4AF3

Human Aurora B Kinase in complex with INCENP and VX-680

• PDB DOI:  https://doi.org/10.2210/pdb4AF3/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-01-16 Released: 2012-04-11 
• Deposition Author(s): Elkins, J.M., Vollmar, M., Wang, J., Picaud, S., Arrowsmith, C.H., Edwards, A., Bountra, C., von Delft, F., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.264 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 

Literature

Crystal Structure of Human Aurora B in Complex with Incenp and Vx-680.

Elkins, J.M., Santaguida, S., Musacchio, A., Knapp, S.

(2012) J Med Chem 55: 7841

• PubMed: 22920039 
• DOI: https://doi.org/10.1021/jm3008954
• Primary Citation of Related Structures:  
  4AF3


• PubMed Abstract: 
  

  We present the structure of the human Aurora B kinase domain in complex with the C-terminal Aurora-binding region of human INCENP and the Aurora kinase inhibitor VX-680. The structure unexpectedly reveals a dimeric arrangement of the Aurora B:INCENP complex, which was confirmed to exist in solution by analytical ultracentrifugation. The dimerization involves a domain swap of the activation loop, resulting in a different conformation of the DFG motif as compared to that seen in other kinase complexes with VX-680. The binding of INCENP differs significantly from that seen in the Xenopus laevis Aurora B:INCENP complex currently used as a model for structure-based design for this important oncology target.

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Organizational Affiliation: 

Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 42.4 kDa 
• Atom Count: 2,427 
• Modelled Residue Count: 296 
• Deposited Residue Count: 363 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AURORA KINASE B	A	292	Homo sapiens	Mutation(s): 1  Gene Names: AURKB, AIK2, AIM1, AIRK2, ARK2, STK1, STK12, STK5 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96GD4 (Homo sapiens) Explore Q96GD4  Go to UniProtKB:  Q96GD4
PHAROS:  Q96GD4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
INNER CENTROMERE PROTEIN	B [auth D]	71	Homo sapiens	Mutation(s): 0  Gene Names: INCENP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQS7 (Homo sapiens) Explore Q9NQS7  Go to UniProtKB:  Q9NQS7
PHAROS:  Q9NQS7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VX6	C [auth A]	CYCLOPROPANECARBOXYLIC ACID {4-[4-(4-METHYL-PIPERAZIN-1-YL)-6-(5-METHYL-2H-PYRAZOL-3-YLAMINO)-PYRIMIDIN-2-YLSULFANYL]-PHENYL}-AMIDE C23 H28 N8 O S GCIKSSRWRFVXBI-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
VX6	BindingDB:  4AF3	Ki: min: 0.02, max: 18 (nM) from 3 assay(s)
		Kd: min: 7, max: 7.4 (nM) from 2 assay(s)
		IC50: min: 17, max: 55 (nM) from 7 assay(s)
	PDBBind:  4AF3	IC50: 31 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.264 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.145	α = 90
b = 80.145	β = 90
c = 92.542	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
SAWAYA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-11 
Deposition Author(s): Elkins, J.M., Vollmar, M., Wang, J., Picaud, S., Arrowsmith, C.H., Edwards, A., Bountra, C., von Delft, F., Knapp, S.

Revision History  

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2012-09-26
  Changes: Database references, Structure summary
• Version 1.2: 2018-01-24
  Changes: Structure summary