2IWI

CRYSTAL STRUCTURE OF THE HUMAN PIM2 IN COMPLEX WITH A RUTHENIUM ORGANOMETALLIC LIGAND RU1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

Starting Model: experimental
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This is version 1.6 of the entry. See complete history


Literature

Crystal structure of the PIM2 kinase in complex with an organoruthenium inhibitor.

Bullock, A.N.Russo, S.Amos, A.Pagano, N.Bregman, H.Debreczeni, J.E.Lee, W.H.von Delft, F.Meggers, E.Knapp, S.

(2009) PLoS One 4: e7112-e7112

  • DOI: https://doi.org/10.1371/journal.pone.0007112
  • Primary Citation of Related Structures:  
    2IWI

  • PubMed Abstract: 

    The serine/threonine kinase PIM2 is highly expressed in human leukemia and lymphomas and has been shown to positively regulate survival and proliferation of tumor cells. Its diverse ATP site makes PIM2 a promising target for the development of anticancer agents. To date our knowledge of catalytic domain structures of the PIM kinase family is limited to PIM1 which has been extensively studied and which shares about 50% sequence identity with PIM2. Here we determined the crystal structure of PIM2 in complex with an organoruthenium complex (inhibition in sub-nanomolar level). Due to its extraordinary shape complementarity this stable organometallic compound is a highly potent inhibitor of PIM kinases. The structure of PIM2 revealed several differences to PIM1 which may be explored further to generate isoform selective inhibitors. It has also demonstrated how an organometallic inhibitor can be adapted to the binding site of protein kinases to generate highly potent inhibitors. This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.


  • Organizational Affiliation

    University of Oxford, Structural Genomics Consortium, Oxford, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SERINE/THREONINE-PROTEIN KINASE PIM-2
A, B
312Homo sapiensMutation(s): 0 
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P1W9 (Homo sapiens)
Explore Q9P1W9 
Go to UniProtKB:  Q9P1W9
PHAROS:  Q9P1W9
GTEx:  ENSG00000102096 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P1W9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.07α = 90
b = 153.07β = 90
c = 78.6γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-02
    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: 2018-01-24
    Changes: Database references, Structure summary
  • Version 1.4: 2018-02-28
    Changes: Database references, Source and taxonomy
  • Version 1.5: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.6: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description