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 

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Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    5UJ2

  • 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 activity against the S282T resistance mutant ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Genome polyproteinC [auth A]572Hepacivirus CMutation(s): 5 
EC: 3.4.22 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q99IB8 (Hepatitis C virus genotype 2a (isolate JFH-1))
Explore Q99IB8 
Go to UniProtKB:  Q99IB8
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*AP*UP*AP*AP*AP*UP*UP*U)-3')B [auth P], A [auth T]8Escherichia coli
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    8B4 (Subject of Investigation/LOI)
    Query on 8B4

    Download Ideal Coordinates CCD File 
    E [auth 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 Ideal Coordinates CCD File 
    D [auth P], F [auth A], G [auth A]MANGANESE (II) ION
    Mn
    WAEMQWOKJMHJLA-UHFFFAOYSA-N
     Ligand Interaction
    CL
    Query on CL

    Download Ideal Coordinates CCD File 
    H [auth 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



    Ligand Structure Quality Assessment  



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

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