2XNN

Structure of Nek2 bound to CCT242430


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Benzimidazole Inhibitors Induce a Dfg-Out Conformation of Never in Mitosis Gene A-Related Kinase 2 (Nek2) without Binding to the Back Pocket and Reveal a Nonlinear Structure-Activity Relationship.

Solanki, S.Innocenti, P.Mas-Droux, C.Boxall, K.Barillari, C.Van Montfort, R.L.Aherne, G.W.Bayliss, R.Hoelder, S.

(2011) J.Med.Chem. 54: 1626

  • DOI: 10.1021/jm1011726
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We describe herein the structure-activity relationship (SAR) and cocrystal structures of a series of Nek2 inhibitors derived from the published polo-like kinase 1 (Plk1) inhibitor (R)-1. Our studies reveal a nonlinear SAR for Nek2 and our cocrystal s ...

    We describe herein the structure-activity relationship (SAR) and cocrystal structures of a series of Nek2 inhibitors derived from the published polo-like kinase 1 (Plk1) inhibitor (R)-1. Our studies reveal a nonlinear SAR for Nek2 and our cocrystal structures show that compounds in this series bind to a DFG-out conformation of Nek2 without extending into the enlarged back pocket commonly found in this conformation. These observations were further investigated, and structure-based design led to Nek2 inhibitors derived from (R)-1 with more than a hundred-fold selectivity against Plk1.


    Organizational Affiliation

    The Institute of Cancer Research, Cancer Research UK Cancer Therapeutics Unit, 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 3 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
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
430
Query on 430

Download SDF File 
Download CCD File 
A
5-(1H-benzimidazol-1-yl)-3-{(1R)-1-[2-(trifluoromethyl)phenyl]ethoxy}thiophene-2-carboxamide
C21 H16 F3 N3 O2 S
SQYKBXHMNBHADB-GFCCVEGCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
430IC50: >50000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 101.210α = 90.00
b = 56.850β = 133.21
c = 80.400γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-30
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance