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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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 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEASE/HELICASE NS3 (P70)A, B187Hepatitis C virus (isolate 1)Mutation(s): 0 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26662
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NONSTRUCTURAL PROTEIN NS4A (P4)C, D16Hepatitis C virus (isolate 1)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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26662
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / 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		 Ligand Interaction
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		 Ligand Interaction
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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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