4WF8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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: 10.1021/cb5006118
  • Primary Citation of Related Structures:  
  • Also Cited By: 5EQS

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NS3 protein
A
192Hepacivirus CMutation(s): 0 
Find proteins for X2G809 (Hepacivirus C)
Go to UniProtKB:  X2G809
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
2R9
Query on 2R9

Download SDF File 
Download CCD File 
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
Asunaprevir
C35 H46 Cl N5 O9 S
XRWSZZJLZRKHHD-WVWIJVSJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.350α = 90.00
b = 60.893β = 90.00
c = 80.875γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
SCALEPACKdata scaling
HKL-2000data reduction
DENZOdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesF31-GM103259
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesRO1-AI085051

Revision History 

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