1DY9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.207 

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Ligand Structure Quality Assessment 


This is version 1.4 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEASE/HELICASE NS3 (P70)A, B187Hepatitis C virus (isolate Taiwan)Mutation(s): 0 
Gene Names: HCV
EC: 3.4.22 (PDB Primary Data), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese))
Explore P26662 
Go to UniProtKB:  P26662
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NONSTRUCTURAL PROTEIN NS4A (P4)C, D16Hepatitis C virus (isolate Taiwan)Mutation(s): 2 
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 P26662 (Hepatitis C virus genotype 1b (isolate Japanese))
Explore P26662 
Go to UniProtKB:  P26662
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2ZF (Subject of Investigation/LOI)
Query on 2ZF

Download Ideal Coordinates CCD File 
E [auth A], F [auth B]N-(tert-butoxycarbonyl)-L-alpha-glutamyl-N-[(1R)-1-(carboxycarbonyl)-3,3-difluoropropyl]-L-leucinamide
C21 H33 F2 N3 O9
WXVMZATZAOHPFR-AVGNSLFASA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
2ZF BindingDB:  1DY9 IC50: 330 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000426 (2ZF)
Query on PRD_000426
E [auth A], F [auth B]BOC-GLU-LEU-FKI, PEPTIDE INHIBITORPeptide-like / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.207 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.35α = 90
b = 94.35β = 90
c = 82.37γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata 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: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.4: 2019-10-09
    Changes: Data collection, Other