6XZK

Structure of zVDR LBD-Calcitriol in complex with chimera 13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.224 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 2.2 of the entry. See complete history


Literature

Structural Basis for alpha-Helix Mimicry and Inhibition of Protein-Protein Interactions with Oligourea Foldamers.

Cussol, L.Mauran-Ambrosino, L.Buratto, J.Belorusova, A.Y.Neuville, M.Osz, J.Fribourg, S.Fremaux, J.Dolain, C.Goudreau, S.R.Rochel, N.Guichard, G.

(2021) Angew Chem Int Ed Engl 60: 2296-2303

  • DOI: https://doi.org/10.1002/anie.202008992
  • Primary Citation of Related Structures:  
    6HFA, 6XZH, 6XZI, 6XZJ, 6XZK, 6XZV

  • PubMed Abstract: 

    Efficient optimization of a peptide lead into a drug candidate frequently needs further transformation to augment properties such as bioavailability. Among the different options, foldamers, which are sequence-based oligomers with precise folded conformation, have emerged as a promising technology. We introduce oligourea foldamers to reduce the peptide character of inhibitors of protein-protein interactions (PPI). However, the precise design of such mimics is currently limited by the lack of structural information on how these foldamers adapt to protein surfaces. We report a collection of X-ray structures of peptide-oligourea hybrids in complex with ubiquitin ligase MDM2 and vitamin D receptor and show how such hybrid oligomers can be designed to bind with high affinity to protein targets. This work should enable the generation of more effective foldamer-based disruptors of PPIs in the context of peptide lead optimization.


  • Organizational Affiliation

    Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607, Pessac, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vitamin D3 receptor A302Danio rerioMutation(s): 0 
Gene Names: vdranr1i1avdr
UniProt
Find proteins for Q9PTN2 (Danio rerio)
Explore Q9PTN2 
Go to UniProtKB:  Q9PTN2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9PTN2
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GLU-ASN-ALA-UIA-URL-URY-URV-UZN-LYS9synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
VDX BindingDB:  6XZK Kd: 1200 (nM) from 1 assay(s)
EC50: 5.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.224 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.112α = 90
b = 66.112β = 90
c = 262.488γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

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 VDXClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release
  • Version 1.1: 2021-09-01
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-01-24
    Changes: Refinement description
  • Version 2.2: 2024-11-06
    Changes: Structure summary