2XWY

Structure of MK-3281, a Potent Non-Nucleoside Finger-Loop Inhibitor, in complex with the Hepatitis C Virus NS5B Polymerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of (7R)-14-Cyclohexyl-7-{[2-(Dimethylamino)Ethyl] (Methyl)Amino}-7,8-Dihydro-6H-Indolo[1,2-E][1,5] Benzoxazocine -11-Carboxylic Acid (Mk-3281), a Potent and Orally Bioavailable Finger-Loop Inhibitor of the Hepatitis C Virus Ns5B Polymerase

Narjes, F.Crescenzi, B.Ferrara, M.Habermann, J.Colarusso, S.Del Rosario Rico Ferreira, M.Stansfield, I.Mackay, A.C.Conte, I.Ercolani, C.Zaramella, S.Palumbi, M.C.Meuleman, P.Leroux-Roels, G.Giuliano, C.Fiore, F.Di Marco, S.Baiocco, P.Koch, U.Migliaccio, G.Altamura, S.Laufer, R.De Francesco, R.Rowley, M.

(2011) J Med Chem 54: 289

  • DOI: https://doi.org/10.1021/jm1013105
  • Primary Citation of Related Structures:  
    2XWY

  • PubMed Abstract: 

    Infections caused by hepatitis C virus (HCV) are a significant world health problem for which novel therapies are in urgent demand. The polymerase of HCV is responsible for the replication of viral genome and has been a prime target for drug discovery efforts. Here, we report on the further development of tetracyclic indole inhibitors, binding to an allosteric site on the thumb domain. Structure-activity relationship (SAR) studies around an indolo-benzoxazocine scaffold led to the identification of compound 33 (MK-3281), an inhibitor with good potency in the HCV subgenomic replication assay and attractive molecular properties suitable for a clinical candidate. The compound caused a consistent decrease in viremia in vivo using the chimeric mouse model of HCV infection.


  • Organizational Affiliation

    Istituto Di Ricerche Di Biologia Molecolare, P. Angeletti SpA (Merck Research Laboratories, Rome), Pomezia, Italy. Frank.Narjes@astrazeneca.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-DIRECTED RNA POLYMERASE537Hepacivirus hominisMutation(s): 0 
EC: 2.7.7.48
UniProt
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK))
Explore P26663 
Go to UniProtKB:  P26663
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26663
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IB8
Query on IB8

Download Ideal Coordinates CCD File 
B [auth A](7R)-14-cyclohexyl-7-{[2-(dimethylamino)ethyl](methyl)amino}-7,8-dihydro-6H-indolo[1,2-e][1,5]benzoxazocine-11-carboxylic acid
C29 H37 N3 O3
YQUCBFIQSJVCOR-JOCHJYFZSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
IB8 PDBBind:  2XWY IC50: 6000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.983α = 90
b = 94.272β = 90
c = 95.145γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-22
    Type: Initial release
  • Version 1.1: 2011-10-26
    Changes: Database references, Version format compliance
  • Version 1.2: 2019-04-03
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description