4A92

Full-length HCV NS3-4A protease-helicase in complex with a macrocyclic protease inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Macrocyclic Hcv Ns3/4A Protease Inhibitor Interacts with Protease and Helicase Residues in the Complex with its Full- Length Target.

Schiering, N.D'Arcy, A.Villard, F.Simic, O.Kamke, M.Monnet, G.Hassiepen, U.Svergun, D.I.Pulfer, R.Eder, J.Raman, P.Bodendorf, U.

(2011) Proc.Natl.Acad.Sci.USA 108: 21052

  • DOI: 10.1073/pnas.1110534108

  • PubMed Abstract: 
  • Hepatitis C virus (HCV) infection is a global health burden with over 170 million people infected worldwide. In a significant portion of patients chronic hepatitis C infection leads to serious liver diseases, including fibrosis, cirrhosis, and hepato ...

    Hepatitis C virus (HCV) infection is a global health burden with over 170 million people infected worldwide. In a significant portion of patients chronic hepatitis C infection leads to serious liver diseases, including fibrosis, cirrhosis, and hepatocellular carcinoma. The HCV NS3 protein is essential for viral polyprotein processing and RNA replication and hence viral replication. It is composed of an N-terminal serine protease domain and a C-terminal helicase/NTPase domain. For full activity, the protease requires the NS4A protein as a cofactor. HCV NS3/4A protease is a prime target for developing direct-acting antiviral agents. First-generation NS3/4A protease inhibitors have recently been introduced into clinical practice, markedly changing HCV treatment options. To date, crystal structures of HCV NS3/4A protease inhibitors have only been reported in complex with the protease domain alone. Here, we present a unique structure of an inhibitor bound to the full-length, bifunctional protease-helicase NS3/4A and show that parts of the P4 capping and P2 moieties of the inhibitor interact with both protease and helicase residues. The structure sheds light on inhibitor binding to the more physiologically relevant form of the enzyme and supports exploring inhibitor-helicase interactions in the design of the next generation of HCV NS3/4A protease inhibitors. In addition, small angle X-ray scattering confirmed the observed protease-helicase domain assembly in solution.


    Organizational Affiliation

    Expertise Platform Proteases, Novartis Institutes for BioMedical Research, Fabrikstrasse 16, CH-4002 Basel, Switzerland. nikolaus.schiering@novartis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERINE PROTEASE NS3
A, B
666Hepatitis C virus genotype 1bEC: 3.6.1.15, 3.4.22.-, 3.6.4.13, 2.7.7.48, 3.4.21.98
Find proteins for P26663 (Hepatitis C virus genotype 1b)
Go to UniProtKB:  P26663
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
F9K
Query on F9K

Download SDF File 
Download CCD File 
A, B
(1'R,2R,2'S,6S,24AS)-17-FLUORO-6-(1-METHYL-2-OXOPIPERIDINE-3-CARBOXAMIDO)-19,19-DIOXIDO-5,21,24-TRIOXO-2'-VINYL-1,2,3,5,6,7,8,9,10,11,12,13,14,20,21,23,24,24A-OCTADECAHYDROSPIRO[BENZO[S]PYRROLO[2,1-G][1,2,5,8,18]THIATETRAAZACYCLOICOSINE-22,1'-CYCLOPRO-2-CARBOXYLATEPAN]-2-YL 4-FLUOROISOINDOLINE
C42 H51 F2 N7 O9 S
JSGPAIBYTVNGSI-ZBBLQTOUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 91.972α = 90.00
b = 110.470β = 90.00
c = 137.227γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2012-01-11
    Type: Other