Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 7660.14 
• Atom Count: 538 
• Residue Count: 64 
• Unique protein chains: 2

3L36

PIE12 D-peptide against HIV entry

• DOI: 10.2210/pdb3L36/pdb

• Classification: DE NOVO PROTEIN


• 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 
• R-Value Work: 0.243 

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: 10.1128/JVI.01339-10
• Primary Citation of Related Structures:  
  3MGN, 3L37, 3L35


• 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
GP41 N-PEPTIDE	A	47	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
HIV ENTRY INHIBITOR PIE12	H	17	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

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

Modified Residues  12 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NH2	A, H	NON-POLYMER	H2 N		--
DCY	H	D-PEPTIDE LINKING	C3 H7 N O2 S		--
DPR	H	D-PEPTIDE LINKING	C5 H9 N O2		--
DLY	H	D-PEPTIDE LINKING	C6 H14 N2 O2		--
DHI	H	D-PEPTIDE LINKING	C6 H10 N3 O2		--
DLE	H	D-PEPTIDE LINKING	C6 H13 N O2		--
DGL	H	D-PEPTIDE LINKING	C5 H9 N O4		--
DGN	H	D-PEPTIDE LINKING	C5 H10 N2 O3		--
DAS	H	D-PEPTIDE LINKING	C4 H7 N O4		--
DTR	H	D-PEPTIDE LINKING	C11 H12 N2 O2		--
DTY	H	D-PEPTIDE LINKING	C9 H11 N O3		--
ACE	A, H	NON-POLYMER	C2 H4 O		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.278 
• R-Value Work: 0.243 
• Space Group: P 3 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 41.117	α = 90.00
b = 41.117	β = 90.00
c = 81.731	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-12-16 
• 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
  Type: Version format compliance