4RCP

Crystal structure of Plk1 Polo-box domain in complex with PL-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A new class of peptidomimetics targeting the polo-box domain of polo-like kinase 1.

Ahn, M.Han, Y.H.Park, J.E.Kim, S.Lee, W.C.Lee, S.J.Gunasekaran, P.Cheong, C.Shin, S.Y.Kim, H.Y.Ryu, E.K.Murugan, R.N.Kim, N.H.Bang, J.K.

(2015) J Med Chem 58: 294-304

  • DOI: 10.1021/jm501147g
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Recent progress in the development of peptide-derived Polo-like kinase (Plk1) polo-box domain (PBD) inhibitors has led to the synthesis of multiple peptide ligands with high binding affinity and selectivity. However, few systematic analyses have been ...

    Recent progress in the development of peptide-derived Polo-like kinase (Plk1) polo-box domain (PBD) inhibitors has led to the synthesis of multiple peptide ligands with high binding affinity and selectivity. However, few systematic analyses have been conducted to identify key Plk1 residues and characterize their interactions with potent Plk1 peptide inhibitors. We performed systematic deletion analysis using the most potent 4j peptide and studied N-terminal capping of the minimal peptide with diverse organic moieties, leading to the identification of the peptidomimetic 8 (AB-103) series with high binding affinity and selectivity. To evaluate the bioavailability of short peptidomimetic ligands, PEGylated 8 series were synthesized and incubated with HeLa cells to test for cellular uptake, antiproliferative activity, and Plk1 kinase inhibition. Finally, crystallographic studies of the Plk1 PBD in complex with peptidomimetics 8 and 22 (AB-103-5) revealed the presence of two hydrogen bond interactions responsible for their high binding affinity and selectivity.


    Organizational Affiliation

    Division of Magnetic Resonance, Korea Basic Science Institute , 804-1, Yangcheong Ri, Ochang, Chungbuk, Cheongwon 363-883, Republic of Korea.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase PLK1A228Homo sapiensMutation(s): 0 
Gene Names: PLKPLK1
EC: 2.7.11.21
Find proteins for P53350 (Homo sapiens)
Explore P53350 
Go to UniProtKB:  P53350
NIH Common Fund Data Resources
PHAROS  P53350
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PL-2B5N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001254
Query on PRD_001254
BPL-2P /  Inhibitor

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Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
56A
Query on 56A
BL-PEPTIDE LINKINGC20 H29 N3 O2HIS
TPO
Query on TPO
BL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.39α = 90
b = 61.27β = 103.27
c = 51.26γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2014-11-19
    Changes: Structure summary
  • Version 1.2: 2015-01-21
    Changes: Database references