7B4D

Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273C/S240R double mutant bound to DNA and MQ: R273C/S240R-DNA-MQ


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.172 

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This is version 1.2 of the entry. See complete history


Literature

Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ).

Degtjarik, O.Golovenko, D.Diskin-Posner, Y.Abrahmsen, L.Rozenberg, H.Shakked, Z.

(2021) Nat Commun 12: 7057-7057

  • DOI: https://doi.org/10.1038/s41467-021-27142-6
  • Primary Citation of Related Structures:  
    6ZNC, 7B46, 7B47, 7B48, 7B49, 7B4A, 7B4B, 7B4C, 7B4D, 7B4E, 7B4F, 7B4G, 7B4H, 7B4N

  • PubMed Abstract: 

    In response to genotoxic stress, the tumor suppressor p53 acts as a transcription factor by regulating the expression of genes critical for cancer prevention. Mutations in the gene encoding p53 are associated with cancer development. PRIMA-1 and eprenetapopt (APR-246/PRIMA-1 MET ) are small molecules that are converted into the biologically active compound, methylene quinuclidinone (MQ), shown to reactivate mutant p53 by binding covalently to cysteine residues. Here, we investigate the structural basis of mutant p53 reactivation by MQ based on a series of high-resolution crystal structures of cancer-related and wild-type p53 core domains bound to MQ in their free state and in complexes with their DNA response elements. Our data demonstrate that MQ binds to several cysteine residues located at the surface of the core domain. The structures reveal a large diversity in MQ interaction modes that stabilize p53 and its complexes with DNA, leading to a common global effect that is pertinent to the restoration of non-functional p53 proteins.


  • Organizational Affiliation

    Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100, Rehovot, Israel.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellular tumor antigen p53200Homo sapiensMutation(s): 2 
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
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA targetB [auth C]12synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QN8 (Subject of Investigation/LOI)
Query on QN8

Download Ideal Coordinates CCD File 
E [auth A](2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one
C8 H13 N O
LGOHLIRGPFPGKT-ZCFIWIBFSA-N
QNN (Subject of Investigation/LOI)
Query on QNN

Download Ideal Coordinates CCD File 
D [auth A],
F [auth A],
G [auth A]
(2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one
C8 H13 N O
LGOHLIRGPFPGKT-LURJTMIESA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.587α = 90
b = 50.164β = 92.598
c = 34.231γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Aprea Therapeutics AB--

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-08
    Type: Initial release
  • Version 1.1: 2021-12-15
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description