9GFI | pdb_00009gfi

hRAR alpha LBD-AM580 complex with staple peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.272 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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
Retinoic acid receptor alpha236Homo sapiensMutation(s): 0 
Gene Names: RARANR1B1
UniProt & NIH Common Fund Data Resources
Find proteins for P10276 (Homo sapiens)
Explore P10276 
Go to UniProtKB:  P10276
PHAROS:  P10276
GTEx:  ENSG00000131759 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10276
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Stapled peptide-like ligand10synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EQN (Subject of Investigation/LOI)
Query on EQN

Download Ideal Coordinates CCD File 
C [auth A]4-{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino}benzoic acid
C22 H25 N O3
SZWKGOZKRMMLAJ-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
HRG
Query on HRG
B
L-PEPTIDE LINKINGC7 H16 N4 O2ARG
NLE
Query on NLE
B
L-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.272 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.51α = 90
b = 62.06β = 105.57
c = 49.35γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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