4KTC

NS3/NS4A protease with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Danoprevir (ITMN-191/R7227), a Highly Selective and Potent Inhibitor of Hepatitis C Virus (HCV) NS3/4A Protease.

Jiang, Y.Andrews, S.W.Condroski, K.R.Buckman, B.Serebryany, V.Wenglowsky, S.Kennedy, A.L.Madduru, M.R.Wang, B.Lyon, M.Doherty, G.A.Woodard, B.T.Lemieux, C.Do, M.G.Zhang, H.Ballard, J.Vigers, G.Brandhuber, B.J.Stengel, P.Josey, J.A.Beigelman, L.Blatt, L.Seiwert, S.D.

(2014) J.Med.Chem. 57: 1753-1769

  • DOI: 10.1021/jm400164c

  • PubMed Abstract: 
  • HCV serine protease NS3 represents an attractive drug target because it is not only essential for viral replication but also implicated in the viral evasion of the host immune response pathway through direct cleavage of key proteins in the human inna ...

    HCV serine protease NS3 represents an attractive drug target because it is not only essential for viral replication but also implicated in the viral evasion of the host immune response pathway through direct cleavage of key proteins in the human innate immune system. Through structure-based drug design and optimization, macrocyclic peptidomimetic molecules bearing both a lipophilic P2 isoindoline carbamate and a P1/P1' acylsulfonamide/acylsulfamide carboxylic acid bioisostere were prepared that possessed subnanomolar potency against the NS3 protease in a subgenomic replicon-based cellular assay (Huh-7). Danoprevir (compound 49) was selected as the clinical development candidate for its favorable potency profile across multiple HCV genotypes and key mutant strains and for its good in vitro ADME profiles and in vivo target tissue (liver) exposures across multiple animal species. X-ray crystallographic studies elucidated several key features in the binding of danoprevir to HCV NS3 protease and proved invaluable to our iterative structure-based design strategy.


    Organizational Affiliation

    Array BioPharma , 3200 Walnut Street, Boulder, Colorado 80301, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine protease NS3
A, C
190Hepatitis C virus genotype 1b (isolate Japanese)Mutation(s): 0 
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese))
Go to UniProtKB:  P26662
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NS4A peptide
B, D
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
1X3
Query on 1X3

Download SDF File 
Download CCD File 
A, C
(2R,6S,13aR,14aR,16aS)-6-{[(cyclopentyloxy)carbonyl]amino}-14a-[(cyclopropylsulfonyl)carbamoyl]-5,16-dioxooctadecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diazacyclopentadecin-2-yl 3,4-dihydroisoquinoline-2(1H)-carboxylate
C37 H51 N5 O9 S
VQZYSHWAKCNHJX-IVYVMHIUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1X3IC50: 1 nM BINDINGMOAD
1X3IC50: 1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.206 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 72.988α = 90.00
b = 72.988β = 90.00
c = 127.480γ = 120.00
Software Package:
Software NamePurpose
MLPHAREphasing
SCALAdata scaling
CrystalCleardata collection
REFMACrefinement
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2014-03-26
    Type: Database references