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 8WFP | pdb_00008wfp

Crystal structure of polo-like kinase(PLK1)PBD in complex with DD-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 
    0.229 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8WFP

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

Literature

Degradation of Polo-like Kinase 1 by the Novel Poly-Arginine N-Degron Pathway PROTAC Regulates Tumor Growth in Nonsmall Cell Lung Cancer.

Gunasekaran, P., Hwang, Y.S., Lee, G.H., Park, J., Kim, J.G., La, Y.K., Park, N.Y., Kothandaraman, R., Yim, M.S., Choi, J., Kim, H.N., Park, I.Y., Lee, S.J., Kim, M.H., Cha-Molstad, H., Shin, S.Y., Ryu, E.K., Bang, J.K.

(2024) J Med Chem 67: 3307-3320

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01493
  • Primary Citation Related Structures: 
    8WFP

  • PubMed Abstract: 

    Polo-like kinase 1 (PLK1), which is crucial in cell cycle regulation, is considered a promising anticancer drug target. Herein, we present the N-degron pathway-based proteolysis targeting chimera (PROTAC) for PLK1 degradation, targeting the Polo-box domain (PBD). We identified DD-2 as the most potent PROTAC that selectively induces PLK1 degradation in cancer cells, including HeLa and nonsmall cell lung cancer (NSCLC), through the N-degron pathway. DD-2 exhibited significant in vitro anticancer effects, inducing G2/M arrest and apoptosis in HeLa and NSCLC cell lines. DD-2 showed significant tumor growth inhibition in a xenograft mouse model using HeLa and NSCLC cell lines, highlighting its potential in cancer treatment. Furthermore, the combination of DD-2 with tyrosine kinase inhibitor (TKI), osimertinib, effectively suppressed tumor growth in double-mutated H1975 cell lines, emphasizing DD-2's potential in combination cancer therapies. Collectively, this study demonstrates the potential of the N-degron pathway, especially using DD-2, for targeted cancer therapies.


  • Organizational Affiliation: 
    • Division of Magnetic Resonance, Korea Basic Science Institute (KBSI), Ochang, Chungbuk 28119, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 53.42 kDa 
  • Atom Count: 3,961 
  • Modeled Residue Count: 465 
  • Deposited Residue Count: 466 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PLK1
A, B
226Homo 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
DD-1
C, D
7Homo sapiensMutation(s): 0 
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains Modified ResidueModification TypeFormula2D Diagram
TPO
Query on TPO
C, D
THRPhosphorylationC4 H10 N O6 P

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.229 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.829α = 90
b = 35.37β = 89.98
c = 95.545γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHENIXphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2022E0701018

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-25
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary