ISDA

Deposition Date 2009-03-18

Release Date 2009-10-20

Last Version Date 2023-11-01

Entry Detail

PDB ID:

3GNV

Keywords:

TRANSFERASE

Title:

HCV NS5B polymerase in complex with 1,5 benzodiazepine inhibitor 1b

Biological Source:

Source Organism:

Hepatitis C virus isolate (Taxon ID: 420174)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.75 Å

R-Value Free:

0.23

R-Value Work:

0.17

R-Value Observed:

0.17

Space Group:

P 21 21 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RNA-directed RNA polymerase
Chain IDs:A, B
Chain Length:581
Number of Molecules:2
Biological Source:Hepatitis C virus isolate

UniProt ID:O92972 Pfam ID:PF00998 EC:2.7.7.48

Ligand Molecules

GOL

XNZ

Primary Citation

Structure-based design of a benzodiazepine scaffold yields a potent allosteric inhibitor of hepatitis C NS5B RNA polymerase.

Vandyck, K, Cummings, M.D, Nyanguile, O, Boutton, C.W, Vendeville, S, McGowan, D, Devogelaere, B, Amssoms, K, Last, S, Rombauts, K, Tahri, A, Lory, P, Hu, L, Beauchamp, D.A, Simmen, K, Raboisson, P.Show

J.Med.Chem. 52 4099 4102 (2009)

PMID: 19507864 DOI: 10.1021/jm9005548

Abstact

HCV NS5B polymerase, an essential and virus-specific enzyme, is an important target for drug discovery. Using structure-based design, we optimized a 1,5-benzodiazepine NS5B polymerase inhibitor chemotype into a new sulfone-containing scaffold. The design yielded potent inhibitor (S)-4c (K(D) = 0.79 nM), which has approximately 20-fold greater affinity for NS5B than its carbonyl analogue (R)-2c.

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Primary Citation of related structures