4LKM

Crystal structure of Plk1 Polo-box domain in complex with PL-74


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Exploring the binding nature of pyrrolidine pocket-dependent interactions in the polo-box domain of polo-like kinase 1

Murugan, R.N.Ahn, M.Lee, W.C.Kim, H.Y.Song, J.H.Cheong, C.Hwang, E.Seo, J.H.Shin, S.Y.Choi, S.H.Park, J.E.Bang, J.K.

(2013) Plos One 8: e80043-e80043

  • DOI: 10.1371/journal.pone.0080043
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Over the years, a great deal of effort has been focused on the design and synthesis of potent, linear peptide inhibitors targeting the polo-like kinase 1 (Plk1), which is critically involved in multiple mitotic processes and has been established as a ...

    Over the years, a great deal of effort has been focused on the design and synthesis of potent, linear peptide inhibitors targeting the polo-like kinase 1 (Plk1), which is critically involved in multiple mitotic processes and has been established as an adverse prognostic marker for tumor patients. Plk1 localizes to its intracellular anchoring sites via its polo-box domain, and inhibiting the Plk1 polo-box domain has been considered as an approach to circumvent the specificity problems associated with inhibiting the conserved adenosine triphosphate-binding pocket. The polo-box domain consists of two different binding regions, such as the unique, broader pyrrolidine-binding pocket and the conserved, narrow, Tyr-rich hydrophobic channel, among the three Plk polo-box domains (Plks 1-3), respectively. Therefore, the studies that provide insights into the binding nature of the unique, broader pyrrolidine-binding pocket might lead to the development of selective Plk1-inhibitory compounds.


    Organizational Affiliation

    Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase PLK1
A, C
231Homo 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
PL-74
B, D
8N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
5PV
Query on 5PV

Download SDF File 
Download CCD File 
B
5-PHENYLVALERIC ACID
C11 H14 O2
BYHDDXPKOZIZRV-UHFFFAOYSA-N
 Ligand Interaction
LYT
Query on LYT

Download SDF File 
Download CCD File 
B
BUTYLAMINE
C4 H11 N
HQABUPZFAYXKJW-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 2 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001159
Query on PRD_001159
BPL-74Peptide-like / Inhibitor

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PRD_001159
Query on PRD_001159
B,DPL-74Peptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.202 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 79.600α = 90.00
b = 82.000β = 90.00
c = 151.720γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
MOLREPphasing
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-11
    Type: Initial release