5MHQ

CCT068127 in complex with CDK2

• PDB DOI:  https://doi.org/10.2210/pdb5MHQ/pdb

• Classification: CELL CYCLE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-11-25 Released: 2017-12-20 
• Deposition Author(s): Whittaker, S.R., Barlow, C., Martin, M.P., Mancusi, C., Wagner, S., Barrie, E., te Poele, R., Sharp, S., Brown, N., Wilson, S., Clarke, P., Walton, M.I., MacDonald, E., Blagg, J., Noble, M.E.M., Garrett, M.D., Workman, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.226 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 

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

• PubMed: 29063678 
• DOI: https://doi.org/10.1002/1878-0261.12148
• Primary Citation of Related Structures:  
  5MHQ


• 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 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.

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Organizational Affiliation: 

Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.17 kDa 
• Atom Count: 2,799 
• Modelled Residue Count: 292 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	A	306	Homo sapiens	Mutation(s): 0  Gene Names: CDK2, CDKN2 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8QT	B [auth A]	(2~{R},3~{S})-3-[[9-propan-2-yl-6-(pyridin-3-ylmethylamino)purin-2-yl]amino]pentan-2-ol C19 H27 N7 O SCACHXWSWJBIHG-HIFRSBDPSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Binding Affinity Annotations
ID	Source	Binding Affinity
8QT	BindingDB:  5MHQ	IC50: 30 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.226 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.66	α = 90
b = 71.15	β = 90
c = 71.15	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Whittaker, S.R., Barlow, C., Martin, M.P., Mancusi, C., Wagner, S., Barrie, E., te Poele, R., Sharp, S., Brown, N., Wilson, S., Clarke, P., Walton, M.I., MacDonald, E., Blagg, J., Noble, M.E.M., Garrett, M.D., Workman, P.

Revision History  

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