Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.19 kDa 
• Atom Count: 2195 
• Modelled Residue Count: 250 
• Deposited Residue Count: 279 
• Unique protein chains: 1

2XKF

Structure of Nek2 bound to aminopyrazine compound 2

• PDB DOI: 10.2210/pdb2XKF/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-07-07 Released: 2010-10-27 
• Deposition Author(s): Mas-Droux, C., Bayliss, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.222 
• R-Value Work: 0.171 
• R-Value Observed: 0.174 

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

• PubMed: 20936789 
• DOI: 10.1021/jm1008727
• Primary Citation of Related Structures:  
  2XK3, 2XK4, 2XK6, 2XK7, 2XK8, 2XKC, 2XKD, 2XKE, 2XKF


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE NEK2	A	279	Homo sapiens	Mutation(s): 0  Gene Names: NEK2, NEK2A, NLK1 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BX1	B [auth A]	1-[3-amino-6-(3,4,5-trimethoxyphenyl)pyrazin-2-yl]piperidine-4-carboxylic acid C19 H24 N4 O5 FFHSQDAETWTILU-UHFFFAOYSA-N
CL	C [auth A], D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
BX1	Binding MOAD:  2XKF	IC50: 870 (nM) from 1 assay(s)
	PDBBind:  2XKF	IC50: 870 (nM) from 1 assay(s)
	BindingDB:  2XKF	IC50: min: 410, max: 940 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.222 
• R-Value Work: 0.171 
• R-Value Observed: 0.174 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.234	α = 90
b = 56.956	β = 127.88
c = 73.493	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-07-07 
• Released Date: 2010-10-27 
Deposition Author(s): Mas-Droux, C., Bayliss, R.

Revision History  

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