Crystal structure of Pim1 with Quercetagetin

Experimental Data Snapshot

  • Resolution: 2.44 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Characterization of a potent and selective small-molecule inhibitor of the PIM1 kinase.

Holder, S.Zemskova, M.Zhang, C.Tabrizizad, M.Bremer, R.Neidigh, J.W.Lilly, M.B.

(2007) Mol Cancer Ther 6: 163-172

  • DOI: https://doi.org/10.1158/1535-7163.MCT-06-0397
  • Primary Citation of Related Structures:  
    2O3P, 2O63, 2O64, 2O65

  • PubMed Abstract: 

    The pim-1 kinase is a true oncogene that has been implicated in the development of leukemias, lymphomas, and prostate cancer, and is the target of drug development programs. We have used experimental approaches to identify a selective, cell-permeable, small-molecule inhibitor of the pim-1 kinase to foster basic and translational studies of the enzyme. We used an ELISA-based kinase assay to screen a diversity library of potential kinase inhibitors. The flavonol quercetagetin (3,3',4',5,6,7-hydroxyflavone) was identified as a moderately potent, ATP-competitive inhibitor (IC(50), 0.34 micromol/L). Resolution of the crystal structure of PIM1 in complex with quercetagetin or two other flavonoids revealed a spectrum of binding poses and hydrogen-bonding patterns in spite of strong similarity of the ligands. Quercetagetin was a highly selective inhibitor of PIM1 compared with PIM2 and seven other serine-threonine kinases. Quercetagetin was able to inhibit PIM1 activity in intact RWPE2 prostate cancer cells in a dose-dependent manner (ED(50), 5.5 micromol/L). RWPE2 cells treated with quercetagetin showed pronounced growth inhibition at inhibitor concentrations that blocked PIM1 kinase activity. Furthermore, the ability of quercetagetin to inhibit the growth of other prostate epithelial cell lines varied in proportion to their levels of PIM1 protein. Quercetagetin can function as a moderately potent and selective, cell-permeable inhibitor of the pim-1 kinase, and may be useful for proof-of-concept studies to support the development of clinically useful PIM1 inhibitors.

  • Organizational Affiliation

    Center for Molecular Biology and Gene Therapy, Loma Linda University School of Medicine, 11234 Anderson Street, Loma Linda, CA 92354, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proto-oncogene serine/threonine-protein kinase Pim-1293Homo 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 MYU

Download Ideal Coordinates CCD File 
C15 H10 O8
Query on IMD

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
C3 H5 N2
Binding Affinity Annotations 
IDSourceBinding Affinity
MYU Binding MOAD:  2O64 IC50: 340 (nM) from 1 assay(s)
PDBBind:  2O64 IC50: 340 (nM) from 1 assay(s)
BindingDB:  2O64 IC50: min: 339, max: 340 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.44 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.755α = 90
b = 97.755β = 90
c = 80.97γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations