Crystal structure of Plk1 Polo-box domain in complex with PL-42

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.199 

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Development of cyclic peptomer inhibitors targeting the polo-box domain of polo-like kinase 1.

Murugan, R.N.Park, J.E.Lim, D.Ahn, M.Cheong, C.Kwon, T.Nam, K.Y.Choi, S.H.Kim, B.Y.Yoon, D.Y.Yaffe, M.B.Yu, D.Y.Lee, K.S.Bang, J.K.

(2013) Bioorg Med Chem 21: 2623-2634

  • DOI: https://doi.org/10.1016/j.bmc.2013.02.020
  • Primary Citation of Related Structures:  
    4HAB, 4HY2

  • PubMed Abstract: 

    The polo-box domain (PBD) of polo-like kinase 1 (Plk1) is essentially required for the function of Plk1 in cell proliferation. The availability of the phosphopeptide-binding pocket on PBD provides a unique opportunity to develop novel protein-protein interaction inhibitors. Recent identification of a minimal 5-residue-long phosphopeptide, PLHSpT, as a Plk1 PBD-specific ligand has led to the development of several peptide-based inhibitors, but none of them is cyclic peptide. Through the combination of single-peptoid mimics and thio-ether bridged cyclization, we successfully demonstrated for the first time two cyclic peptomers, PL-116 and PL-120, dramatically improved the binding affinity without losing mono-specificity against Plk1 PBD in comparison with the linear parental peptide, PLHSpT. These cyclic peptomers could serve as promising templates for future drug designs to inhibit Plk1 PBD.

  • Organizational Affiliation

    Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk 363-883, Cheongwon, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PLK1225Homo sapiensMutation(s): 0 
Gene Names: PLKPLK1
UniProt & NIH Common Fund Data Resources
Find proteins for P53350 (Homo sapiens)
Explore P53350 
Go to UniProtKB:  P53350
PHAROS:  P53350
GTEx:  ENSG00000166851 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53350
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PL-42B [auth D]7synthetic constructMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on TPO
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.4253α = 90
b = 50.2621β = 101.5152
c = 57.4562γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
SERGUIdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-03
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description, Source and taxonomy