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: 2.40 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.216 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.8 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

  • DOI: https://doi.org/10.1074/jbc.275.10.7152
  • Primary Citation of Related Structures:  
    1DXP, 1DY8, 1DY9

  • 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, 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEASE/HELICASE NS3 (P70)
A, B
187Hepatitis C virus (isolate Taiwan)Mutation(s): 0 
Gene Names: HCV
EC: 3.4.22
UniProt
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese))
Explore P26662 
Go to UniProtKB:  P26662
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26662
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NONSTRUCTURAL PROTEIN NS4A (P4)
C, D
16Hepatitis C virus (isolate Taiwan)Mutation(s): 2 
Gene Names: HCV
UniProt
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese))
Explore P26662 
Go to UniProtKB:  P26662
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26662
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0F7
Query on 0F7

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]
N-[(benzyloxy)carbonyl]-L-isoleucyl-N-[(1R)-1-(carboxycarbonyl)-3,3-difluoropropyl]-L-leucinamide
C25 H35 F2 N3 O7
IXLOEMUNKMDCDV-CAIZAGQASA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
0F7 BindingDB:  1DY8 IC50: 1700 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.216 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.82α = 90
b = 93.82β = 90
c = 80.95γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-11-30
    Changes: Other
  • Version 1.3: 2014-03-12
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2019-01-30
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2019-02-06
    Changes: Data collection, Experimental preparation
  • Version 1.6: 2019-07-10
    Changes: Data collection, Derived calculations
  • Version 1.7: 2019-07-24
    Changes: Data collection
  • Version 1.8: 2023-12-06
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description