4X7Q

PIM2 kinase in complex with Compound 1s


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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:  

  • 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. Electronic address: al_ishchenko@yahoo.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase pim-2
B, A
312Homo sapiensMutation(s): 0 
Gene Names: PIM2
EC: 2.7.11.1
Find proteins for Q9P1W9 (Homo sapiens)
Go to Gene View: PIM2
Go to UniProtKB:  Q9P1W9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
3YR
Query on 3YR

Download SDF File 
Download CCD File 
A, 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3YRIC50: 14 nM (100) BINDINGDB
3YRIC50: 14 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.196 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 142.265α = 90.00
b = 142.265β = 90.00
c = 61.750γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Database references, Derived calculations, Refinement description, Source and taxonomy