Crystal structure of human Pim-1 kinase in complex with an azaspiro pyrazinyl-indazole inhibitor.

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


The discovery of novel 3-(pyrazin-2-yl)-1H-indazoles as potent pan-Pim kinase inhibitors.

Wang, H.L.Cee, V.J.Chavez, F.Lanman, B.A.Reed, A.B.Wu, B.Guerrero, N.Lipford, J.R.Sastri, C.Winston, J.Andrews, K.L.Huang, X.Lee, M.R.Mohr, C.Xu, Y.Zhou, Y.Tasker, A.S.

(2015) Bioorg Med Chem Lett 25: 834-840

  • DOI: https://doi.org/10.1016/j.bmcl.2014.12.068
  • Primary Citation of Related Structures:  
    4RPV, 4WRS

  • PubMed Abstract: 

    The three Pim kinases are a small family of serine/threonine kinases regulating several signaling pathways that are fundamental to tumorigenesis. As such, the Pim kinases are a very attractive target for pharmacological inhibition in cancer therapy. Herein, we describe our efforts toward the development of a potent, pan-Pim inhibitor. The synthesis and hit-to-lead SAR development from a 3-(pyrazin-2-yl)-1H-indazole derived hit 2 to the identification of a series of potent, pan-Pim inhibitors such as 13o are described.

  • Organizational Affiliation

    Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA. Electronic address: huiw@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 3U1

Download Ideal Coordinates CCD File 
D [auth A]3-{6-[(4R)-6-azaspiro[2.5]oct-4-yloxy]pyrazin-2-yl}-5-(2,6-difluorophenyl)-1H-indazole
C24 H21 F2 N5 O
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
C3 H8 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
3U1 BindingDB:  4WRS IC50: min: 0.4, max: 1 (nM) from 2 assay(s)
Binding MOAD:  4WRS IC50: 0.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.815α = 90
b = 97.815β = 90
c = 80.585γ = 120
Software Package:
Software NamePurpose

Structure Validation

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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: 2015-02-11
    Changes: Database references
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Other, Source and taxonomy, Structure summary