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 

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Ligand Structure Quality Assessment 


This is version 1.2 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-DIRECTED RNA POLYMERASEA537Hepacivirus CMutation(s): 0 
EC: 2.7.7.48 (PDB Primary Data), 3.4.22 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
UniProt
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK))
Explore P26663 
Go to UniProtKB:  P26663
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IB8 (Subject of Investigation/LOI)
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
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
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