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 

wwPDB Validation 3D Report Full Report


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:  

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase PLK1
A, B, C
223Homo sapiensMutation(s): 0 
Gene Names: PLK1 (PLK)
EC: 2.7.11.21
Find proteins for P53350 (Homo sapiens)
Go to Gene View: PLK1
Go to UniProtKB:  P53350
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PL-49
D, E, F
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CXS
Query on CXS
Download SDF File 
Download CCD File 
A, B, C
3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
C9 H19 N O3 S
PJWWRFATQTVXHA-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000780
Query on PRD_000780		D,E,FPL-49Peptide-like / Enzyme inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.260 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 95.043α = 90.00
b = 95.043β = 90.00
c = 240.580γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
SERGUIdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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