5EQS

Crystal structure of a genotype 1a/3a chimeric HCV NS3/4A protease in complex with Asunaprevir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.839 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular and Dynamic Mechanism Underlying Drug Resistance in Genotype 3 Hepatitis C NS3/4A Protease.

Soumana, D.I.Kurt Yilmaz, N.Ali, A.Prachanronarong, K.L.Schiffer, C.A.

(2016) J.Am.Chem.Soc. 138: 11850-11859

  • DOI: 10.1021/jacs.6b06454
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Hepatitis C virus (HCV), affecting an estimated 150 million people worldwide, is the leading cause of viral hepatitis, cirrhosis and hepatocellular carcinoma. HCV is genetically diverse with six genotypes (GTs) and multiple subtypes of different glob ...

    Hepatitis C virus (HCV), affecting an estimated 150 million people worldwide, is the leading cause of viral hepatitis, cirrhosis and hepatocellular carcinoma. HCV is genetically diverse with six genotypes (GTs) and multiple subtypes of different global distribution and prevalence. Recent development of direct-acting antivirals against HCV including NS3/4A protease inhibitors (PIs) has greatly improved treatment outcomes for GT-1. However, all current PIs exhibit significantly lower potency against GT-3. Lack of structural data on GT-3 protease has limited our ability to understand PI failure in GT-3. In this study the molecular basis for reduced potency of current inhibitors against GT-3 NS3/4A protease is elucidated with structure determination, molecular dynamics simulations and inhibition assays. A chimeric GT-1a3a NS3/4A protease amenable to crystallization was engineered to recapitulate decreased sensitivity of GT-3 protease to PIs. High-resolution crystal structures of this GT-1a3a bound to 3 PIs, asunaprevir, danoprevir and vaniprevir, had only subtle differences relative to GT-1 despite orders of magnitude loss in affinity. In contrast, hydrogen-bonding interactions within and with the protease active site and dynamic fluctuations of the PIs were drastically altered. The correlation between loss of intermolecular dynamics and inhibitor potency suggests a mechanism where polymorphisms between genotypes (or selected mutations) in the drug target confer resistance through altering the intermolecular dynamics of the protein-inhibitor complex.


    Related Citations: 
    • Structural analysis of asunaprevir resistance in HCV NS3/4A protease.
      Soumana, D.I.,Ali, A.,Schiffer, C.A.
      (2014) ACS Chem. Biol. 9: 2485


    Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NS3 protease
A
192Hepacivirus CMutation(s): 3 
Find proteins for A0A0B4WYC6 (Hepacivirus C)
Go to UniProtKB:  A0A0B4WYC6
Small Molecules
Ligands 2 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
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: 1.839 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.115α = 90.00
b = 60.334β = 90.00
c = 79.646γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement

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 Allergy and Infectious DiseasesUnited StatesR01-AI085051

Revision History 

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2016-11-30
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence