8A92

p53-Y220C Core Domain in Complex with a Bromo-trifluoro-pyrazole-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Revisiting a challenging p53 binding site: a diversity-optimized HEFLib reveals diverse binding modes in T-p53C-Y220C.

Stahlecker, J.Klett, T.Schwer, M.Jaag, S.Dammann, M.Ernst, L.N.Braun, M.B.Zimmermann, M.O.Kramer, M.Lammerhofer, M.Stehle, T.Coles, M.Boeckler, F.M.

(2022) RSC Med Chem 13: 1575-1586

  • DOI: https://doi.org/10.1039/d2md00246a
  • Primary Citation of Related Structures:  
    8A92

  • PubMed Abstract: 

    The cellular tumor antigen p53 is a key component in cell cycle control. The mutation Y220C heavily destabilizes the protein thermally but yields a druggable crevice. We have screened the diversity-optimized halogen-enriched fragment library against T-p53C-Y220C with STD-NMR and DSF to identify hits, which we validated by 1 H, 15 N-HSQC NMR. We could identify four hits binding in the Y220C cleft, one hit binding covalently and four hits binding to an uncharacterized binding site. Compound 1151 could be crystallized showing a flip of C220 and thus opening subsite 3. Additionally, 4482 was identified to alkylate cysteines. Data shows that the diversity-optimized HEFLib leads to multiple diverse hits. The identified scaffolds can be used to further optimize interactions with T-p53C-Y220C and increase thermal stability.


  • Organizational Affiliation

    Department of Protein Evolution, Max Planck Institute for Biology Tübingen Max-Planck-Ring 5 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
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 
D [auth A],
G [auth B]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
LE9 (Subject of Investigation/LOI)
Query on LE9

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
4-bromanyl-5-(trifluoromethyl)-1H-pyrazol-3-amine
C4 H3 Br F3 N3
ZHAMWMKUYVFDJH-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 
E [auth A],
H [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.077α = 90
b = 71.109β = 90
c = 105.226γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
XDSdata scaling

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: 2022-11-09
    Type: Initial release
  • Version 1.1: 2023-01-11
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description