3AVI

Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structures of novel allosteric peptide inhibitors of HIV integrase identify new interactions at the LEDGF binding site.

Rhodes, D.I., Peat, T.S., Vandegraaff, N., Jeevarajah, D., Newman, J., Martyn, J., Coates, J.A., Ede, N.J., Rea, P., Deadman, J.J.

(2011) Chembiochem 12: 2311-2315

  • DOI: 10.1002/cbic.201100350
  • Primary Citation of Related Structures:  
    3AV9, 3AVA, 3AVB, 3AVC, 3AVF, 3AVG, 3AVH, 3AVI, 3AVJ, 3AVK, 3AVL, 3AVM, 3AVN

  • PubMed Abstract: 

    • An optimised method of solution cyclisation gave us access to a series of peptides including SLKIDNLD (2). We investigated the crystallographic complexes of the HIV integrase (HIV-IN) catalytic core domain with 13 of the peptides and identified multiple interactions at the binding site, including hydrogen bonds with residues Thr125 and Gln95, that have not previously been described as being accessible within the binding site ...

    An optimised method of solution cyclisation gave us access to a series of peptides including SLKIDNLD (2). We investigated the crystallographic complexes of the HIV integrase (HIV-IN) catalytic core domain with 13 of the peptides and identified multiple interactions at the binding site, including hydrogen bonds with residues Thr125 and Gln95, that have not previously been described as being accessible within the binding site. We show that the peptides inhibit the interaction of lens epithelium-derived growth factor (LEDGF) with HIV-IN in a proximity AlphaScreen assay and in an assay for the LEDGF enhancement of HIV-IN strand transfer. The interactions identified represent a potential framework for the development of new HIV-IN inhibitors.

    Organizational Affiliation: 

    Avexa Ltd, 576 Swan Street, Melbourne 3121, Australia.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IntegraseA, B183Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)Mutation(s): 3 
Gene Names: gag-pol
EC: 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LEDGF peptideC [auth D], D [auth F]8Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000821
Query on PRD_000821		C [auth D], D [auth F]SLKIDNMD peptideCyclic peptide / Enzyme inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.995α = 90
b = 70.995β = 90
c = 66.996γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2012-12-12
    Changes: Other
  • Version 1.2: 2013-06-19
    Changes: Database references