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: 2.9 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.184 

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

  • 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. Electronic address: tkirschberg@gilead.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Genome polyprotein
A
572Hepatitis C virus genotype 2aEC: 3.6.1.15, 3.4.22.-, 3.6.4.13, 2.7.7.48, 3.4.21.98
Find proteins for Q99IB8 (Hepatitis C virus genotype 2a)
Go to UniProtKB:  Q99IB8
Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*UP*AP*AP*AP*UP*UP*U)-3')T,P8Escherichia coli
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
8B4
Query on 8B4

Download SDF File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.184 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 141.760α = 90.00
b = 141.760β = 90.00
c = 91.110γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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