3VKX

Structure of PCNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Identification of small molecule proliferating cell nuclear antigen (PCNA) inhibitor that disrupts interactions with PIP-box proteins and inhibits DNA replication

Punchihewa, C.Inoue, A.Hishiki, A.Fujikawa, Y.Connelly, M.Evison, B.Shao, Y.Heath, R.Kuraoka, I.Rodrigues, P.Hashimoto, H.Kawanishi, M.Sato, M.Yagi, T.Fujii, N.

(2012) J Biol Chem 287: 14289-14300

  • DOI: https://doi.org/10.1074/jbc.M112.353201
  • Primary Citation of Related Structures:  
    3VKX

  • PubMed Abstract: 

    We have discovered that 3,3',5-triiodothyronine (T3) inhibits binding of a PIP-box sequence peptide to proliferating cell nuclear antigen (PCNA) protein by competing for the same binding site, as evidenced by the co-crystal structure of the PCNA-T3 complex at 2.1 Å resolution. Based on this observation, we have designed a novel, non-peptide small molecule PCNA inhibitor, T2 amino alcohol (T2AA), a T3 derivative that lacks thyroid hormone activity. T2AA inhibited interaction of PCNA/PIP-box peptide with an IC(50) of ~1 μm and also PCNA and full-length p21 protein, the tightest PCNA ligand protein known to date. T2AA abolished interaction of PCNA and DNA polymerase δ in cellular chromatin. De novo DNA synthesis was inhibited by T2AA, and the cells were arrested in S-phase. T2AA inhibited growth of cancer cells with induction of early apoptosis. Concurrently, Chk1 and RPA32 in the chromatin are phosphorylated, suggesting that T2AA causes DNA replication stress by stalling DNA replication forks. T2AA significantly inhibited translesion DNA synthesis on a cisplatin-cross-linked template in cells. When cells were treated with a combination of cisplatin and T2AA, a significant increase in phospho(Ser(139))histone H2AX induction and cell growth inhibition was observed.


  • Organizational Affiliation

    Department of Chemical Biology and Therapeutics, St Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proliferating cell nuclear antigen261Homo sapiensMutation(s): 0 
Gene Names: PCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P12004 (Homo sapiens)
Explore P12004 
Go to UniProtKB:  P12004
PHAROS:  P12004
GTEx:  ENSG00000132646 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12004
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T3
Query on T3

Download Ideal Coordinates CCD File 
B [auth A]3,5,3'TRIIODOTHYRONINE
C15 H12 I3 N O4
AUYYCJSJGJYCDS-LBPRGKRZSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
T3 BindingDB:  3VKX IC50: 3600 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.107α = 90
b = 143.107β = 90
c = 143.107γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2013-08-14
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection