5M55

Nek2 bound to arylaminopurine 71


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-guided design of purine-based probes for selective Nek2 inhibition.

Coxon, C.R.Wong, C.Bayliss, R.Boxall, K.Carr, K.H.Fry, A.M.Hardcastle, I.R.Matheson, C.J.Newell, D.R.Sivaprakasam, M.Thomas, H.Turner, D.Yeoh, S.Wang, L.Z.Griffin, R.J.Golding, B.T.Cano, C.

(2017) Oncotarget 8: 19089-19124

  • DOI: 10.18632/oncotarget.13249
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nek2 (NIMA-related kinase 2) is a cell cycle-dependent serine/threonine protein kinase that regulates centrosome separation at the onset of mitosis. Overexpression of Nek2 is common in human cancers and suppression can restrict tumor cell growth and ...

    Nek2 (NIMA-related kinase 2) is a cell cycle-dependent serine/threonine protein kinase that regulates centrosome separation at the onset of mitosis. Overexpression of Nek2 is common in human cancers and suppression can restrict tumor cell growth and promote apoptosis. Nek2 inhibition with small molecules, therefore, offers the prospect of a new therapy for cancer. To achieve this goal, a better understanding of the requirements for selective-inhibition of Nek2 is required. 6-Alkoxypurines were identified as ATP-competitive inhibitors of Nek2 and CDK2. Comparison with CDK2-inhibitor structures indicated that judicious modification of the 6-alkoxy and 2-arylamino substituents could achieve discrimination between Nek2 and CDK2. In this study, a library of 6-cyclohexylmethoxy-2-arylaminopurines bearing carboxamide, sulfonamide and urea substituents on the 2-arylamino ring was synthesized. Few of these compounds were selective for Nek2 over CDK2, with the best result being obtained for 3-((6-(cyclohexylmethoxy)-9H-purin-2-yl)amino)-N,N-dimethylbenzamide (CDK2 IC50 = 7.0 μM; Nek2 IC50 = 0.62 μM) with >10-fold selectivity. Deletion of the 6-substituent abrogated activity against both Nek2 and CDK2. Nine compounds containing an (E)-dialkylaminovinyl substituent at C-6, all showed selectivity for Nek2, e.g. (E)-6-(2-(azepan-1-yl)vinyl)-N-phenyl-9H-purin-2-amine (CDK2 IC50 = 2.70 μM; Nek2 IC50 = 0.27 μM). Structural biology of selected compounds enabled a partial rationalization of the observed structure activity relationships and mechanism of Nek2 activation. This showed that carboxamide 11 is the first reported inhibitor of Nek2 in the DFG-in conformation.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of Leicester, Leicester, UK.,Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK.,Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, Surrey, UK.,Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Newcastle upon Tyne, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase Nek2
A
279Homo sapiensMutation(s): 0 
Gene Names: NEK2 (NEK2A, NLK1)
EC: 2.7.11.1
Find proteins for P51955 (Homo sapiens)
Go to Gene View: NEK2
Go to UniProtKB:  P51955
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
7GG
Query on 7GG

Download SDF File 
Download CCD File 
A
6-[(~{Z})-2-(diethylamino)ethenyl]-~{N}-phenyl-7~{H}-purin-2-amine
C17 H20 N6
SHKLUCMYFCYADL-KHPPLWFESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
7GGIC50: 240 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 100.300α = 90.00
b = 57.610β = 132.99
c = 79.920γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-10-20 
  • Released Date: 2016-11-02 
  • Deposition Author(s): Bayliss, R.

Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC24461/A10285

Revision History 

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2016-11-23
    Type: Database references
  • Version 1.2: 2017-05-03
    Type: Database references