3L36 | pdb_00003l36

PIE12 D-peptide against HIV entry

• PDB DOI: https://doi.org/10.2210/pdb3L36/pdb

• Classification: DE NOVO PROTEIN
• Mutation(s): No 


• Deposited: 2009-12-16 Released: 2010-11-03 
• Deposition Author(s): Welch, B.D., Redman, J.S., Paul, S., Whitby, F.G., Weinstock, M.T., Reeves, J.D., Lie, Y.S., Eckert, D.M., Hill, C.P., Root, M.J., Kay, M.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.278 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

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

• PubMed: 20719956 
• DOI: https://doi.org/10.1128/JVI.01339-10
• Primary Citation of Related Structures:  
  3L35, 3L36, 3L37, 3MGN


• 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 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.

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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.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 7.66 kDa 
• Atom Count: 587 
• Modelled Residue Count: 64 
• Deposited Residue Count: 64 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GP41 N-PEPTIDE	A	47	N/A	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV ENTRY INHIBITOR PIE12	B [auth H]	17	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CXS	C [auth H]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C9 H19 N O3 S PJWWRFATQTVXHA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.278 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.117	α = 90
b = 41.117	β = 90
c = 81.731	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-03 
Deposition Author(s): Welch, B.D., Redman, J.S., Paul, S., Whitby, F.G., Weinstock, M.T., Reeves, J.D., Lie, Y.S., Eckert, D.M., Hill, C.P., Root, M.J., Kay, M.S.

Revision History  

• Version 1.0: 2010-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary