ISDA

Entry Detail

PDB ID:

3QGD

Keywords:

Title:

Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase complex with (2E)-3-(4-{[(1-{[(13-cyclohexyl-6-oxo-6,7-dihydro-5H-indolo[1,2-d][1,4]benzodiazepin-10-yl)carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-enoic acid and (2R)-4-(2,6-dimethoxypyrimidin-4-yl)-1-[(4-ethylphenyl)sulfonyl]-N-(4-methoxybenzyl)piperazine-2-carboxamide

Biological Source:

Source Organism:

Hepatitis C virus subtype 1b

Host Organism:

Escherichia coli

PDB Version:

Deposition Date:

2011-01-24

Release Date:

2011-04-20

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.60 Å

R-Value Free:

0.26

R-Value Work:

0.23

R-Value Observed:

0.23

Space Group:

P 21 21 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:RNA-directed RNA polymerase
Chain IDs:A, B
Chain Length:574
Number of Molecules:2
Biological Source:Hepatitis C virus subtype 1b

UniProt ID:Q9WMX2 Pfam ID:PF00998

Ligand Molecules

23E

26S

SO4

Primary Citation

Investigation of the mode of binding of a novel series of N-benzyl-4-heteroaryl-1-(phenylsulfonyl)piperazine-2-carboxamides to the hepatitis C virus polymerase.

Gentles, R.G, Sheriff, S, Beno, B.R, Wan, C, Kish, K, Ding, M, Zheng, X, Chupak, L, Poss, M.A, Witmer, M.R, Morin, P, Wang, Y.K, Rigat, K, Lemm, J, Voss, S, Liu, M, Pelosi, L, Roberts, S.B, Gao, M, Kadow, J.F.Show

Bioorg.Med.Chem.Lett. 21 2212 2215 (2011)

PMID: 21441029 DOI: 10.1016/j.bmcl.2011.03.011

Abstact

Structure based rationales for the activities of potent N-benzyl-4-heteroaryl-1-(phenylsulfonyl)piperazine-2-carboxamide inhibitors of the hepatitis C viral polymerase are described herein. These compounds bind to the hepatitis C virus non-structural protein 5B (NS5B), and co-crystal structures of select examples from this series with NS5B are reported. Comparison of co-crystal structures of a potent analog with both NS5B genotype 1a and genotype 1b provides a possible explanation for the genotype-selectivity observed with this compound class and suggests opportunities for the further optimization of the series.

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Primary Citation of related structures