2XK7

Structure of Nek2 bound to aminopyrazine compound 23


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.992 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Aminopyrazine Inhibitors Binding to an Unusual Inactive Conformation of the Mitotic Kinase Nek2: Sar and Structural Characterization.

Whelligan, D.K.Solanki, S.Taylor, D.Thomson, D.W.Cheung, K.M.Boxall, K.Mas-Droux, C.Barillari, C.Burns, S.Grummitt, C.G.Collins, I.Van Montfort, R.L.Aherne, G.W.Bayliss, R.Hoelder, S.

(2010) J.Med.Chem. 53: 7682

  • DOI: 10.1021/jm1008727
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report herein the first systematic exploration of inhibitors of the mitotic kinase Nek2. Starting from HTS hit aminopyrazine 2, compounds with improved activity were identified using structure-based design. Our structural biology investigations re ...

    We report herein the first systematic exploration of inhibitors of the mitotic kinase Nek2. Starting from HTS hit aminopyrazine 2, compounds with improved activity were identified using structure-based design. Our structural biology investigations reveal two notable observations. First, 2 and related compounds bind to an unusual, inactive conformation of the kinase which to the best of our knowledge has not been reported for other types of kinase inhibitors. Second, a phenylalanine residue at the center of the ATP pocket strongly affects the ability of the inhibitor to bind to the protein. The implications of these observations are discussed, and the work described here defines key features for potent and selective Nek2 inhibition, which will aid the identification of more advanced inhibitors of Nek2.


    Organizational Affiliation

    Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, United Kingdom.




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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
30E
Query on 30E

Download SDF File 
Download CCD File 
A
(3R,4R)-1-[3-amino-6-(3,4,5-trimethoxyphenyl)pyrazin-2-yl]-3-ethylpiperidine-4-carboxylic acid
C21 H28 N4 O5
MQOJTCBESRAKQA-GXTWGEPZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
30EIC50: 1500 nM BINDINGMOAD
30EIC50: 1500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.992 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 101.200α = 90.00
b = 56.770β = 127.61
c = 74.140γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-27
    Type: Initial release
  • Version 1.1: 2011-05-19
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance