4AF3

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


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 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    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. jon.elkins@sgc.ox.ac.uk



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AURORA KINASE BA292Homo sapiensMutation(s): 1 
Gene Names: AURKBAIK2AIM1AIRK2ARK2STK1STK12STK5
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96GD4
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
INNER CENTROMERE PROTEINB [auth D]71Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NQS7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VX6
Query on VX6

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding 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 = 80.145α = 90
b = 80.145β = 90
c = 92.542γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
SAWAYAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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