5KZI

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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 1.1 of the entry. See complete history


Literature

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: 10.1016/j.bmcl.2016.09.067
  • Primary Citation of Related Structures:  
    5KZI

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1A286Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6YN (Subject of Investigation/LOI)
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
MLPJIYXHHVPOPK-AWEZNQCLSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
6YN Binding MOAD:  5KZI IC50: 0.07 (nM) from 1 assay(s)
BindingDB:  5KZI IC50: min: 0.07, max: 403 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2016-07-25 
  • 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