3BWF

Crystal structure of the human Pim1 in complex with an osmium compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Similar biological activities of two isostructural ruthenium and osmium complexes.

Maksimoska, J.Williams, D.S.Atilla-Gokcumen, G.E.Smalley, K.S.Carroll, P.J.Webster, R.D.Filippakopoulos, P.Knapp, S.Herlyn, M.Meggers, E.

(2008) Chemistry 14: 4816-4822

  • DOI: 10.1002/chem.200800294
  • Primary Citation of Related Structures:  
    3BWF

  • PubMed Abstract: 
  • In this study, we probe and verify the concept of designing unreactive bioactive metal complexes, in which the metal possesses a purely structural function, by investigating the consequences of replacing ruthenium in a bioactive half-sandwich kinase ...

    In this study, we probe and verify the concept of designing unreactive bioactive metal complexes, in which the metal possesses a purely structural function, by investigating the consequences of replacing ruthenium in a bioactive half-sandwich kinase inhibitor scaffold by its heavier congener osmium. The two isostructural complexes are compared with respect to their anticancer properties in 1205 Lu melanoma cells, activation of the Wnt signaling pathway, IC(50) values against the protein kinases GSK-3beta and Pim-1, and binding modes to the protein kinase Pim-1 by protein crystallography. It was found that the two congeners display almost indistinguishable biological activities, which can be explained by their nearly identical three-dimensional structures and their identical mode of action as protein kinase inhibitors. This is a unique example in which the replacement of a metal in an anticancer scaffold by its heavier homologue does not alter its biological activity.


    Organizational Affiliation

    Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene serine/threonine-protein kinase Pim-1A313N/AMutation(s): 1 
Gene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Explore P11309 
Go to UniProtKB:  P11309
NIH Common Fund Data Resources
PHAROS  P11309
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DWC
Query on DWC

Download CCD File 
A
PYRIDOCARBAZOLE CYCLOPENTADIENYL OS(CO) COMPLEX
C23 H9 N3 O4 Os
PAWFNOQPRXIUSH-LZOTZQNHCM
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DWCIC50 :  0.20000000298023224   nM  PDBBind
DWCIC50:  0.6000000238418579   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.458α = 90
b = 98.458β = 90
c = 81.362γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-06-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance