4WH8

Crystal Structure of HCV NS3/4A protease in complex with an Asunaprevir P1-P3 macrocyclic analog.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

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Ligand Structure Quality Assessment 


This is version 3.1 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: 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyprotein
A, B
198hepatitis C virus genotype 1aMutation(s): 0 
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3M7
Query on 3M7

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
tert-butyl {(2R,4S,6S,12Z,13aS,14aR,16aS)-2-[(7-chloro-4-methoxyisoquinolin-1-yl)oxy]-14a-[(cyclopropanesulfonyl)carbamoyl]-5,16-dioxo-1,2,3,5,6,7,8,9,10,11,13a,14,14a,15,16,16a-hexadecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diazacyclopentadecin-6-yl}carbamate
C36 H46 Cl N5 O9 S
ZFAXEHOMXOFIQU-HGSGLVRESA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.412α = 90
b = 54.975β = 90.09
c = 59.859γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
PDB_EXTRACTdata extraction
HKL-3000data scaling
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-12-03
    Changes: Database references
  • Version 2.0: 2017-09-06
    Changes: Atomic model, Author supporting evidence, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2019-12-11
    Changes: Author supporting evidence
  • Version 3.0: 2022-10-26
    Changes: Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary
  • Version 3.1: 2024-05-22
    Changes: Data collection