Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 49789.16 
• Atom Count: 3252 
• Residue Count: 438 
• Unique protein chains: 1

3ZME

Structure of the p53 core domain mutant Y220C bound to the small molecule PhiKan7242

• DOI: 10.2210/pdb3ZME/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): 5 


• Deposited: 2013-02-07 Released: 2013-05-08 
• Deposition Author(s): Joerger, A.C., Wilcken, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.175 
• R-Value Work: 0.155 

Literature

Small molecule induced reactivation of mutant p53 in cancer cells.

Liu, X., Wilcken, R., Joerger, A.C., Chuckowree, I.S., Amin, J., Spencer, J., Fersht, A.R.

(2013) Nucleic Acids Res. 41: 6034-6044

• PubMed: 23630318 
• DOI: 10.1093/nar/gkt305


• PubMed Abstract: 
  

The p53 cancer mutant Y220C is an excellent paradigm for rescuing the function of conformationally unstable p53 mutants because it has a unique surface crevice that can be targeted by small-molecule stabilizers. Here, we have identified a compound, PK7088, which is active in vitro: PK7088 bound to the mutant with a dissociation constant of 140 μM and raised its melting temperature, and we have determined the binding mode of a close structural analogue by X-ray crystallography. We showed that PK7088 is biologically active in cancer cells carrying the Y220C mutant by a battery of tests. PK7088 increased the amount of folded mutant protein with wild-type conformation, as monitored by immunofluorescence, and restored its transcriptional functions. It induced p53-Y220C-dependent growth inhibition, cell-cycle arrest and apoptosis. Most notably, PK7088 increased the expression levels of p21 and the proapoptotic NOXA protein. PK7088 worked synergistically with Nutlin-3 on up-regulating p21 expression, whereas Nutlin-3 on its own had no effect, consistent with its mechanism of action. PK7088 also restored non-transcriptional apoptotic functions of p53 by triggering nuclear export of BAX to the mitochondria. We suggest a set of criteria for assigning activation of p53.

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Related Citations: 

• Structural Basis for Understanding Oncogenic P53 Mutations and Designing Rescue Drugs.
  Joerger, A.C.,Ang, H.C.,Fersht, A.R.
  (2006) Proc.Natl.Acad.Sci.USA 103: 15056




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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cellular tumor antigen p53	A, B	219	Homo sapiens	Mutation(s): 5  Gene Names: TP53 (P53)
Find proteins for P04637 (Homo sapiens) Go to Gene View: TP53 Go to UniProtKB:  P04637

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
QC5	A, B	2-(4-(4-fluorophenyl)-5-(1H-pyrrol-1-yl)-1H-pyrazol-1-yl)-N,N-dimethylethanamine C17 H19 F N4 ZCQVHVWVDAEXBJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.175 
• R-Value Work: 0.155 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 65.138	α = 90.00
b = 71.023	β = 90.00
c = 105.324	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-07 
• Released Date: 2013-05-08 
• Deposition Author(s): Joerger, A.C., Wilcken, R.

Revision History 

• Version 1.0: 2013-05-08
  Type: Initial release
• Version 1.1: 2013-05-15
  Type: Database references, Source and taxonomy
• Version 1.2: 2013-07-17
  Type: Database references
• Version 1.3: 2018-12-12
  Type: Data collection, Database references, Source and taxonomy, Structure summary
• Version 1.4: 2019-05-08
  Type: Data collection, Experimental preparation
• Version 1.5: 2019-05-15
  Type: Data collection, Experimental preparation