1W3C

Crystal structure of the Hepatitis C Virus NS3 Protease in complex with a peptidomimetic inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.177 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The Design and Enzyme-Bound Crystal Structure of Indoline Based Peptidomimetic Inhibitors of Hepatitis C Virus Ns3 Protease

Ontoria, J.M.Di Marco, S.Conte, I.Di Francesco, M.E.Gardelli, C.Koch, U.Matassa, V.G.Poma, M.Steinkuhler, C.Volpari, C.Harper, S.

(2004) J Med Chem 47: 6443

  • DOI: https://doi.org/10.1021/jm049435d
  • Primary Citation of Related Structures:  
    1W3C

  • PubMed Abstract: 

    The design of a series of peptidomimetic inhibitors of the hepatitis C virus NS3 protease is described. These inhibitors feature an indoline-2-carboxamide as a novel heterocyclic replacement for the P3 amino acid residue and N-terminal capping group of tripeptide based inhibitors. The crystal structure of the ternary NS3/NS4A/inhibitor complex for the most active molecule in this series highlights its suitability as an N-terminal capping group of a dipeptide inhibitor of the NS3 protease.


  • Organizational Affiliation

    IRBM-MRL Rome, Via Pontina km 30,600, 00040 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 1)Mutation(s): 0 
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
Expand
  • 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 1)Mutation(s): 2 
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DN2
Query on DN2

Download Ideal Coordinates CCD File 
F [auth B]3-({(2S)-2-[({(1S)-1-[({(1S)-1-[(R)-CARBOXY(HYDROXY)METHYL]-3,3-DIFLUOROPROPYL}AMINO)CARBONYL]-3-METHYLBUTYL}AMINO)CARBONYL]-2,3-DIHYDRO-1H-INDOL-2-YL}METHYL)THIOPHENE-2-CARBOXYLIC ACID
C26 H31 F2 N3 O7 S
BEFPIHVRQQQFFB-QUPVEMFASA-N
DN1
Query on DN1

Download Ideal Coordinates CCD File 
E [auth A]3-({(2S)-2-[({(1R)-1-[({(1R)-1-[(R)-CARBOXY(HYDROXY)METHYL]-3,3-DIFLUOROPROPYL}AMINO)CARBONYL]-3-METHYLBUTYL}AMINO)CARB ONYL]-2,3-DIHYDRO-1H-INDOL-2-YL}METHYL)THIOPHENE-2-CARBOXYLIC ACID
C26 H31 F2 N3 O7 S
BEFPIHVRQQQFFB-DUFVWYDBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.177 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.411α = 90
b = 92.411β = 90
c = 80.007γ = 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: 2004-12-09
    Type: Initial release
  • Version 1.1: 2015-09-16
    Changes: Data collection, Database references, Derived calculations, Other, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary