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 4O6W | pdb_00004o6w

Peptide-Based Inhibitors of Plk1 Polo-box Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.215 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4O6W

This is version 1.1 of the entry. See complete history. 

Literature

Mono-anionic phosphopeptides produced by unexpected histidine alkylation exhibit high plk1 polo-box domain-binding affinities and enhanced antiproliferative effects in hela cells.

Qian, W.J., Park, J.E., Lim, D., Lai, C.C., Kelley, J.A., Park, S.Y., Lee, K.W., Yaffe, M.B., Lee, K.S., Burke, T.R.

(2014) Biopolymers 102: 444-455

  • DOI: https://doi.org/10.1002/bip.22569
  • Primary Citation Related Structures: 
    4O6W

  • PubMed Abstract: 

    Binding of polo-like kinase 1 (Plk1) polo-box domains (PBDs) to phosphothreonine (pThr)/phosphoserine (pSer)-containing sequences is critical for the proper function of Plk1. Although high-affinity synthetic pThr-containing peptides provide starting points for developing PBD-directed inhibitors, to date the efficacy of such peptides in whole cell assays has been poor. This potentially reflects limited cell membrane permeability arising, in part, from the di-anionic nature of the phosphoryl group or its mimetics. In our current article we report the unanticipated on-resin N(τ)-alkylation of histidine residues already bearing a N(π)- alkyl group. This resulted in cationic imidazolium-containing pThr peptides, several of which exhibit single-digit nanomolar PBD-binding affinities in extracellular assays and improved antimitotic efficacies in intact cells. We enhanced the cellular efficacies of these peptides further by applying bio-reversible pivaloyloxymethyl (POM) phosphoryl protection. New structural insights presented in our current study, including the potential utility of intramolecular charge masking, may be useful for the further development of PBD-binding peptides and peptide mimetics.


  • Organizational Affiliation: 
    • Chemical Biology Laboratory, Center for Cancer Research, National Institutes of Health, NCI at Frederick, Frederick, MD, 21702.

Macromolecule Content 

  • Total Structure Weight: 28.22 kDa 
  • Atom Count: 2,144 
  • Modeled Residue Count: 224 
  • Deposited Residue Count: 244 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PLK1237Homo sapiensMutation(s): 0 
Gene Names: PLK1, PLK
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
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptide-Based inhibitorB [auth C]7N/AMutation(s): 0 
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
2SO
Query on 2SO
B [auth C]L-PEPTIDE LINKINGC24 H38 N3 O4HIS
TPO
Query on TPO
B [auth C]L-PEPTIDE LINKINGC4 H10 N O6 PTHR

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.215 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.819α = 90
b = 51.275β = 101.19
c = 58.006γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
AMoREphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Data collection, Database references, Derived calculations, Structure summary