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


Ligand Structure Quality Assessment 


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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymeraseA, B563Hepatitis 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)
UniProt
Find proteins for O92972 (Hepatitis C virus genotype 1b (strain HC-J4))
Explore O92972 
Go to UniProtKB:  O92972
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0LN (Subject of Investigation/LOI)
Query on 0LN

Download Ideal Coordinates CCD File 
C [auth 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 Ideal Coordinates CCD File 
D [auth A] , E [auth A] , F [auth A] , G [auth A] , J [auth B] , K [auth B] , L [auth B] , M [auth B] , 
D [auth A], E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A], I [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
0LN Binding MOAD:  4DRU Kd: 2.4 (nM) from 1 assay(s)
BindingDB:  4DRU Kd: 2.4 (nM) from 1 assay(s)
IC50: 26 (nM) from 1 assay(s)
EC50: 79 (nM) from 1 assay(s)
PDBBind:  4DRU Kd: 2.4 (nM) from 1 assay(s)
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



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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