4X7Q

PIM2 kinase in complex with Compound 1s

• PDB DOI: https://doi.org/10.2210/pdb4X7Q/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-12-09 Released: 2015-02-11 
• Deposition Author(s): Marcotte, D.J., Silvian, L.F.

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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 

Starting Model: experimental

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

• PubMed: 25575657 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

Biogen Idec, 14 Cambridge Center, Cambridge, MA 02142, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 69.53 kDa 
• Atom Count: 3,680 
• Modelled Residue Count: 460 
• Deposited Residue Count: 624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-2	A [auth B], B [auth A]	312	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3YR	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
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
3YR	BindingDB:  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 = 142.265	α = 90
b = 142.265	β = 90
c = 61.75	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-11 
Deposition Author(s): Marcotte, D.J., Silvian, L.F.

Revision History  

• 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
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description