4XHK

PIM1 kinase in complex with Compound 1s


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

wwPDB Validation 3D Report Full Report



Literature

Structure-based design of low-nanomolar PIM kinase inhibitors.

Ishchenko, A.Zhang, L.Le Brazidec, J.Y.Fan, J.Chong, J.H.Hingway, A.Raditsis, A.Singh, L.Elenbaas, B.Hong, V.S.Marcotte, D.Silvian, L.Enyedy, I.Chao, J.

(2015) Bioorg Med Chem Lett 25: 474-480

  • DOI: 10.1016/j.bmcl.2014.12.041
  • Primary Citation of Related Structures:  
    4X7Q, 4XHK

  • PubMed Abstract: 
  • PIM kinases are implicated in variety of cancers by promoting cell survival and proliferation and are targets of interest for therapeutic intervention. We have identified a low-nanomolar pan-PIM inhibitor (PIM1/2/3 potency 5:14:2nM) using structure b ...

    PIM kinases are implicated in variety of cancers by promoting cell survival and proliferation and are targets of interest for therapeutic intervention. We have identified a low-nanomolar pan-PIM inhibitor (PIM1/2/3 potency 5:14:2nM) using structure based modeling. The crystal structure of this compound with PIM1 confirmed the predicted binding mode and protein-ligand interactions except those in the acidic ribose pocket. We show the SAR suggesting the importance of having a hydrogen bond donor in this pocket for inhibiting PIM2; however, this interaction is not important for inhibiting PIM1 or PIM3. In addition, we report the discovery of a new class of PIM inhibitors by using computational de novo design tool implemented in MOE software (Chemical Computing Group). These inhibitors have a different interaction profile.


    Organizational Affiliation

    Biogen Idec, 14 Cambridge Center, Cambridge, MA 02142, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1B315Homo 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
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3YR
Query on 3YR

Download CCD File 
B
2-(2,6-difluorophenyl)-N-{4-[(3S)-pyrrolidin-3-yloxy]pyridin-3-yl}-1,3-thiazole-4-carboxamide
C19 H16 F2 N4 O2 S
DNXZIJKGPFJRAA-NSHDSACASA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
BL-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3YRIC50:  5   nM  Binding MOAD
3YRIC50:  5   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.99α = 90
b = 96.99β = 90
c = 80.772γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-11
    Type: Initial release