5FDL

Crystal Structure of K103N/Y181C Mutant HIV-1 Reverse Transcriptase (RT) in Complex with IDX899


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of the Aryl-phospho-indole IDX899, a Highly Potent Anti-HIV Non-nucleoside Reverse Transcriptase Inhibitor.

Dousson, C.Alexandre, F.R.Amador, A.Bonaric, S.Bot, S.Caillet, C.Convard, T.da Costa, D.Lioure, M.P.Roland, A.Rosinovsky, E.Maldonado, S.Parsy, C.Trochet, C.Storer, R.Stewart, A.Wang, J.Mayes, B.A.Musiu, C.Poddesu, B.Vargiu, L.Liuzzi, M.Moussa, A.Jakubik, J.Hubbard, L.Seifer, M.Standring, D.

(2016) J.Med.Chem. 59: 1891-1898

  • DOI: 10.1021/acs.jmedchem.5b01430

  • PubMed Abstract: 
  • Here, we describe the design, synthesis, biological evaluation, and identification of a clinical candidate non-nucleoside reverse transcriptase inhibitors (NNRTIs) with a novel aryl-phospho-indole (APhI) scaffold. NNRTIs are recommended components of ...

    Here, we describe the design, synthesis, biological evaluation, and identification of a clinical candidate non-nucleoside reverse transcriptase inhibitors (NNRTIs) with a novel aryl-phospho-indole (APhI) scaffold. NNRTIs are recommended components of highly active antiretroviral therapy (HAART) for the treatment of HIV-1. Since a major problem associated with NNRTI treatment is the emergence of drug resistant virus, this work focused on optimization of the APhI against clinically relevant HIV-1 Y181C and K103N mutants and the Y181C/K103N double mutant. Optimization of the phosphinate aryl substituent led to the discovery of the 3-Me,5-acrylonitrile-phenyl analogue RP-13s (IDX899) having an EC50 of 11 nM against the Y181C/K103N double mutant.


    Organizational Affiliation

    IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
P51 Reverse transcriptase
A
557Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
P66 Reverse transcriptase
B
440Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5DV
Query on 5DV

Download SDF File 
Download CCD File 
A
methyl (R)-(2-carbamoyl-5-chloro-1H-indol-3-yl)[3-(2-cyanoethyl)-5-methylphenyl]phosphinate
C20 H19 Cl N3 O3 P
KJQCBIWCQKNBKR-MUUNZHRXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.243 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 118.260α = 90.00
b = 154.790β = 90.00
c = 154.730γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PHASERphasing
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2016-03-23
    Type: Database references