5KGW

HIV1 catalytic core domain in complex with inhibitor: (2~{S})-2-[3-(3,4-dihydro-2~{H}-chromen-6-yl)-1-methyl-indol-2-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.194 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Indole-based allosteric inhibitors of HIV-1 integrase.

Patel, P.A.Kvaratskhelia, N.Mansour, Y.Antwi, J.Feng, L.Koneru, P.Kobe, M.J.Jena, N.Shi, G.Mohamed, M.S.Li, C.Kessl, J.J.Fuchs, J.R.

(2016) Bioorg Med Chem Lett 26: 4748-4752

  • DOI: https://doi.org/10.1016/j.bmcl.2016.08.037
  • Primary Citation of Related Structures:  
    5KGW, 5KGX

  • PubMed Abstract: 

    Employing a scaffold hopping approach, a series of allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) have been synthesized based on an indole scaffold. These compounds incorporate the key elements utilized in quinoline-based ALLINIs for binding to the IN dimer interface at the principal LEDGF/p75 binding pocket. The most potent of these compounds displayed good activity in the LEDGF/p75 dependent integration assay (IC50=4.5μM) and, as predicted based on the geometry of the five- versus six-membered ring, retained activity against the A128T IN mutant that confers resistance to many quinoline-based ALLINIs.


  • Organizational Affiliation

    Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Department of Chemistry, The Ohio State University, Columbus, OH 43210, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrase163Human immunodeficiency virus 1Mutation(s): 1 
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CAF
Query on CAF
A
L-PEPTIDE LINKINGC5 H12 As N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.194 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.196α = 90
b = 72.196β = 90
c = 65.981γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-11-02
    Changes: Non-polymer description
  • Version 1.2: 2018-03-07
    Changes: Data collection, Derived calculations