6TVW

Structure of native gp41 derived peptide fusion inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.234 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Systematic Evaluation of Fluorination as Modification for Peptide-Based Fusion Inhibitors against HIV-1 Infection.

Huhmann, S.Nyakatura, E.K.Rohrhofer, A.Moschner, J.Schmidt, B.Eichler, J.Roth, C.Koksch, B.

(2021) Chembiochem 22: 3443-3451

  • DOI: https://doi.org/10.1002/cbic.202100417
  • Primary Citation of Related Structures:  
    6TVQ, 6TVU, 6TVW

  • PubMed Abstract: 

    With the emergence of novel viruses, the development of new antivirals is more urgent than ever. A key step in human immunodeficiency virus type 1 (HIV-1) infection is six-helix bundle formation within the envelope protein subunit gp41. Selective disruption of bundle formation by peptides has been shown to be effective; however, these drugs, exemplified by T20, are prone to rapid clearance from the patient. The incorporation of non-natural amino acids is known to improve these pharmacokinetic properties. Here, we evaluate a peptide inhibitor in which a critical Ile residue is replaced by fluorinated analogues. We characterized the influence of the fluorinated analogues on the biophysical properties of the peptide. Furthermore, we show that the fluorinated peptides can block HIV-1 infection of target cells at nanomolar levels. These findings demonstrate that fluorinated amino acids are appropriate tools for the development of novel peptide therapeutics.


  • Organizational Affiliation

    Freie Universität Berlin, Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Arnimallee 20, 14195, Berlin, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoproteinA [auth CCC]38Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q5VGF0 (Human immunodeficiency virus 1)
Explore Q5VGF0 
Go to UniProtKB:  Q5VGF0
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UniProt GroupQ5VGF0
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MET-THR-TRP-MET-GLU-TRP-ASP-ARG-GLUB [auth DDD]15Human immunodeficiency virus 1Mutation(s): 0 
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ASN-ASN-TYR-THR-SER-LEU-ILE-HIS-SER-LEU-ILE-GLU-GLUC [auth DbD]15Human immunodeficiency virus 1Mutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O0B (Subject of Investigation/LOI)
Query on O0B

Download Ideal Coordinates CCD File 
D [auth DbD](2~{S},3~{S})-2-azanyl-5,5,5-tris(fluoranyl)-3-methyl-pentanal
C6 H10 F3 N O
LTCCWCHCWMGFFS-CRCLSJGQSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.234 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.706α = 90
b = 44.706β = 90
c = 208.857γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
ACORNphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection, Derived calculations