4HCO

Human Plk1-PBD in complex with Thymoquinone at the phophopeptide binding site

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


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


Literature

Thymoquinone Blocks pSer/pThr Recognition by Plk1 Polo-Box Domain As a Phosphate Mimic

Yin, Z., Song, Y., Rehse, P.H.

(2013) ACS Chem Biol 8: 303-308

  • DOI: 10.1021/cb3004379
  • Primary Citation of Related Structures:  
    4H5X, 4H71, 4HCO

  • PubMed Abstract: 

    • Phosphorylation-dependent protein-protein interaction has rarely been targeted in medicinal chemistry. Thymoquinone, a naturally occurring antitumor agent, disrupts prephosphorylated substrate recognition by the polo-box domain of polo-like kinase 1, a key mitotic regulator responsible for various carcinogenesis when overexpressed ...

    Phosphorylation-dependent protein-protein interaction has rarely been targeted in medicinal chemistry. Thymoquinone, a naturally occurring antitumor agent, disrupts prephosphorylated substrate recognition by the polo-box domain of polo-like kinase 1, a key mitotic regulator responsible for various carcinogenesis when overexpressed. Here, crystallographic studies reveal that the phosphoserine/phosphothreonine recognition site of the polo-box domain is the binding pocket for thymoquinone and its analogue poloxime. Both small molecules displace phosphopeptides bound with the polo-box domain in a slow but noncovalent binding mode. A conserved water bridge and a cation-π interaction were found as their competition strategy against the phosphate group. This mechanism sheds light on small-molecule intervention of phospho-recognition by the polo-box domain of polo-like kinase 1 and other phospho-binding proteins in general.

    Organizational Affiliation: 

    School of Life Science and Technology, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, Jiangsu 210009, China.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PLK1 A, B240Homo sapiensMutation(s): 0 
Gene Names: PLK1, PLK
EC: 2.7.11.21
Find proteins for P53350 (Homo sapiens)
Explore P53350 
Go to UniProtKB:  P53350
NIH Common Fund Data Resources
PHAROS:  P53350
GTEx:  ENSG00000166851
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMW
Query on IMW
Download Ideal Coordinates CCD File 
A
2-methyl-5-(1-methylethyl)cyclohexa-2,5-diene-1,4-dione
C10 H12 O2
KEQHJBNSCLWCAE-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IMWIC50 :  47380   nM  PDBBind
IMWIC50:  2180   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.26α = 90
b = 102.15β = 93.96
c = 67.74γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2012-10-01 
  • Released Date: 2012-10-10 
    • Deposition Author(s): Yin, Z., Rehse, P.H.
  • This entry supersedes: 4H70

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2013-03-06
    Changes: Database references