Crystal structure of human Pim-1 kinase in complex with an aminooxadiazole-indole inhibitor.

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


The discovery and optimization of aminooxadiazoles as potent Pim kinase inhibitors.

Wurz, R.P.Pettus, L.H.Jackson, C.Wu, B.Wang, H.L.Herberich, B.Cee, V.Lanman, B.A.Reed, A.B.Chavez, F.Nixey, T.Laszlo, J.Wang, P.Nguyen, Y.Sastri, C.Guerrero, N.Winston, J.Lipford, J.R.Lee, M.R.Andrews, K.L.Mohr, C.Xu, Y.Zhou, Y.Reid, D.L.Tasker, A.S.

(2015) Bioorg Med Chem Lett 25: 847-855

  • DOI: https://doi.org/10.1016/j.bmcl.2014.12.067
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    High levels of Pim expression have been implicated in several hematopoietic and solid tumor cancers. These findings suggest that inhibition of Pim signaling by a small molecule Pim-1,2 inhibitor could provide patients with therapeutic benefit. Herein, we describe our progress towards this goal starting from the highly Pim-selective indole-thiadiazole compound (1), which was derived from a nonselective hit identified in a high throughput screening campaign. Optimization of this compound's potency and its pharmacokinetic properties resulted in the discovery of compound 29. Cyclopropane 29 was found to exhibit excellent enzymatic potency on the Pim-1 and Pim-2 isoforms (Ki values of 0.55nM and 0.28nM, respectively), and found to inhibit the phosphorylation of BAD in the Pim-overexpressing KMS-12 cell line (IC50=150nM). This compound had moderate clearance and bioavailability in rat (CL=2.42L/kg/h; %F=24) and exhibited a dose-dependent inhibition of p-BAD in KMS-12 tumor pharmacodynamic (PD) model with an EC50 value of 6.74μM (18μg/mL) when dosed at 10, 30, 100 and 200mg/kg po in mice.

  • Organizational Affiliation

    Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA. Electronic address: rwurz@amgen.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1286Homo sapiensMutation(s): 0 
Gene Names: PIM1
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens)
Explore P11309 
Go to UniProtKB:  P11309
PHAROS:  P11309
GTEx:  ENSG00000137193 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11309
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 38W

Download Ideal Coordinates CCD File 
B [auth A]N-tert-butyl-5-[3-(4-cyclopropylpyrimidin-2-yl)-1H-indol-5-yl]-1,3,4-oxadiazol-2-amine
C21 H22 N6 O
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
38W BindingDB:  4TY1 IC50: 1.58 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.081α = 90
b = 95.081β = 90
c = 80.842γ = 120
Software Package:
Software NamePurpose

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2015-02-04 
  • Deposition Author(s): Mohr, C.

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-02-18
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Refinement description