3UIX

Crystal structure of Pim1 kinase in complex with small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

wwPDB Validation 3D Report Full Report



Literature

A novel pim-1 kinase inhibitor targeting residues that bind the substrate Peptide.

Tsuganezawa, K.Watanabe, H.Parker, L.Yuki, H.Taruya, S.Nakagawa, Y.Kamei, D.Mori, M.Ogawa, N.Tomabechi, Y.Handa, N.Honma, T.Yokoyama, S.Kojima, H.Okabe, T.Nagano, T.Tanaka, A.

(2012) J Mol Biol 417: 240-252

  • DOI: 10.1016/j.jmb.2012.01.036
  • Primary Citation of Related Structures:  
    3UIX

  • PubMed Abstract: 
  • A new screening method using fluorescent correlation spectroscopy was developed to select kinase inhibitors that competitively inhibit the binding of a fluorescently labeled substrate peptide. Using the method, among approximately 700 candidate compo ...

    A new screening method using fluorescent correlation spectroscopy was developed to select kinase inhibitors that competitively inhibit the binding of a fluorescently labeled substrate peptide. Using the method, among approximately 700 candidate compounds selected by virtual screening, we identified a novel Pim-1 kinase inhibitor targeting its peptide binding residues. X-ray crystal analysis of the complex structure of Pim-1 with the inhibitor indicated that the inhibitor actually binds to the ATP-binding site and also forms direct interactions with residues (Asp128 and Glu171) that bind the substrate peptide. These interactions, which cause small side-chain movements, seem to affect the binding ability of the fluorescently labeled substrate. The compound inhibited Pim-1 kinase in vitro, with an IC(50) value of 150 nM. Treatment of cultured leukemia cells with the compound reduced the amount of p21 and increased the amount of p27, due to Pim-1 inhibition, and then triggered apoptosis after cell-cycle arrest at the G(1)/S phase. This screening method may be widely applicable for the identification of various new Pim-1 kinase inhibitors targeting the residues that bind the substrate peptide.


    Organizational Affiliation

    RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene serine/threonine-protein kinase pim-1A298Homo sapiensMutation(s): 0 
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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Q17
Query on Q17

Download CCD File 
A
2-{4-[(3-aminopropyl)amino]quinazolin-2-yl}phenol
C17 H18 N4 O
VIQWLKJTZBWAFF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Q17IC50:  151   nM  Binding MOAD
Q17IC50 :  151   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.006α = 90
b = 97.006β = 90
c = 80.898γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-11-06 
  • Released Date: 2012-04-11 
  • Deposition Author(s): Parker, L.J.

Revision History 

  • Version 1.0: 2012-04-11
    Type: Initial release