1CZQ

CRYSTAL STRUCTURE OF THE D10-P1/IQN17 COMPLEX: A D-PEPTIDE INHIBITOR OF HIV-1 ENTRY BOUND TO THE GP41 COILED-COIL POCKET.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibiting HIV-1 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: 103-115

  • Primary Citation of Related Structures:  2Q3I, 2Q5U, 2Q7C

  • 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.


    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 THE HYDROPHOBIC POCKET OF HIV GP41 AND GCN4-PIQI
A
46N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
D-PEPTIDE INHIBITOR
D
17N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
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  8 Unique
IDChainsTypeFormula2D DiagramParent
DCY
Query on DCY
D
D-PEPTIDE LINKINGC3 H7 N O2 S

--

DHI
Query on DHI
D
D-PEPTIDE LINKINGC6 H10 N3 O2

--

DLE
Query on DLE
D
D-PEPTIDE LINKINGC6 H13 N O2

--

DGL
Query on DGL
D
D-PEPTIDE LINKINGC5 H9 N O4

--

DAL
Query on DAL
D
D-PEPTIDE LINKINGC3 H7 N O2

--

DTR
Query on DTR
D
D-PEPTIDE LINKINGC11 H12 N2 O2

--

DAR
Query on DAR
D
D-PEPTIDE LINKINGC6 H15 N4 O2

--

ACE
Query on ACE
A, D
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.214 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 41.829α = 90.00
b = 41.829β = 90.00
c = 84.817γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-10-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance