2XNM

Structure of NEK2 bound to CCT

• PDB DOI: https://doi.org/10.2210/pdb2XNM/pdb

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


• Deposited: 2010-08-05 Released: 2011-03-30 
• Deposition Author(s): Mas-Droux, C., Bayliss, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.196 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

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

• PubMed: 21366329 
• DOI: https://doi.org/10.1021/jm1011726
• Primary Citation of Related Structures:  
  2XNM, 2XNN, 2XNO, 2XNP


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.93 kDa 
• Atom Count: 2,458 
• Modelled Residue Count: 258 
• Deposited Residue Count: 279 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE NEK2	A	279	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000117650

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WGZ	B [auth A]	5-{6-[(1-METHYLPIPERIDIN-4-YL)OXY]-1H-BENZIMIDAZOL-1-YL}-3-{(1R)-1-[2-(TRIFLUOROMETHYL)PHENYL]ETHOXY}THIOPHENE-2-CARBOXAMIDE C27 H27 F3 N4 O3 S SWIVJTVGOIXUKC-MRXNPFEDSA-N
TRS	M [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	K [auth A], L [auth A], N [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
WGZ	BindingDB:  2XNM	IC50: min: 25, max: 200 (nM) from 4 assay(s)
	PDBBind:  2XNM	IC50: 160 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.196 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.8	α = 90
b = 56.83	β = 133.21
c = 81.3	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-30 
Deposition Author(s): Mas-Droux, C., Bayliss, R.

Revision History  

• Version 1.0: 2011-03-30
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other