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 
  • R-Value Observed: 0.199 

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Ligand Structure Quality Assessment 


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:  
    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 based modeling ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-2B [auth A],
A [auth B]		312Homo sapiensMutation(s): 0 
Gene Names: PIM2
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3YR
Query on 3YR
Download Ideal Coordinates CCD File 
C [auth B],
D [auth A]		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
PO4
Query on PO4
Download Ideal Coordinates CCD File 
E [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3YR BindingDB:  4X7Q IC50: 14 (nM) from 1 assay(s)
Binding MOAD:  4X7Q IC50: 14 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.265α = 90
b = 142.265β = 90
c = 61.75γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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