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 

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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
  • Primary Citation of Related Structures:  
    3EYD

  • 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 processed with the help of serine protease NS3 to produce mature virus ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HCV NS3A, C200hepatitis C virus genotype 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)
UniProt
Find proteins for P26664 (Hepatitis C virus genotype 1a (isolate 1))
Explore P26664 
Go to UniProtKB:  P26664
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26664
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HCV NS4a peptideB, D23N/AMutation(s): 1 
UniProt
Find proteins for P26664 (Hepatitis C virus genotype 1a (isolate 1))
Explore P26664 
Go to UniProtKB:  P26664
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26664
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BE8
Query on BE8
Download Ideal Coordinates CCD File 
F [auth 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 Ideal Coordinates CCD File 
E [auth A],
G [auth C]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
BE8 PDBBind:  3EYD Ki: 0.2 (nM) from 1 assay(s)
BindingDB:  3EYD Ki: 0.2 (nM) from 1 assay(s)
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations