4YUR

Crystal Structure of Plk4 Kinase Domain Bound to Centrinone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

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This is version 1.1 of the entry. See complete history


Literature

Cell biology. Reversible centriole depletion with an inhibitor of Polo-like kinase 4.

Wong, Y.L.Anzola, J.V.Davis, R.L.Yoon, M.Motamedi, A.Kroll, A.Seo, C.P.Hsia, J.E.Kim, S.K.Mitchell, J.W.Mitchell, B.J.Desai, A.Gahman, T.C.Shiau, A.K.Oegema, K.

(2015) Science 348: 1155-1160

  • DOI: https://doi.org/10.1126/science.aaa5111
  • Primary Citation of Related Structures:  
    4YUR

  • PubMed Abstract: 

    Centrioles are ancient organelles that build centrosomes, the major microtubule-organizing centers of animal cells. Extra centrosomes are a common feature of cancer cells. To investigate the importance of centrosomes in the proliferation of normal and cancer cells, we developed centrinone, a reversible inhibitor of Polo-like kinase 4 (Plk4), a serine-threonine protein kinase that initiates centriole assembly. Centrinone treatment caused centrosome depletion in human and other vertebrate cells. Centrosome loss irreversibly arrested normal cells in a senescence-like G1 state by a p53-dependent mechanism that was independent of DNA damage, stress, Hippo signaling, extended mitotic duration, or segregation errors. In contrast, cancer cell lines with normal or amplified centrosome numbers could proliferate indefinitely after centrosome loss. Upon centrinone washout, each cancer cell line returned to an intrinsic centrosome number "set point." Thus, cells with cancer-associated mutations fundamentally differ from normal cells in their response to centrosome loss.


  • Organizational Affiliation

    Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PLK4278Homo sapiensMutation(s): 0 
Gene Names: PLK4SAKSTK18
EC: 2.7.11.21
UniProt & NIH Common Fund Data Resources
Find proteins for O00444 (Homo sapiens)
Explore O00444 
Go to UniProtKB:  O00444
PHAROS:  O00444
GTEx:  ENSG00000142731 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00444
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4J7
Query on 4J7

Download Ideal Coordinates CCD File 
B [auth A]2-({2-fluoro-4-[(2-fluoro-3-nitrobenzyl)sulfonyl]phenyl}sulfanyl)-5-methoxy-N-(3-methyl-1H-pyrazol-5-yl)-6-(morpholin-4-yl)pyrimidin-4-amine
C26 H25 F2 N7 O6 S2
HHJSKDRCUMVWKF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.805α = 90
b = 125.805β = 90
c = 125.805γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy