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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: 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.


  • 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
MoleculeChains Sequence LengthOrganismDetailsImage
AURORA KINASE B292Homo sapiensMutation(s): 1 
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
GTEx:  ENSG00000178999 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96GD4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
INNER CENTROMERE PROTEINB [auth D]71Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQS7 (Homo sapiens)
Explore Q9NQS7 
Go to UniProtKB:  Q9NQS7
PHAROS:  Q9NQS7
GTEx:  ENSG00000149503 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NQS7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / 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
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

View Full Validation Report



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
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description