9GF9

S-Protease complexed with stapled peptide-like ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 
    0.252 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SO4Click on this verticalbar to view details

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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease pancreatic
A, B, C, D, E
101Bos taurusMutation(s): 0 
EC: 4.6.1.18
UniProt
Find proteins for P61823 (Bos taurus)
Explore P61823 
Go to UniProtKB:  P61823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61823
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease pancreatic
G, H, I, J, K
17Bos taurusMutation(s): 3 
EC: 4.6.1.18
UniProt
Find proteins for P61823 (Bos taurus)
Explore P61823 
Go to UniProtKB:  P61823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61823
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth G]
CA [auth J]
DA [auth L]
M [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
HRG
Query on HRG
G, H, I, J, K
L-PEPTIDE LINKINGC7 H16 N4 O2ARG
NLE
Query on NLE
G, H, I, J, K
L-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free:  0.252 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.232α = 88.19
b = 44.358β = 87.8
c = 93.694γ = 67.11
Software Package:
Software NamePurpose
BUSTERrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SO4Click on this verticalbar to view details

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