Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.51 kDa 
• Atom Count: 2362 
• Residue Count: 250 
• Unique protein chains: 1

4IBI

Ebola virus VP35 bound to small molecule

• DOI: 10.2210/pdb4IBI/pdb

• Classification: TRANSCRIPTION/TRANSCRIPTION inhibitor
• Organism(s): Ebola virus - Mayinga, Zaire, 1976
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-12-08 Released: 2014-03-19 
• Deposition Author(s): Brown, C.S., Leung, D.W., Xu, W., Borek, D.M., Otwinowski, Z., Ramanan, P., Stubbs, A.J., Peterson, D.S., Binning, J.M., Amarasinghe, G.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.237 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

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

• PubMed: 24495995 
• 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 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.

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Organizational Affiliation: 

Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase cofactor VP35	A, B	129	Ebola virus - Mayinga, Zaire, 1976	Mutation(s): 0  Gene Names: VP35
Find proteins for Q05127 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05127  Go to UniProtKB:  Q05127

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1D8	A, B	3-{(2S)-2-(7-chloro-1,3-benzodioxol-5-yl)-4-hydroxy-5-oxo-3-[3-(trifluoromethyl)benzoyl]-2,5-dihydro-1H-pyrrol-1-yl}benzoic acid C26 H15 Cl F3 N O7 XYQJDZQSXLXEJQ-FQEVSTJZSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
1D8	Kd:  73000   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.237 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.302	α = 90
b = 65.451	β = 90
c = 72.653	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-12-08 
• Released Date: 2014-03-19 
Deposition Author(s): Brown, C.S., Leung, D.W., Xu, W., Borek, D.M., Otwinowski, Z., Ramanan, P., Stubbs, A.J., Peterson, D.S., Binning, J.M., Amarasinghe, G.K.

Revision History 

• Version 1.0: 2014-03-19
  Type: Initial release
  
• Version 1.1: 2014-05-14
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Refinement description