5KGX

HIV1 catalytic core domain in complex with an 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: 2.67 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


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: 10.1016/j.bmcl.2016.08.037
  • Structures With Same Primary Citation

  • 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 ...

    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. Electronic address: fuchs.42@osu.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IntegraseA163Human immunodeficiency virus 1Mutation(s): 2 
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)
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7SK
Query on 7SK

Download CCD File 
A
(2S)-tert-butoxy[3-(3,4-dihydro-2H-1-benzopyran-6-yl)-1-methyl-1H-indol-2-yl]acetic acid
C24 H27 N O4
JEETZBQOULTRJG-QFIPXVFZSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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: 2.67 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.191 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.109α = 90
b = 72.109β = 90
c = 65.713γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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