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

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Discovery of imidazopyridazines as potent Pim-1/2 kinase inhibitors.

Wurz, R.P.Sastri, C.D'Amico, D.C.Herberich, B.Jackson, C.L.Pettus, L.H.Tasker, A.S.Wu, B.Guerrero, N.Lipford, J.R.Winston, J.T.Yang, Y.Wang, P.Nguyen, Y.Andrews, K.L.Huang, X.Lee, M.R.Mohr, C.Zhang, J.D.Reid, D.L.Xu, Y.Zhou, Y.Wang, H.L.

(2016) Bioorg Med Chem Lett 26: 5580-5590

  • DOI: https://doi.org/10.1016/j.bmcl.2016.09.067
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    High levels of Pim expression have been implicated in several hematopoietic and solid tumor cancers, suggesting that inhibition of Pim signaling could provide patients with therapeutic benefit. Herein, we describe our progress towards this goal using a screening hit (rac-1) as a starting point. Modification of the indazole ring resulted in the discovery of a series of imidazopyridazine-based Pim inhibitors exemplified by compound 22m, which was found to be a subnanomolar inhibitor of the Pim-1 and Pim-2 isoforms (IC 50 values of 0.024nM and 0.095nM, respectively) and to potently inhibit the phosphorylation of BAD in a cell line that expresses high levels of all Pim isoforms, KMS-12-BM (IC 50 =28nM). Profiling of Pim-1 and Pim-2 expression levels in a panel of multiple myeloma cell lines and correlation of these data with the potency of compound 22m in a proliferation assay suggests that Pim-2 inhibition would be advantageous for this indication.

  • 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 6YN

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[4-[(3~{S})-3-azanylpiperidin-1-yl]pyridin-3-yl]-2-[2,6-bis(fluoranyl)phenyl]imidazo[1,5-b]pyridazin-7-amine
C22 H21 F2 N7
Binding Affinity Annotations 
IDSourceBinding Affinity
6YN Binding MOAD:  5KZI IC50: 0.07 (nM) from 1 assay(s)
BindingDB:  5KZI IC50: min: 0.07, max: 0.08 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.998α = 90
b = 95.998β = 90
c = 81.251γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2016-11-09 
  • Deposition Author(s): Mohr, C.

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references