4XHK | pdb_00004xhk

PIM1 kinase in complex with Compound 1s

• PDB DOI: https://doi.org/10.2210/pdb4XHK/pdb

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


• Deposited: 2015-01-05 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: 1.90 Å
• R-Value Free: 
  0.184 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

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 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].
Biogen Idec, 14 Cambridge Center, Cambridge, MA 02142, USA.
Biogen Idec, 14 Cambridge Center, Cambridge, MA 02142, USA; EMD Serono Research and Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA.
Biogen Idec, 14 Cambridge Center, Cambridge, MA 02142, USA; Department of Chemistry, Keimyung University, 1095 Dalgubeoldaero, Dalseo-Gu, Daegu 704-701, Republic of Korea.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 36.37 kDa 
• Atom Count: 2,507 
• Modeled Residue Count: 270 
• Deposited Residue Count: 315 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-1	A [auth B]	315	Homo sapiens	Mutation(s): 0  Gene Names: PIM1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens) Explore P11309  Go to UniProtKB:  P11309
PHAROS:  P11309 GTEx:  ENSG00000137193

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3YR	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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A [auth B]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.184 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.99	α = 90
b = 96.99	β = 90
c = 80.772	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
HKL-2000	data reduction

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: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2024-10-16
  Changes: Structure summary