4WSY | pdb_00004wsy

Crystal structure of human Pim-1 kinase in complex with a thiazolamine-indazole inhibitor.

• PDB DOI: https://doi.org/10.2210/pdb4WSY/pdb

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


• Deposited: 2014-10-28 Released: 2015-02-11 
• Deposition Author(s): Mohr, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.224 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Discovery of 5-(1H-indol-5-yl)-1,3,4-thiadiazol-2-amines as potent PIM inhibitors.

Wu, B., Wang, H.L., Cee, V.J., Lanman, B.A., Nixey, T., Pettus, L., Reed, A.B., Wurz, R.P., Guerrero, N., Sastri, C., Winston, J., Lipford, J.R., Lee, M.R., Mohr, C., Andrews, K.L., Tasker, A.S.

(2015) Bioorg Med Chem Lett 25: 775-780

• PubMed: 25616902 
• DOI: https://doi.org/10.1016/j.bmcl.2014.12.091
• Primary Citation Related Structures: 
  4WSY, 4WT6


• PubMed Abstract: 
  

  PIM kinases are a family of Ser/Thr kinases that are implicated in tumorigenesis. The discovery of a new class of PIM inhibitors, 5-(1H-indol-5-yl)-1,3,4-thiadiazol-2-amines, is discussed with optimized compounds showing excellent potency against all three PIM isoforms.

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Organizational Affiliation: 
• Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA. Electronic address: [e-mail].
Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA.
Department of Oncology, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA.
Department of Molecular Structure and Characterization, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.5 kDa 
• Atom Count: 2,336 
• Modeled Residue Count: 273 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-1	A	286	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3U5	B [auth A]	5-[3-(quinolin-3-yl)-2H-indazol-5-yl]-1,3-thiazol-2-amine C19 H13 N5 S GQCHSJRNLCGUAC-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.224 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.291	α = 90
b = 97.291	β = 90
c = 80.489	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
HKL-2000	data scaling
SCALEPACK	data scaling
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-11 
Deposition Author(s): Mohr, C.

Revision History  

• Version 1.0: 2015-02-11
  Type: Initial release
  
• Version 1.1: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Other, Source and taxonomy