5UJ2

Crystal structure of HCV NS5B genotype 2A JFH-1 isolate with S15G E86Q E87Q C223H V321I mutations and Delta8 neta hairpoin loop deletion in complex with GS-639476 (diphsohate version of GS-9813), Mn2+ and symmetrical primer template 5'-AUAAAUUU


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of a 2'-fluoro-2'-C-methyl C-nucleotide HCV polymerase inhibitor and a phosphoramidate prodrug with favorable properties.

Kirschberg, T.A.Metobo, S.Clarke, M.O.Aktoudianakis, V.Babusis, D.Barauskas, O.Birkus, G.Butler, T.Byun, D.Chin, G.Doerffler, E.Edwards, T.E.Fenaux, M.Lee, R.Lew, W.Mish, M.R.Murakami, E.Park, Y.Squires, N.H.Tirunagari, N.Wang, T.Whitcomb, M.Xu, J.Yang, H.Ye, H.Zhang, L.Appleby, T.C.Feng, J.Y.Ray, A.S.Cho, A.Kim, C.U.

(2017) Bioorg Med Chem Lett 27: 1840-1847

  • DOI: 10.1016/j.bmcl.2017.02.037
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A series of 2'-fluorinated C-nucleosides were prepared and tested for anti-HCV activity. Among them, the triphosphate of 2'-fluoro-2'-C-methyl adenosine C-nucleoside (15) was a potent and selective inhibitor of the NS5B polymerase and maintained acti ...

    A series of 2'-fluorinated C-nucleosides were prepared and tested for anti-HCV activity. Among them, the triphosphate of 2'-fluoro-2'-C-methyl adenosine C-nucleoside (15) was a potent and selective inhibitor of the NS5B polymerase and maintained activity against the S282T resistance mutant. A number of phosphoramidate prodrugs were then prepared and evaluated leading to the identification of the 1-aminocyclobutane-1-carboxylic acid isopropyl ester variant (53) with favorable pharmacokinetic properties including efficient liver delivery in animals.


    Organizational Affiliation

    Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Genome polyprotein
A
572Hepacivirus CMutation(s): 5 
Find proteins for R9TEU1 (Hepacivirus C)
Go to UniProtKB:  R9TEU1
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*UP*AP*AP*AP*UP*UP*U)-3')P, T8Escherichia coli
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8B4
Query on 8B4

Download CCD File 
P
(1S)-1-(4-aminoimidazo[2,1-f][1,2,4]triazin-7-yl)-1,4-anhydro-2-deoxy-2-fluoro-5-O-[(S)-hydroxy(phosphonooxy)phosphoryl]-2-methyl-D-ribitol
C11 H16 F N5 O9 P2
ITUZUOFEWXEZBP-HGIWHZBTSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
A, P
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.76α = 90
b = 141.76β = 90
c = 91.11γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-04-12
    Changes: Database references