4DRU

HCV NS5B in complex with macrocyclic INDOLE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-based macrocyclization yields hepatitis C virus NS5B inhibitors with improved binding affinities and pharmacokinetic properties.

Cummings, M.D.Lin, T.I.Hu, L.Tahri, A.McGowan, D.Amssoms, K.Last, S.Devogelaere, B.Rouan, M.C.Vijgen, L.Berke, J.M.Dehertogh, P.Fransen, E.Cleiren, E.van der Helm, L.Fanning, G.Van Emelen, K.Nyanguile, O.Simmen, K.Raboisson, P.Vendeville, S.

(2012) Angew Chem Int Ed Engl 51: 4637-4640


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase
A, B
563Hepatitis C virus isolate HC-J4Mutation(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)
Find proteins for O92972 (Hepatitis C virus genotype 1b (strain HC-J4))
Go to UniProtKB:  O92972
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0LN
Query on 0LN

Download CCD File 
A
13-cyclohexyl-3-methoxy-17,22-dimethyl-7H-10,6-(methanoiminothioiminobutanoiminomethano)indolo[2,1-a][2]benzazepine-14,23-dione 16,16-dioxide
C32 H38 N4 O5 S
LTHKMHZATSPXJT-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0LNKd:  2.4000000953674316   nM  PDBBind
0LNKd:  2.4000000953674316   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.13α = 90
b = 106.643β = 90
c = 133.286γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2012-08-15
    Changes: Database references