1DY8

Inhibition of the Hepatitis C Virus NS3/4A Protease. The Crystal Structures of Two Protease-Inhibitor Complexes (inhibitor II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Inhibition of the Hepatitis C Virus Ns3/4A Protease the Crystal Structures of Two Protease-Inhibitor Complexes

Di Marco, S.Rizzi, M.Volpari, C.Walsh, M.Narjes, F.Colarusso, S.De Francesco, R.Matassa, V.G.Sollazzo, M.

(2000) J.Biol.Chem. 275: 7152

  • Primary Citation of Related Structures:  
  • Also Cited By: 1OL0, 2A4G, 2A4R, 2A4Q, 1W3C

  • PubMed Abstract: 
  • The hepatitis C virus NS3 protein contains a serine protease domain with a chymotrypsin-like fold, which is a target for development of therapeutics. We report the crystal structures of this domain complexed with NS4A cofactor and with two potent, re ...

    The hepatitis C virus NS3 protein contains a serine protease domain with a chymotrypsin-like fold, which is a target for development of therapeutics. We report the crystal structures of this domain complexed with NS4A cofactor and with two potent, reversible covalent inhibitors spanning the P1-P4 residues. Both inhibitors bind in an extended backbone conformation, forming an anti-parallel beta-sheet with one enzyme beta-strand. The P1 residue contributes most to the binding energy, whereas P2-P4 side chains are partially solvent exposed. The structures do not show notable rearrangements of the active site upon inhibitor binding. These results are significant for the development of antivirals.


    Organizational Affiliation

    Biotechnology, Via Pontina Km 30.600, 00040 Pomezia, Rome, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEASE/HELICASE NS3 (P70)
A, B
187Hepatitis C virus genotype 1b (isolate Japanese)Mutation(s): 0 
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese))
Go to UniProtKB:  P26662
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NONSTRUCTURAL PROTEIN NS4A (P4)
C, D
16Hepatitis C virus genotype 1b (isolate Japanese)Mutation(s): 2 
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese))
Go to UniProtKB:  P26662
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0F7
Query on 0F7

Download SDF File 
Download CCD File 
A, B
N-[(benzyloxy)carbonyl]-L-isoleucyl-N-[(1R)-1-(carboxycarbonyl)-3,3-difluoropropyl]-L-leucinamide
C25 H35 F2 N3 O7
IXLOEMUNKMDCDV-CAIZAGQASA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000271 (0F7)
Query on PRD_000271
A,BCBZ-ILE-LEU-FKI, peptide inhibitorPeptide-like / Inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0F7IC50: 1700 nM (88) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.221 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 93.820α = 90.00
b = 93.820β = 90.00
c = 80.950γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-01-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-11-30
    Type: Other
  • Version 1.3: 2014-03-12
    Type: Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2019-01-30
    Type: Data collection, Experimental preparation
  • Version 1.5: 2019-02-06
    Type: Data collection, Experimental preparation