5MMB

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ434 (compound 6p)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-Guided Optimization of HIV Integrase Strand Transfer Inhibitors.

Zhao, X.Z.Smith, S.J.Maskell, D.P.Metifiot, M.Pye, V.E.Fesen, K.Marchand, C.Pommier, Y.Cherepanov, P.Hughes, S.H.Burke, T.R.

(2017) J. Med. Chem. 60: 7315-7332

  • DOI: 10.1021/acs.jmedchem.7b00596
  • Primary Citation of Related Structures:  5MMA, 5NO1

  • PubMed Abstract: 
  • Integrase mutations can reduce the effectiveness of the first-generation FDA-approved integrase strand transfer inhibitors (INSTIs), raltegravir (RAL) and elvitegravir (EVG). The second-generation agent, dolutegravir (DTG), has enjoyed considerable c ...

    Integrase mutations can reduce the effectiveness of the first-generation FDA-approved integrase strand transfer inhibitors (INSTIs), raltegravir (RAL) and elvitegravir (EVG). The second-generation agent, dolutegravir (DTG), has enjoyed considerable clinical success; however, resistance-causing mutations that diminish the efficacy of DTG have appeared. Our current findings support and extend the substrate envelope concept that broadly effective INSTIs can be designed by filling the envelope defined by the DNA substrates. Previously, we explored 1-hydroxy-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamides as an INSTI scaffold, making a limited set of derivatives, and concluded that broadly effective INSTIs can be developed using this scaffold. Herein, we report an extended investigation of 6-substituents as well the first examples of 7-substituted analogues of this scaffold. While 7-substituents are not well-tolerated, we have identified novel substituents at the 6-position that are highly effective, with the best compound (6p) retaining better efficacy against a broad panel of known INSTI resistant mutants than any analogues we have previously described.


    Organizational Affiliation

    Chromatin Structure and Mobile DNA, The Francis Crick Institute , London NW1 1AT, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PFV INTEGRASE
A, B
395Human spumaretrovirusGene Names: pol
EC: 3.1.26.4, 3.1.-.-, 2.7.7.49, 2.7.7.7, 2.7.7.-, 3.4.23.-
Find proteins for P14350 (Human spumaretrovirus)
Go to UniProtKB:  P14350
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')C19synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')D17synthetic construct
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEZ
Query on HEZ

Download SDF File 
Download CCD File 
A, B
HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
OUY
Query on OUY

Download SDF File 
Download CCD File 
A
methyl 3-[5-azanyl-6-[[2,4-bis(fluoranyl)phenyl]methylcarbamoyl]-8-oxidanyl-7-oxidanylidene-1,8-naphthyridin-3-yl]propanoate
C20 H18 F2 N4 O5
JVWFVALMCGSXOC-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.184 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 160.490α = 90.00
b = 160.490β = 90.00
c = 123.830γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
Aimlessdata scaling
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Database references