Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 49.4 kDa 
• Atom Count: 3,777 
• Modelled Residue Count: 389 
• Deposited Residue Count: 438 
• Unique protein chains: 1

 2X0U

STRUCTURE OF THE P53 CORE DOMAIN MUTANT Y220C BOUND TO A 2-amino substituted benzothiazole scaffold

• PDB DOI: 10.2210/pdb2X0U/pdb

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


• Deposited: 2009-12-17 Released: 2010-01-26 
• Deposition Author(s): Joerger, A.C., Kaar, J.L., Basse, N., Fersht, A.R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.193 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

Literature

Toward the Rational Design of P53-Stabilizing Drugs: Probing the Surface of the Oncogenic Y220C Mutant.

Basse, N., Kaar, J.L., Settanni, G., Joerger, A.C., Rutherford, T.J., Fersht, A.R.

(2010) Chem Biol 17: 46

• PubMed: 20142040 
• DOI: 10.1016/j.chembiol.2009.12.011
• Primary Citation of Related Structures:  
  2X0U, 2X0V, 2X0W


• PubMed Abstract: 
  

The p53 cancer mutation Y220C induces formation of a cavity on the protein's surface that can accommodate stabilizing small molecules. We combined fragment screening and molecular dynamics to assess the druggability of p53-Y220C and map ligand interaction sites within the mutational cavity. Elucidation of the binding mode of fragment hits by crystallography yielded a clear picture of how a drug might dock in the cavity. Simulations that solvate the protein with isopropanol found additional sites that extend the druggable surface. Moreover, structural observations and simulation revealed the dynamic landscape of the cavity, which improves our understanding of the impact of the mutation on p53 stability. This underpins the importance of considering flexibility of the cavity in screening for optimized ligands. Our findings provide a blueprint for the design of effective drugs that rescue p53-Y220C.

---

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 U S A 103: 15056

---

Organizational Affiliation: 

Medical Research Council Centre for Protein Engineering, Cambridge, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELLULAR TUMOR ANTIGEN P53	A, B	219	Homo sapiens	Mutation(s): 5  Gene Names: TP53, P53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens) Explore P04637  Go to UniProtKB:  P04637
PHAROS:  P04637

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X0U	D [auth B]	6,7-DIHYDRO[1,4]DIOXINO[2,3-F][1,3]BENZOTHIAZOL-2-AMINE C9 H8 N2 O2 S IURPFIBKOPUBIT-UHFFFAOYSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.193 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.06	α = 90
b = 71.14	β = 90
c = 105.41	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-26 
Deposition Author(s): Joerger, A.C., Kaar, J.L., Basse, N., Fersht, A.R.

Revision History  

• Version 1.0: 2010-01-26
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation, Other