3EYD

Structure of HCV NS3-4A Protease with an Inhibitor Derived from a Boronic Acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Potent inhibitors of HCV-NS3 protease derived from boronic acids.

Venkatraman, S.Wu, W.Prongay, A.Girijavallabhan, V.George Njoroge, F.

(2009) Bioorg Med Chem Lett 19: 180-183

  • DOI: 10.1016/j.bmcl.2008.10.124
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Chronic hepatitis C infection is the leading causes for cirrhosis of the liver and hepatocellular carcinoma, leading to liver failure and liver transplantation. The etiological agent, HCV virus produces a single positive strand of RNA that is process ...

    Chronic hepatitis C infection is the leading causes for cirrhosis of the liver and hepatocellular carcinoma, leading to liver failure and liver transplantation. The etiological agent, HCV virus produces a single positive strand of RNA that is processed with the help of serine protease NS3 to produce mature virus. Inhibition of NS3 protease can be potentially used to develop effective drugs for HCV infections. Numerous efforts are now underway to develop potent inhibitors of HCV protease that contain ketoamides as serine traps. Herein we report the synthesis of a series of potent inhibitors that contain a boronic acid as a serine trap. The activity of these compounds were optimized to 200pM. X-ray structure of compound 17 bound to NS3 protease is also discussed.


    Organizational Affiliation

    Schering Plough Research Institute, K15-MS 3545, Kenilworth, NJ 07033, USA. Srikanth.Venkatraman@spcorp.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HCV NS3
A, C
200Hepatitis C virus subtype 1aMutation(s): 0 
Gene Names: ns3
EC: 3.4.22 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P26664 (Hepatitis C virus genotype 1a (isolate 1))
Go to UniProtKB:  P26664
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HCV NS4a peptide
B, D
23N/AMutation(s): 1 
Find proteins for P26664 (Hepatitis C virus genotype 1a (isolate 1))
Go to UniProtKB:  P26664
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BE8
Query on BE8

Download CCD File 
A
[(1R)-2-cyclobutyl-1-({[(1R,2S,5S)-3-(N-{[(1S)-2,2-dimethyl-1-{[methyl(methylsulfonyl)amino]methyl}propyl]carbamoyl}-3-methyl-L-valyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hex-2-yl]carbonyl}amino)ethyl]boronic acid
C29 H54 B N5 O7 S
KGZWDDBJGGJYLY-WKOLOUIMSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BE8Ki :  0.20000000298023224   nM  PDBBind
BE8Ki:  0.20000000298023224   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.180 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 224.483α = 90
b = 224.483β = 90
c = 75.786γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
X-PLORmodel building
X-PLORrefinement
HKL-2000data reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance