4WRS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1016/j.bmcl.2014.12.068
  • Primary Citation of Related Structures:  

  • 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. ...

    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.,Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA. Electronic address: vcee@amgen.com.,Department of Oncology, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA.,Department of Molecular Structure and Characterization, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA.,Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA.,Department of Pharmacokinetics and Drug Metabolism, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase pim-1
A
286Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Go to Gene View: PIM1
Go to UniProtKB:  P11309
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3U1
Query on 3U1

Download SDF File 
Download CCD File 
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
FCGLYPSBPNFQRF-FQEVSTJZSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3U1IC50: 0.4 - 1 nM (100) BINDINGDB
3U1IC50: 0.4 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.179 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 97.815α = 90.00
b = 97.815β = 90.00
c = 80.585γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-10-25 
  • Released Date: 2015-02-04 
  • Deposition Author(s): Mohr, C.

Revision History 

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-02-11
    Type: Database references