ISDA

Deposition Date 2016-02-24

Release Date 2016-12-14

Last Version Date 2024-10-23

Entry Detail

PDB ID:

5IDK

Keywords:

VIRAL PROTEIN

Title:

Crystal structure of West Nile Virus NS2B-NS3 protease in complex with a capped dipeptide boronate inhibitor

Biological Source:

Source Organism:

West Nile virus (Taxon ID: 11082)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.50 Å

R-Value Free:

0.18

R-Value Work:

0.15

R-Value Observed:

0.16

Space Group:

P 21 21 21

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Genome polyprotein,SERINE PROTEASE SUBUNIT NS2B, SERINE PROTEASE NS3
Chain IDs:A, B, C
Chain Length:230
Number of Molecules:3
Biological Source:West Nile virus

UniProt ID:P06935 Pfam ID:PF00949, PF01002 EC:2.7.7.48

Ligand Molecules

6A8

DMS

GOL

Primary Citation

Peptide-Boronic Acid Inhibitors of Flaviviral Proteases: Medicinal Chemistry and Structural Biology.

Nitsche, C, Zhang, L, Weigel, L.F, Schilz, J, Graf, D, Bartenschlager, R, Hilgenfeld, R, Klein, C.D.Show

J. Med. Chem. 60 511 516 (2017)

PMID: 27966962 DOI: 10.1021/acs.jmedchem.6b01021

Abstact

A thousand-fold affinity gain is achieved by introduction of a C-terminal boronic acid moiety into dipeptidic inhibitors of the Zika, West Nile, and dengue virus proteases. The resulting compounds have Ki values in the two-digit nanomolar range, are not cytotoxic, and inhibit virus replication. Structure-activity relationships and a high resolution X-ray cocrystal structure with West Nile virus protease provide a basis for the design of optimized covalent-reversible inhibitors aimed at emerging flaviviral pathogens.

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