4WT6 | pdb_00004wt6

Crystal structure of human Pim-1 kinase in complex with a thiadiazolamine-indole inhibitor.

• PDB DOI: https://doi.org/10.2210/pdb4WT6/pdb

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


• Deposited: 2014-10-29 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: 
  0.211 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (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 of 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].

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 33.53 kDa 
• Atom Count: 2,401 
• Modelled 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
3U6	B [auth A]	6-[5-(5-amino-1,3,4-thiadiazol-2-yl)-1H-indol-3-yl]-N-cyclopentylpyridin-2-amine C20 H20 N6 S LYSVYDGAEVIKAF-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3U6	BindingDB:  4WT6	IC50: min: 12, max: 111 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.211 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.184	α = 90
b = 98.184	β = 90
c = 80.8	γ = 120

Software Package:

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

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, Structure summary