NEK2-EDE bound to CCT248662

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

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Ligand Structure Quality Assessment 

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Design of Potent and Selective Hybrid Inhibitors of the Mitotic Kinase Nek2: Structure-Activity Relationship, Structural Biology, and Cellular Activity.

Innocenti, P.Cheung, K.M.Solanki, S.Mas-Droux, C.Rowan, F.Yeoh, S.Boxall, K.Westlake, M.Pickard, L.Hardy, T.Baxter, J.E.Aherne, G.W.Bayliss, R.Fry, A.M.Hoelder, S.

(2012) J Med Chem 55: 3228

  • DOI: https://doi.org/10.1021/jm201683b
  • Primary Citation of Related Structures:  
    4A4X, 4AFE

  • PubMed Abstract: 

    We report herein a series of Nek2 inhibitors based on an aminopyridine scaffold. These compounds have been designed by combining key elements of two previously discovered chemical series. Structure based design led to aminopyridine (R)-21, a potent and selective inhibitor able to modulate Nek2 activity in cells.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SERINE/THREONINE-PROTEIN KINASE NEK2279Homo sapiensMutation(s): 3 
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on JUP

Download Ideal Coordinates CCD File 
C28 H27 F3 N4 O2 S
Binding Affinity Annotations 
IDSourceBinding Affinity
JUP BindingDB:  4A4X IC50: min: 37, max: 2700 (nM) from 3 assay(s)
PDBBind:  4A4X IC50: 59 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.223α = 90
b = 56.909β = 127.12
c = 74.408γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other