6CBI

PCNA in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Rational Design of a 310-Helical PIP-Box Mimetic Targeting PCNA, the Human Sliding Clamp.

Wegener, K.L.McGrath, A.E.Dixon, N.E.Oakley, A.J.Scanlon, D.B.Abell, A.D.Bruning, J.B.

(2018) Chemistry 24: 11325-11331

  • DOI: 10.1002/chem.201801734
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The human sliding clamp (PCNA) controls access to DNA for many proteins involved in DNA replication and repair. Proteins are recruited to the PCNA surface by means of a short, conserved peptide motif known as the PCNA-interacting protein box (PIP-box ...

    The human sliding clamp (PCNA) controls access to DNA for many proteins involved in DNA replication and repair. Proteins are recruited to the PCNA surface by means of a short, conserved peptide motif known as the PCNA-interacting protein box (PIP-box). Inhibitors of these essential protein-protein interactions may be useful as cancer therapeutics by disrupting DNA replication and repair in these highly proliferative cells. PIP-box peptide mimetics have been identified as a potentially rapid route to potent PCNA inhibitors. Here we describe the rational design and synthesis of the first PCNA peptidomimetic ligands, based on the high affinity PIP-box sequence from the natural PCNA inhibitor p21. These mimetics incorporate covalent i,i+4 side-chain/side-chain lactam linkages of different lengths, designed to constrain the peptides into the 3 10 -helical structure required for PCNA binding. NMR studies confirmed that while the unmodified p21 peptide had little defined structure in solution, mimetic ACR2 pre-organized into 3 10 -helical structure prior to interaction with PCNA. ACR2 displayed higher affinity binding than most known PIP-box peptides, and retains the native PCNA binding mode, as observed in the co-crystal structure of ACR2 bound to PCNA. This study offers a promising new strategy for PCNA inhibitor design for use as anti-cancer therapeutics.


    Organizational Affiliation

    Institute for Photonics and Advanced Sensing (IPAS), Department of Chemistry, and the Centre for Nanoscale BioPhotonics, The University of Adelaide, South Australia, 5005, Australia.,Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, NSW, 2522, Australia.,Department of Chemistry, The University of Adelaide, South Australia, 5005, Australia.,Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proliferating cell nuclear antigen
A, C, E, B, D, F
261Homo sapiensMutation(s): 0 
Gene Names: PCNA
Find proteins for P12004 (Homo sapiens)
Go to Gene View: PCNA
Go to UniProtKB:  P12004
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS
H, I, J, K
14Homo sapiensMutation(s): 0 
Gene Names: CDKN1A (CAP20, CDKN1, CIP1, MDA6, PIC1, SDI1, WAF1)
Find proteins for P38936 (Homo sapiens)
Go to Gene View: CDKN1A
Go to UniProtKB:  P38936
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DAB
Query on DAB
H, I, J, K
L-PEPTIDE LINKINGC4 H10 N2 O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.260α = 90.00
b = 144.820β = 90.00
c = 174.480γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
MOSFLMdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-08-01
    Type: Data collection, Database references
  • Version 1.2: 2018-08-29
    Type: Data collection, Database references