4DFW

Oxime-based Post Solid-phase Peptide Diversification: Identification of High Affinity Polo-like Kinase 1 (Plk1) Polo-box Domain Binding Peptides


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Oxime-based Post Solid-phase Peptide Diversification: Identification of High Affinity Polo-like Kinase 1 (Plk1) Polo-box Domain Binding Peptides

Liu, F.Park, J.-E.Qian, W.-J.Lim, D.Scharow, A.Berg, T.Yaffe, M.B.Lee, K.S.Burke, T.R.

(2012) Chem.Biol. --: --

  • DOI: 10.1021/cb200469a

  • PubMed Abstract: 
  • In an effort to develop improved binding antagonists of the polo-like kinase 1 (Plk1) polo-box domain (PBD), we optimized interactions of the known high affinity 5-mer peptide PLHSpT using oxime-based post solid-phase peptide diversification of the N ...

    In an effort to develop improved binding antagonists of the polo-like kinase 1 (Plk1) polo-box domain (PBD), we optimized interactions of the known high affinity 5-mer peptide PLHSpT using oxime-based post solid-phase peptide diversification of the N-terminal Pro residue. This allowed us to achieve up to two orders of magnitude potency enhancement. An X-ray crystal structure of the highest affinity analogue in complex with Plk1 PBD revealed new binding interactions in a hydrophobic channel that had been occluded in X-ray structures of the unliganded protein. This study represents an important example where amino acid modification by post solid-phase oxime ligation can facilitate the development of protein-protein interaction inhibitors by identifying new binding pockets that would not otherwise be accessible to coded amino acid residues.


    Organizational Affiliation

    Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, USA.




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
Peptide
D
7N/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
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
D
NON-POLYMERH2 N

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TPO
Query on TPO
D
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
0LF
Query on 0LF
D
L-PEPTIDE LINKINGC15 H21 N O3PRO
ACE
Query on ACE
D
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.155 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 35.665α = 76.44
b = 34.844β = 86.95
c = 47.097γ = 69.14
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
StructureStudiodata collection
AMoREphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-28
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Database references, Structure summary