4IBB

Ebola virus VP35 bound to small molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

In Silico Derived Small Molecules Bind the Filovirus VP35 Protein and Inhibit Its Polymerase Cofactor Activity.

Brown, C.S.Lee, M.S.Leung, D.W.Wang, T.Xu, W.Luthra, P.Anantpadma, M.Shabman, R.S.Melito, L.M.Macmillan, K.S.Borek, D.M.Otwinowski, Z.Ramanan, P.Stubbs, A.J.Peterson, D.S.Binning, J.M.Tonelli, M.Olson, M.A.Davey, R.A.Ready, J.M.Basler, C.F.Amarasinghe, G.K.

(2014) J Mol Biol 426: 2045-2058

  • DOI: 10.1016/j.jmb.2014.01.010
  • Primary Citation of Related Structures:  
    4IBE, 4IBF, 4IBG, 4IBI, 4IBJ, 4IBK, 4IBB, 4IBC, 4IBD

  • PubMed Abstract: 
  • The Ebola virus (EBOV) genome only encodes a single viral polypeptide with enzymatic activity, the viral large (L) RNA-dependent RNA polymerase protein. However, currently, there is limited information about the L protein, which has hampered the deve ...

    The Ebola virus (EBOV) genome only encodes a single viral polypeptide with enzymatic activity, the viral large (L) RNA-dependent RNA polymerase protein. However, currently, there is limited information about the L protein, which has hampered the development of antivirals. Therefore, antifiloviral therapeutic efforts must include additional targets such as protein-protein interfaces. Viral protein 35 (VP35) is multifunctional and plays important roles in viral pathogenesis, including viral mRNA synthesis and replication of the negative-sense RNA viral genome. Previous studies revealed that mutation of key basic residues within the VP35 interferon inhibitory domain (IID) results in significant EBOV attenuation, both in vitro and in vivo. In the current study, we use an experimental pipeline that includes structure-based in silico screening and biochemical and structural characterization, along with medicinal chemistry, to identify and characterize small molecules that target a binding pocket within VP35. NMR mapping experiments and high-resolution x-ray crystal structures show that select small molecules bind to a region of VP35 IID that is important for replication complex formation through interactions with the viral nucleoprotein (NP). We also tested select compounds for their ability to inhibit VP35 IID-NP interactions in vitro as well as VP35 function in a minigenome assay and EBOV replication. These results confirm the ability of compounds identified in this study to inhibit VP35-NP interactions in vitro and to impair viral replication in cell-based assays. These studies provide an initial framework to guide development of antifiloviral compounds against filoviral VP35 proteins.


    Organizational Affiliation

    Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address: gamarasinghe@path.wustl.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase cofactor VP35AB129Ebola virus - Mayinga, Zaire, 1976Mutation(s): 0 
Gene Names: VP35
Find proteins for Q05127 (Zaire ebolavirus (strain Mayinga-76))
Explore Q05127 
Go to UniProtKB:  Q05127
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1DK
Query on 1DK

Download CCD File 
A, B
{4-[(5R)-3-hydroxy-2-oxo-4-(thiophen-2-ylcarbonyl)-5-(2,4,5-trimethylphenyl)-2,5-dihydro-1H-pyrrol-1-yl]phenyl}acetic acid
C26 H23 N O5 S
BCVUJQWONQBDJX-HSZRJFAPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1DKKd:  270700   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.48α = 90
b = 65.81β = 90
c = 72.227γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2014-03-19
    Changes: Structure summary
  • Version 1.2: 2014-05-14
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description, Structure summary