Crystal structure of HCV NS3/4A protease variant R155K in complex with Asunaprevir

Experimental Data Snapshot

  • Resolution: 1.99 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

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Structural Analysis of Asunaprevir Resistance in HCV NS3/4A Protease.

Soumana, D.I.Ali, A.Schiffer, C.A.

(2014) ACS Chem Biol 9: 2485-2490

  • DOI: https://doi.org/10.1021/cb5006118
  • Primary Citation of Related Structures:  
    4WF8, 4WH6, 4WH8

  • PubMed Abstract: 

    Asunaprevir (ASV), an isoquinoline-based competitive inhibitor targeting the hepatitis C virus (HCV) NS3/4A protease, is very potent in vivo. However, the potency is significantly compromised by the drug resistance mutations R155K and D168A. In this study three crystal structures of ASV and an analogue were determined to analyze the structural basis of drug resistance susceptibility. These structures revealed that ASV makes extensive contacts with Arg155 outside the substrate envelope. Arg155 in turn is stabilized by Asp168, and thus when either residue is mutated, the enzyme's interaction with ASV's P2* isoquinoline is disrupted. Adding a P1-P3 macrocycle to ASV enhances the inhibitor's resistance barrier, likely due to poising the inhibitor to its bound conformation. Macrocyclic inhibitors with P2* extension moieties avoiding interaction with the protease S2 residues including Arg155 must be chosen for future design of more robust protease inhibitors.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyprotein200hepatitis C virus genotype 1aMutation(s): 0 
Find proteins for A8DG50 (hepatitis C virus genotype 1a)
Explore A8DG50 
Go to UniProtKB:  A8DG50
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8DG50
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2R9

Download Ideal Coordinates CCD File 
E [auth A]N-(tert-butoxycarbonyl)-3-methyl-L-valyl-(4R)-4-[(7-chloro-4-methoxyisoquinolin-1-yl)oxy]-N-{(1R,2S)-1-[(cyclopropylsulfonyl)carbamoyl]-2-ethenylcyclopropyl}-L-prolinamide
C35 H46 Cl N5 O9 S
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
O4 S
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Binding Affinity Annotations 
IDSourceBinding Affinity
2R9 BindingDB:  4WH6 EC50: min: 1.2, max: 4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.99 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.924α = 90
b = 58.415β = 90
c = 60.09γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesRO1-AI085051
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF31-GM103259

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2014-12-03
    Changes: Database references
  • Version 1.2: 2015-09-09
    Changes: Data collection
  • Version 1.3: 2015-11-25
    Changes: Non-polymer description
  • Version 1.4: 2017-09-06
    Changes: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.5: 2019-12-11
    Changes: Author supporting evidence