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 
  • R-Value Observed: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Structures With Same Primary Citation

  • 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), 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, B, C, D, E, F
261Homo sapiensMutation(s): 0 
Gene Names: PCNA
Find proteins for P12004 (Homo sapiens)
Go to UniProtKB:  P12004
NIH Common Fund Data Resources
PHAROS  P12004
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
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: CDKN1ACAP20CDKN1CIP1MDA6PIC1SDI1WAF1
Find proteins for P38936 (Homo sapiens)
Go to UniProtKB:  P38936
NIH Common Fund Data Resources
PHAROS  P38936
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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,KL-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 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.26α = 90
b = 144.82β = 90
c = 174.48γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-29
    Changes: Derived calculations