4AFE | pdb_00004afe

Nek2 bound to hybrid compound 21

• PDB DOI: https://doi.org/10.2210/pdb4AFE/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-01-19 Released: 2012-04-25 
• Deposition Author(s): Yeoh, S., Innocenti, P., Hoelder, S., Bayliss, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.248 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

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

• PubMed: 22404346 
• DOI: https://doi.org/10.1021/jm201683b
• Primary Citation 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.

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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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.22 kDa 
• Atom Count: 2,131 
• Modeled Residue Count: 253 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GGY	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
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.248 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.039	α = 90
b = 56.724	β = 127.1
c = 74.279	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-25 
Deposition Author(s): Yeoh, S., Innocenti, P., Hoelder, S., Bayliss, R.

Revision History  

• Version 1.0: 2012-04-25
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description