Human Nek2 kinase Apo

Experimental Data Snapshot

  • Resolution: 2.33 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Insights Into the Conformational Variability and Regulation of Human Nek2 Kinase.

Westwood, I.Cheary, D.M.Baxter, J.E.Richards, M.W.Van Montfort, R.L.Fry, A.M.Bayliss, R.

(2009) J Mol Biol 386: 476

  • DOI: https://doi.org/10.1016/j.jmb.2008.12.033
  • Primary Citation of Related Structures:  
    2W5A, 2W5B, 2W5H

  • PubMed Abstract: 

    The Nek family of serine/threonine kinases regulates centrosome and cilia function; in addition, several of its members are potential targets for drug discovery. Nek2 is dimeric, is cell cycle regulated and functions in the separation of centrosomes at G2/M. Here, we report the crystal structures of wild-type human Nek2 kinase domain bound to ADP at 1.55-A resolution and T175A mutant in apo form as well as that bound to a non-hydrolyzable ATP analog. These show that regions of the Nek2 structure around the nucleotide-binding site can adopt several different but well-defined conformations. None of the conformations was the same as that observed for the previously reported inhibitor-bound structure, and the two nucleotides stabilized two conformations. The structures suggest mechanisms for the auto-inhibition of Nek2 that we have tested by mutagenesis. Comparison of the structures with Aurora-A and Cdk2 gives insight into the structural mechanism of Nek2 activation. The production of specific inhibitors that target individual kinases of the human genome is an urgent challenge in drug discovery, and Nek2 is especially promising as a cancer target. We not only identify potential challenges to the task of producing Nek2 inhibitors but also propose that the conformational variability provides an opportunity for the design of Nek2 selective inhibitors because one of the conformations may provide a unique target.

  • Organizational Affiliation

    The Institute of Cancer Research, London, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SERINE/THREONINE-PROTEIN KINASE NEK2279Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P51955 (Homo sapiens)
Explore P51955 
Go to UniProtKB:  P51955
PHAROS:  P51955
GTEx:  ENSG00000117650 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51955
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.33 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.739α = 90
b = 56.962β = 133.36
c = 80.612γ = 90
Software Package:
Software NamePurpose

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2008-12-23 
  • Deposition Author(s): Bayliss, R.

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Other