4HAB

Crystal structure of Plk1 Polo-box domain in complex with PL-49

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.260 

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This is version 1.2 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: 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 ...

    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.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PLK1A, B, C223Homo sapiensMutation(s): 0 
Gene Names: PLK, PLK1
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
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PL-49D, E, F7synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
11Q
Query on 11Q		D, E, F L-PEPTIDE LINKINGC12 H21 N O2PRO
TPO
Query on TPO		D, E, F L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000780
Query on PRD_000780		D, E, FPL-49Peptide-like / Enzyme inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.260 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.043α = 90
b = 95.043β = 90
c = 240.58γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
CNSrefinement
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