6NUJ

HIV-1 Integrase Catalytic Core Domain Complexed with Allosteric Inhibitor BI-224436


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors.

Koneru, P.C.Francis, A.C.Deng, N.Rebensburg, S.V.Hoyte, A.C.Lindenberger, J.Adu-Ampratwum, D.Larue, R.C.Wempe, M.F.Engelman, A.N.Lyumkis, D.Fuchs, J.R.Levy, R.M.Melikyan, G.B.Kvaratskhelia, M.

(2019) Elife 8

  • DOI: 10.7554/eLife.46344
  • Primary Citation of Related Structures:  
    6NUJ

  • PubMed Abstract: 
  • Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are a promising new class of antiretroviral agents that disrupt proper viral maturation by inducing hyper-multimerization of IN. Here we show that lead pyridine-based ALLINI KF116 exhibits striking selectivity for IN tetramers versus lower order protein oligomers ...

    Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are a promising new class of antiretroviral agents that disrupt proper viral maturation by inducing hyper-multimerization of IN. Here we show that lead pyridine-based ALLINI KF116 exhibits striking selectivity for IN tetramers versus lower order protein oligomers. IN structural features that are essential for its functional tetramerization and HIV-1 replication are also critically important for KF116 mediated higher-order IN multimerization. Live cell imaging of single viral particles revealed that KF116 treatment during virion production compromises the tight association of IN with capsid cores during subsequent infection of target cells. We have synthesized the highly active (-)-KF116 enantiomer, which displayed EC 50 of ~7 nM against wild type HIV-1 and ~10 fold higher, sub-nM activity against a clinically relevant dolutegravir resistant mutant virus suggesting potential clinical benefits for complementing dolutegravir therapy with pyridine-based ALLINIs.


    Organizational Affiliation

    Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IntegraseA166Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: pol
UniProt
Find proteins for F2WR52 (Human immunodeficiency virus 1)
Explore F2WR52 
Go to UniProtKB:  F2WR52
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L3D (Subject of Investigation/LOI)
Query on L3D

Download Ideal Coordinates CCD File 
B [auth A](2S)-tert-butoxy[4-(2,3-dihydropyrano[4,3,2-de]quinolin-7-yl)-2-methylquinolin-3-yl]acetic acid
C27 H26 N2 O4
MIXIIJCBELCMCZ-VWLOTQADSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAF
Query on CAF
AL-PEPTIDE LINKINGC5 H12 As N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.211α = 90
b = 72.211β = 90
c = 66.079γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data collection
SCALEPACKdata scaling
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI110310

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release