3L37

PIE12 D-peptide against HIV entry


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design of a potent D-peptide HIV-1 entry inhibitor with a strong barrier to resistance.

Welch, B.D.Francis, J.N.Redman, J.S.Paul, S.Weinstock, M.T.Reeves, J.D.Lie, Y.S.Whitby, F.G.Eckert, D.M.Hill, C.P.Root, M.J.Kay, M.S.

(2010) J.Virol. 84: 11235-11244

  • DOI: 10.1128/JVI.01339-10
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The HIV gp41 N-trimer pocket region is an ideal viral target because it is extracellular, highly conserved, and essential for viral entry. Here, we report on the design of a pocket-specific D-peptide, PIE12-trimer, that is extraordinarily elusive to ...

    The HIV gp41 N-trimer pocket region is an ideal viral target because it is extracellular, highly conserved, and essential for viral entry. Here, we report on the design of a pocket-specific D-peptide, PIE12-trimer, that is extraordinarily elusive to resistance and characterize its inhibitory and structural properties. D-peptides (peptides composed of D-amino acids) are promising therapeutic agents due to their insensitivity to protease degradation. PIE12-trimer was designed using structure-guided mirror-image phage display and linker optimization and is the first D-peptide HIV entry inhibitor with the breadth and potency required for clinical use. PIE12-trimer has an ultrahigh affinity for the gp41 pocket, providing it with a reserve of binding energy (resistance capacitor) that yields a dramatically improved resistance profile compared to those of other fusion inhibitors. These results demonstrate that the gp41 pocket is an ideal drug target and establish PIE12-trimer as a leading anti-HIV antiviral candidate.


    Organizational Affiliation

    Department of Biochemistry, University of Utah School of Medicine, 15 N. Medical Drive East, Rm. 4100, Salt Lake City, UT 84112-5650, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GP41 N-PEPTIDE
A
47N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HIV ENTRY INHIBITOR PIE12
H
18N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  12 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
A, H
NON-POLYMERH2 N

--

DCY
Query on DCY
H
D-PEPTIDE LINKINGC3 H7 N O2 S

--

DPR
Query on DPR
H
D-PEPTIDE LINKINGC5 H9 N O2

--

DLY
Query on DLY
H
D-PEPTIDE LINKINGC6 H14 N2 O2

--

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

--

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

--

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

--

DGN
Query on DGN
H
D-PEPTIDE LINKINGC5 H10 N2 O3

--

DAS
Query on DAS
H
D-PEPTIDE LINKINGC4 H7 N O4

--

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

--

DTY
Query on DTY
H
D-PEPTIDE LINKINGC9 H11 N O3

--

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

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.235 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 49.121α = 90.00
b = 49.121β = 90.00
c = 67.687γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance