4WHL

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

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 PLK1
A
237Homo sapiensMutation(s): 0 
Gene Names: PLK1PLK
EC: 2.7.11.21
Find proteins for P53350 (Homo sapiens)
Go to UniProtKB:  P53350
NIH Common Fund Data Resources
PHAROS  P53350
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
C6H5(CH2)8-DERIVATIZED PEPTIDE INHIBITOR
B
5synthetic constructMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002126
Query on PRD_002126
BC6H5(CH2)8-derivatized peptide inhibitorPolypeptide /  Enzyme inhibitor

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.76α = 90
b = 57.76β = 90
c = 137.568γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
ADSCdata collection
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing
HKLdata reduction
HKLdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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
    Changes: Database references
  • Version 1.2: 2015-02-11
    Changes: Structure summary