5IDK

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

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.

(2017) J. Med. Chem. 60: 511-516

  • DOI: 10.1021/acs.jmedchem.6b01021

  • PubMed Abstract: 

    • 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 ...

    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.

    Organizational Affiliation: 

    Medicinal Chemistry, IPMB, Heidelberg University , INF-364, 69120 Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Genome polyprotein,SERINE PROTEASE SUBUNIT NS2B, SERINE PROTEASE NS3
A, B, C
230West Nile virusMutation(s): 0 
Find proteins for P06935 (West Nile virus)
Go to UniProtKB:  P06935
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
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Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
6A8
Query on 6A8
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Download CCD File 
A, B, C
((R)-1-((S)-3-(4-(aminomethyl)phenyl)-2-benzamidopropaneamido)-4-guanidinobutyl)boronic acid, cyclic double ester with glycerol
C25 H35 B N6 O5
UBPZINWFQYNJIA-FKBYEOEOSA-N
 Ligand Interaction
DMS
Query on DMS
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Download CCD File 
B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.420α = 90.00
b = 96.965β = 90.00
c = 187.856γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermanyKL-1356/3-1

Revision History 

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2016-12-28
    Type: Database references
  • Version 1.2: 2017-01-25
    Type: Database references
  • Version 1.3: 2017-07-05
    Type: Refinement description
  • Version 1.4: 2017-09-06
    Type: Author supporting evidence