2JAV

Human Kinase with pyrrole-indolinone ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and Regulation of the Human Nek2 Centrosomal Kinase

Rellos, P.Ivins, F.J.Baxter, J.E.Pike, A.C.W.Nott, T.J.Parkinson, D.-M.Das, S.Howell, S.Fedorov, O.Shen, Q.Y.Fry, A.M.Knapp, S.Smerdon, S.J.

(2007) J Biol Chem 282: 6833

  • DOI: 10.1074/jbc.M609721200
  • Primary Citation of Related Structures:  
    2JAV

  • PubMed Abstract: 
  • The dimeric Ser/Thr kinase Nek2 regulates centrosome cohesion and separation through phosphorylation of structural components of the centrosome, and aberrant regulation of Nek2 activity can lead to aneuploid defects characteristic of cancer cells. Mu ...

    The dimeric Ser/Thr kinase Nek2 regulates centrosome cohesion and separation through phosphorylation of structural components of the centrosome, and aberrant regulation of Nek2 activity can lead to aneuploid defects characteristic of cancer cells. Mutational analysis of autophosphorylation sites within the kinase domain identified by mass spectrometry shows a complex pattern of positive and negative regulatory effects on kinase activity that are correlated with effects on centrosomal splitting efficiency in vivo. The 2.2-A resolution x-ray structure of the Nek2 kinase domain in complex with a pyrrole-indolinone inhibitor reveals an inhibitory helical motif within the activation loop. This helix presents a steric barrier to formation of the active enzyme and generates a surface that may be exploitable in the design of specific inhibitors that selectively target the inactive state. Comparison of this "auto-inhibitory" conformation with similar arrangements in cyclin-dependent kinase 2 and epidermal growth factor receptor kinase suggests a role for dimerization-dependent allosteric regulation that combines with autophosphorylation and protein phosphatase 1c phosphatase activity to generate the precise spatial and temporal control required for Nek2 function in centrosomal maturation.


    Organizational Affiliation

    Structural Genomics Consortium, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE/THREONINE-PROTEIN KINASE NEK2A279Homo sapiensMutation(s): 1 
Gene Names: NEK2NEK2ANLK1
EC: 2.7.11.1
Find proteins for P51955 (Homo sapiens)
Explore P51955 
Go to UniProtKB:  P51955
NIH Common Fund Data Resources
PHAROS  P51955
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5Z5
Query on 5Z5

Download CCD File 
A
5-[(Z)-(5-CHLORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-N-(DIETHYLAMINO)ETHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE
C17 H16 Cl N3 O2
FIRPCWHHIWFKCD-GHXNOFRVSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5Z5IC50:  8000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.634α = 90
b = 56.924β = 95.98
c = 66.012γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation