9GFC | pdb_00009gfc

HDM2 complexed with stapled peptide-like ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.318 (Depositor), 0.306 (DCC) 
  • R-Value Work: 
    0.263 (Depositor) 
  • R-Value Observed: 
    0.266 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9GFC

This is version 1.0 of the entry. See complete history

Literature

Guanidinium-Stapled Helical Peptides for Targeting Protein-Protein Interactions.

Perdriau, C.Luton, A.Zimmeter, K.Neuville, M.Saragaglia, C.Peluso-Iltis, C.Osz, J.Kauffmann, B.Collie, G.W.Rochel, N.Guichard, G.Pasco, M.

(2025) Angew Chem Int Ed Engl 64: e202416348-e202416348

  • DOI: https://doi.org/10.1002/anie.202416348
  • Primary Citation Related Structures: 
    9GF9, 9GFC, 9GFE, 9GFI

  • PubMed Abstract: 

    Peptide stapling has emerged as a versatile approach in drug discovery to reinforce secondary structure elements especially α-helices and improve properties of linear bioactive peptides. Inspired by the prevalence of arginine in protein-protein and protein-DNA interfaces, we investigated guanidinium-stapling as a means to constrain helical peptides. Guanidinium stapling was readily achieved on solid support, utilizing two orthogonally protected lysine or unatural α-amino acid residues with an amino function. This method allows for easy modulation of the nature and size of the staple as well as helix propensity. Evaluating a set of guanidinium-stapled peptides for their interaction with different protein targets identified several binders with increased target affinity. X-ray structure determination of four complexes revealed that all stapled peptides adopt a helical conformation upon protein binding. Notably, the disubstituted guanidinium generally exhibits a distinct cis/trans conformation and, in one instance, retains a conserved hydrogen bond with the protein surface. By identifying, for the first time, the guanidinium moiety as an effective helical peptide stapling group, this research significantly expands the repertoire of α-helix stapling techniques for the creation of useful protein mimics.


  • Organizational Affiliation
    • Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR5248, IECB, 2 rue Robert Escarpit, F-33600, Pessac, France.

Macromolecule Content 

  • Total Structure Weight: 45.23 kDa 
  • Atom Count: 3,180 
  • Modeled Residue Count: 383 
  • Deposited Residue Count: 386 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2
A, B, C, D
86Homo sapiensMutation(s): 0 
Gene Names: MDM2
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens)
Explore Q00987 
Go to UniProtKB:  Q00987
PHAROS:  Q00987
GTEx:  ENSG00000135679 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00987
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Stapled peptide-like ligand
E, F, G
14synthetic constructMutation(s): 0 

Small Molecules

Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
HRG
Query on HRG
E, F, G
L-PEPTIDE LINKINGC7 H16 N4 O2ARG
NLE
Query on NLE
E, F, G
L-PEPTIDE LINKINGC6 H13 N O2LEU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.318 (Depositor), 0.306 (DCC) 
  • R-Value Work:  0.263 (Depositor) 
  • R-Value Observed: 0.266 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.628α = 90
b = 40.736β = 95.86
c = 78.177γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-15-CE07-0010
Agence Nationale de la Recherche (ANR)FranceANR-17-CE07-0020
Agence Nationale de la Recherche (ANR)FranceANR-20-CE18-0038

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release