8RBC | pdb_00008rbc

p53-Y220C Core Domain Covalently Bound to 3-amino-5-chloropyrazine-2,6-dicarbonitrile Soaked at 5 mM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 
    0.260 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Covalent Fragments Acting as Tyrosine Mimics for Mutant p53-Y220C Rescue by Nucleophilic Aromatic Substitution.

Klett, T.Stahlecker, J.Jaag, S.Masberg, B.Knappe, C.Lammerhofer, M.Coles, M.Stehle, T.Boeckler, F.M.

(2024) Acs Pharmacol Transl Sci 7: 3984-3999

  • DOI: https://doi.org/10.1021/acsptsci.4c00414
  • Primary Citation of Related Structures:  
    8RBA, 8RBB, 8RBC

  • PubMed Abstract: 

    The tumor suppressor p53 is frequently mutated in human cancers. The Y220C mutant is the ninth most common p53 cancer mutant and is classified as a structural mutant, as it leads to strong thermal destabilization and degradation by creating a solvent-accessible hydrophobic cleft. To identify small molecules that thermally stabilize p53, we employed DSF to screen S N Ar-type electrophiles from our covalent fragment library (CovLib) for binding to different structural (Y220C, R282W) and DNA contact (R273H) mutants of p53. The reactive fragments SN001, SN006, and SN007 were detected to specifically stabilize Y220C, indicating the arylation of Cys220 in the mutational cleft, as confirmed by X-ray crystallography. The fragments occupy the central cavity and mimic the ring system of the WT tyrosine lost by the mutation. Surpassing previously reported noncovalent ligands, SN001 stabilized T-p53C-Y220C concentration-dependently up to 4.45 °C and, due to its small size, represents a promising starting point for optimization.


  • Organizational Affiliation
    • Lab for Molecular Design & Pharm. Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellular tumor antigen p53
A, B
219Homo sapiensMutation(s): 5 
Gene Names: TP53P53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens)
Explore P04637 
Go to UniProtKB:  P04637
PHAROS:  P04637
GTEx:  ENSG00000141510 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04637
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth B]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
YM0 (Subject of Investigation/LOI)
Query on YM0

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
I [auth B]
3-azanylpyrazine-2,6-dicarbonitrile
C6 H3 N5
SVUGJCIZAIHMMN-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free:  0.260 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.909α = 90
b = 71.088β = 90
c = 107.057γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release
  • Version 1.1: 2025-01-01
    Changes: Database references