1W3C

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1021/jm049435d

  • 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 ...

    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.


    Related Citations: 
    • 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


    Organizational Affiliation

    IRBM-MRL Rome, Via Pontina km 30,600, 00040 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DN1
Query on DN1

Download SDF File 
Download CCD File 
A
3-({(2S)-2-[({(1R)-1-[({(1R)-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
PEPTIDOMIMETIC INHIBITOR
C26 H31 F2 N3 O7 S
BEFPIHVRQQQFFB-DUFVWYDBSA-N
 Ligand Interaction
DN2
Query on DN2

Download SDF File 
Download CCD File 
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
PEPTIDOMIMETIC INHIBITOR
C26 H31 F2 N3 O7 S
BEFPIHVRQQQFFB-QUPVEMFASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.177 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 92.411α = 90.00
b = 92.411β = 90.00
c = 80.007γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-09
    Type: Initial release
  • Version 1.1: 2015-09-16
    Type: Data collection, Database references, Derived calculations, Other, Source and taxonomy, Structure summary, Version format compliance