4WHH

A New Class of Peptidomimetics Targeting the Polo-box Domain of Polo-like kinase 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 2.0 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
  • Primary Citation of Related Structures:  

  • 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 PLK1
A
237Homo 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
C6H5(CH2)8-DERIVATIZED PEPTIDE INHIBITOR
B
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002127
Query on PRD_002127
BC6H5(CH2)8-derivatized peptide inhibitorPolypeptide / Enzyme inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.927α = 90.00
b = 58.300β = 90.00
c = 66.753γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing
ADSCdata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2014-09-22 
  • Released Date: 2014-12-03 
  • Deposition Author(s): Bang, J.K.

Funding OrganizationLocationGrant Number
Korea Basic Science InstituteKorea, Republic OfT34418
Rural Development AdministrationKorea, Republic OfPJ009594

Revision History 

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2015-01-21
    Type: Database references
  • Version 2.0: 2019-03-27
    Type: Data collection, Database references, Derived calculations, Other, Polymer sequence, Source and taxonomy