Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33192.71 
• Atom Count: 2041 
• Residue Count: 279 
• Unique protein chains: 1

2XKF

Structure of Nek2 bound to aminopyrazine compound 2

• DOI: 10.2210/pdb2XKF/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• 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 

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:  
  2XKE, 2XKD, 2XKC, 2XK8, 2XK7, 2XK6, 2XK4, 2XK3


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
SERINE/THREONINE-PROTEIN KINASE NEK2	A	279	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
BX1	A	1-[3-amino-6-(3,4,5-trimethoxyphenyl)pyrazin-2-yl]piperidine-4-carboxylic acid C19 H24 N4 O5 FFHSQDAETWTILU-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
BX1	IC50: 410 - 940 nM (100) BINDINGDB
BX1	IC50: 870 nM BINDINGMOAD
BX1	IC50: 870 nM PDBBIND

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length (Å)	Angle (°)
a = 100.234	α = 90.00
b = 56.956	β = 127.88
c = 73.493	γ = 90.00

Software Package:

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

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance