2Q5U

Crystal structure of IQN17


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibiting HIV Entry: Discovery of D-Peptide Inhibitors that Target the Gp41 Coiled-Coil Pocket

Eckert, D.M.Malashkevich, V.N.Hong, L.H.Carr, P.A.Kim, P.S.

(1999) Cell 99: 103-105

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The HIV-1 gp41 protein promotes viral entry by mediating the fusion of viral and cellular membranes. A prominent pocket on the surface of a central trimeric coiled coil within gp41 was previously identified as a potential target for drugs that inhibi ...

    The HIV-1 gp41 protein promotes viral entry by mediating the fusion of viral and cellular membranes. A prominent pocket on the surface of a central trimeric coiled coil within gp41 was previously identified as a potential target for drugs that inhibit HIV-1 entry. We designed a peptide, IQN17, which properly presents this pocket. Utilizing IQN17 and mirror-image phage display, we identified cyclic, D-peptide inhibitors of HIV-1 infection that share a sequence motif. A 1.5 A cocrystal structure of IQN17 in complex with a D-peptide, and NMR studies, show that conserved residues of these inhibitors make intimate contact with the gp41 pocket. Our studies validate the pocket per se as a target for drug development. IQN17 and these D-peptide inhibitors are likely to be useful for development and identification of a new class of orally bioavailable anti-HIV drugs.


    Related Citations: 
    • Crystal Structure of GCN4-Piqi, a Trimeric Coiled-Coil with Buried Polar Residues.
      Eckert, D.M.,Malashkevich, V.N.,Kim, P.S.
      (1998) J.Mol.Biol. 284: 859
    • Core structure of gp41 from the HIV envelope glycoprotein
      Chan, D.C.,Fass, D.,Berger, J.M.,Kim, P.S.
      (1997) Cell 89: 263


    Organizational Affiliation

    Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fusion protein between yeast variant GCN4 and HIVgp41
A, B, C
46Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for A3F986 (Human immunodeficiency virus 1)
Go to UniProtKB:  A3F986
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A, B, C
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.244 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 45.515α = 90.00
b = 47.895β = 90.00
c = 136.091γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
DENZOdata reduction
REFMACrefinement
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance