4DTK | pdb_00004dtk

Novel and selective pan-PIM kinase inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4DTK/pdb

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


• Deposited: 2012-02-21 Released: 2012-07-11 
• Deposition Author(s): Ferguson, A.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.182 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Literature

Discovery of novel benzylidene-1,3-thiazolidine-2,4-diones as potent and selective inhibitors of the PIM-1, PIM-2, and PIM-3 protein kinases.

Dakin, L.A., Block, M.H., Chen, H., Code, E., Dowling, J.E., Feng, X., Ferguson, A.D., Green, I., Hird, A.W., Howard, T., Keeton, E.K., Lamb, M.L., Lyne, P.D., Pollard, H., Read, J., Wu, A.J., Zhang, T., Zheng, X.

(2012) Bioorg Med Chem Lett 22: 4599-4604

• PubMed: 22727640 
• DOI: https://doi.org/10.1016/j.bmcl.2012.05.098
• Primary Citation Related Structures: 
  4DTK


• PubMed Abstract: 
  

  Novel substituted benzylidene-1,3-thiazolidine-2,4-diones (TZDs) have been identified as potent and highly selective inhibitors of the PIM kinases. The synthesis and SAR of these compounds are described, along with X-ray crystallographic, anti-proliferative, and selectivity data.

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Organizational Affiliation: 
• Oncology iMed Sciences Group, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA.

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: 32.89 kDa 
• Atom Count: 2,494 
• Modeled Residue Count: 273 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-1	A	276	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7LI	I [auth A]	(5Z)-5-{2-[(3R)-3-aminopiperidin-1-yl]-3-(propan-2-yloxy)benzylidene}-1,3-thiazolidine-2,4-dione C18 H23 N3 O3 S ULMRMVZQMKZWKJ-MLJKTZRHSA-N
SO4	J [auth A], K [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.182 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.444	α = 90
b = 97.444	β = 90
c = 81.363	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
BUSTER	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-11 
Deposition Author(s): Ferguson, A.D.

Revision History  

• Version 1.0: 2012-07-11
  Type: Initial release
  
• Version 1.1: 2012-07-25
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations