ISDA

Deposition Date 2017-01-16

Release Date 2017-03-22

Last Version Date 2023-10-04

Entry Detail

PDB ID:

5UJ2

Keywords:

immune system/RNA

Title:

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

Biological Source:

Source Organism:

Escherichia coli (Taxon ID: 562)
Hepatitis C virus (Taxon ID: 11103)

Host Organism:

ESCHERICHIA COLI

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.90 Å

R-Value Free:

0.22

R-Value Work:

0.18

R-Value Observed:

0.18

Space Group:

P 65

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Genome polyprotein
Mutations:S15G E86Q E87Q C223H V321I
Chain IDs:C (auth: A)
Chain Length:572
Number of Molecules:1
Biological Source:Hepatitis C virus

UniProt ID:Q99IB8 Pfam ID:PF00998

Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(*AP*UP*AP*AP*AP*UP*UP*U)-3')
Chain IDs:A (auth: T), B (auth: P)
Chain Length:8
Number of Molecules:2
Biological Source:Escherichia coli

Ligand Molecules

8B4

Primary Citation

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.Show

Bioorg. Med. Chem. Lett. 27 1840 1847 (2017)

PMID: 28274633 DOI: 10.1016/j.bmcl.2017.02.037

Abstact

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.

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Primary Citation of related structures