensurate with inhibition of CDK activity, CCT068127 treatment results in decreased retinoblastoma protein (RB) phosphorylation, reduced phosphorylation of RNA polymerase II, and induction of cell cycle arrest and apoptosis. The transcriptional signature of CCT068127 shows greatest similarity to other small-molecule CDK and also HDAC inhibitors. CCT068127 caused a dramatic loss in expression of DUSP6 phosphatase, alongside elevated ERK phosphorylation and activation of MAPK pathway target genes. MCL1 protein levels are rapidly decreased by CCT068127 treatment and this associates with synergistic antiproliferative activity after combined treatment with CCT068127 and ABT263, a BCL2 family inhibitor. These findings support the rational combination of this series of CDK2/9 inhibitors and BCL2 family inhibitors for the treatment of human cancer.


    Organizational Affiliation

    Cyclacel Ltd., Dundee, UK.,Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK.,Northern Institute for Cancer Research, University of Newcastle upon Tyne, Medical School, Newcastle upon Tyne, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 2
A
306Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8QT
Query on 8QT

Download SDF File 
Download CCD File 
A
(2~{R},3~{S})-3-[[9-propan-2-yl-6-(pyridin-3-ylmethylamino)purin-2-yl]amino]pentan-2-ol
CCT068127
C19 H27 N7 O
SCACHXWSWJBIHG-HIFRSBDPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.660α = 90.00
b = 71.150β = 90.00
c = 71.150γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
xia2data reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Database references
  • Version 1.2: 2018-03-14
    Type: Database references