4HY2 | pdb_00004hy2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.246 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.196 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4HY2

This is version 1.3 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 27 kDa 
  • Atom Count: 1,891 
  • Modeled Residue Count: 222 
  • Deposited Residue Count: 232 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PLK1225Homo sapiensMutation(s): 0 
Gene Names: PLKPLK1
EC: 2.7.11.21
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
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PL-42B [auth D]7synthetic constructMutation(s): 0 

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
1C3
Query on 1C3
B [auth D]L-PEPTIDE LINKINGC15 H21 N O5

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TPO
Query on TPO
B [auth D]L-PEPTIDE LINKINGC4 H10 N O6 PTHR

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.246 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.196 (DCC) 
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
CNSrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection

Structure Validation

View Full Validation Report



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
  • Version 1.3: 2025-03-26
    Changes: Data collection, Database references, Derived calculations, Structure summary