4AFE

Nek2 bound to hybrid compound 21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

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: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE/THREONINE-PROTEIN KINASE NEK2A279Homo sapiensMutation(s): 0 
Gene Names: NEK2NEK2ANLK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P51955 (Homo sapiens)
Explore P51955 
Go to UniProtKB:  P51955
PHAROS:  P51955
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51955
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GGY
Query on GGY

Download Ideal Coordinates CCD File 
B [auth A]4-(2-AMINO-5-{4-[(DIMETHYLAMINO)METHYL]THIOPHEN-2-YL}PYRIDIN-3-YL)-2-{[(1R,2Z)-4,4,4-TRIFLUORO-1-METHYLBUT-2-EN-1-YL]OXY}BENZAMIDE
C24 H25 F3 N4 O2 S
LLEOOSLUHRQCHZ-LMVHVUTASA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GGY PDBBind:  4AFE IC50: 73 (nM) from 1 assay(s)
BindingDB:  4AFE IC50: min: 22, max: 800 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.039α = 90
b = 56.724β = 127.1
c = 74.279γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-25
    Type: Initial release