3LPT

HIV integrase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Rational design of small-molecule inhibitors of the LEDGF/p75-integrase interaction and HIV replication.

Christ, F.Voet, A.Marchand, A.Nicolet, S.Desimmie, B.A.Marchand, D.Bardiot, D.Van der Veken, N.J.Van Remoortel, B.Strelkov, S.V.De Maeyer, M.Chaltin, P.Debyser, Z.

(2010) Nat.Chem.Biol. 6: 442-448

  • DOI: 10.1038/nchembio.370
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lens epithelium-derived growth factor (LEDGF/p75) is a cellular cofactor of HIV-1 integrase that promotes viral integration by tethering the preintegration complex to the chromatin. By virtue of its crucial role in the early steps of HIV replication, ...

    Lens epithelium-derived growth factor (LEDGF/p75) is a cellular cofactor of HIV-1 integrase that promotes viral integration by tethering the preintegration complex to the chromatin. By virtue of its crucial role in the early steps of HIV replication, the interaction between LEDGF/p75 and integrase represents an attractive target for antiviral therapy. We have rationally designed a series of 2-(quinolin-3-yl)acetic acid derivatives (LEDGINs) that act as potent inhibitors of the LEDGF/p75-integrase interaction and HIV-1 replication at submicromolar concentration by blocking the integration step. A 1.84-A resolution crystal structure corroborates the binding of the inhibitor in the LEDGF/p75-binding pocket of integrase. Together with the lack of cross-resistance with two clinical integrase inhibitors, these findings define the 2-(quinolin-3-yl)acetic acid derivatives as the first genuine allosteric HIV-1 integrase inhibitors. Our work demonstrates the feasibility of rational design of small molecules inhibiting the protein-protein interaction between a viral protein and a cellular host factor.


    Organizational Affiliation

    Laboratory for Molecular Virology and Gene Therapy, Division of Molecular Medicine, Katholieke Universiteit Leuven (KULeuven), Leuven, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrase
A
166Human immunodeficiency virus 1Mutation(s): 1 
Find proteins for Q76353 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q76353
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
P03
Query on P03

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Download CCD File 
A
2-[3-[3-(2-hydroxyethoxy)propoxy]propoxy]ethanol
C10 H22 O5
GNAZJSIZGCDIQL-UHFFFAOYSA-N
 Ligand Interaction
723
Query on 723

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Download CCD File 
A
(6-chloro-2-oxo-4-phenyl-1,2-dihydroquinolin-3-yl)acetic acid
C17 H12 Cl N O3
SHDUUQWYFNJIAG-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAF
Query on CAF
A
L-PEPTIDE LINKINGC5 H12 As N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
723IC50: 12200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.231 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.000α = 90.00
b = 72.000β = 90.00
c = 65.490γ = 120.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2015-12-09
    Type: Database references
  • Version 1.3: 2017-11-01
    Type: Refinement description