3BR9

Crystal Structure of HCV NS5B Polymerase with a Novel Pyridazinone Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Novel HCV NS5B polymerase inhibitors derived from 4-(1',1'-dioxo-1',4'-dihydro-1'lambda6-benzo[1',2',4']thiadiazin-3'-yl)-5-hydroxy-2H-pyridazin-3-ones. Part 1: exploration of 7'-substitution of benzothiadiazine.

Zhou, Y.Webber, S.E.Murphy, D.E.Li, L.S.Dragovich, P.S.Tran, C.V.Sun, Z.Ruebsam, F.Shah, A.M.Tsan, M.Showalter, R.E.Patel, R.Li, B.Zhao, Q.Han, Q.Hermann, T.Kissinger, C.R.Lebrun, L.Sergeeva, M.V.Kirkovsky, L.

(2008) Bioorg Med Chem Lett 18: 1413-1418

  • DOI: 10.1016/j.bmcl.2008.01.007
  • Primary Citation of Related Structures:  
    3BR9, 3BSA, 3BSC

  • PubMed Abstract: 
  • 5-Hydroxy-3(2H)-pyridazinone derivatives were investigated as inhibitors of genotype 1 HCV NS5B polymerase. The synthesis, structure-activity relationships (SAR), metabolic stability, and structure-based design approach for this new class of compounds are discussed ...

    5-Hydroxy-3(2H)-pyridazinone derivatives were investigated as inhibitors of genotype 1 HCV NS5B polymerase. The synthesis, structure-activity relationships (SAR), metabolic stability, and structure-based design approach for this new class of compounds are discussed.


    Organizational Affiliation

    Anadys Pharmaceuticals, Inc., 3115 Merryfield Row, San Diego, CA 92121, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymeraseA, B578Hepacivirus CMutation(s): 1 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DEY (Subject of Investigation/LOI)
Query on DEY

Download Ideal Coordinates CCD File 
C [auth A], D [auth B](2R)-2-({3-[5-hydroxy-2-(3-methylbutyl)-3-oxo-6-thiophen-2-yl-2,3-dihydropyridazin-4-yl]-1,1-dioxido-2H-1,2,4-benzothia diazin-7-yl}oxy)propanamide
C23 H25 N5 O6 S2
BPHLZVCJUQBQLM-CYBMUJFWSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
DEY BindingDB:  3BR9 IC50: 62 (nM) from 1 assay(s)
EC50: 210 (nM) from 1 assay(s)
PDBBind:  3BR9 IC50: 62 (nM) from 1 assay(s)
Binding MOAD:  3BR9 IC50: 62 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.502α = 90
b = 104.311β = 90
c = 125.693γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations, Structure summary