5IQ6 | pdb_00005iq6

Crystal structure of Dengue virus serotype 3 RNA dependent RNA polymerase bound to HeE1-2Tyr, a new pyridobenzothizole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5IQ6/pdb

• Classification: HYDROLASE
• Organism(s): dengue virus type 3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-03-10 Released: 2016-10-05 
• Deposition Author(s): Tarantino, D., Mastrangelo, E., Milani, M.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Targeting flavivirus RNA dependent RNA polymerase through a pyridobenzothiazole inhibitor.

Tarantino, D., Cannalire, R., Mastrangelo, E., Croci, R., Querat, G., Barreca, M.L., Bolognesi, M., Manfroni, G., Cecchetti, V., Milani, M.

(2016) Antiviral Res 134: 226-235

• PubMed: 27649989 
• DOI: https://doi.org/10.1016/j.antiviral.2016.09.007
• Primary Citation Related Structures: 
  5IQ6


• PubMed Abstract: 
  

  RNA dependent RNA polymerases (RdRp) are essential enzymes for flavivirus replication. Starting from an in silico docking analysis we identified a pyridobenzothiazole compound, HeE1-2Tyr, able to inhibit West Nile and Dengue RdRps activity in vitro, which proved effective against different flaviviruses in cell culture. Crystallographic data show that HeE1-2Tyr binds between the fingers domain and the priming loop of Dengue virus RdRp (Site 1). Conversely, enzyme kinetics, binding studies and mutational analyses suggest that, during the catalytic cycle and assembly of the RdRp-RNA complex, HeE1-2Tyr might be hosted in a distinct binding site (Site 2). RdRp mutational studies, driven by in silico docking analysis, allowed us to locate the inhibition Site 2 in the thumb domain. Taken together, our results provide innovative concepts for optimization of a new class of anti-flavivirus compounds.

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Organizational Affiliation: 
• Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy; CNR-IBF, Istituto di Biofisica, Via Celoria 26, I-20133, Milano, Italy.
Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Perugia, Italy.
Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy.
UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille university - IRD 190 - Inserm 1207 - EHESP), & Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille, Marseille, France.
Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Perugia, Italy. Electronic address: [e-mail].
Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy; CNR-IBF, Istituto di Biofisica, Via Celoria 26, I-20133, Milano, Italy. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 73.58 kDa 
• Atom Count: 4,884 
• Modeled Residue Count: 576 
• Deposited Residue Count: 628 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA dependent RNA polymerase	A	628	dengue virus type 3	Mutation(s): 0
UniProt
Find proteins for Q6YMS4 (Dengue virus type 3 (strain Sri Lanka/1266/2000)) Explore Q6YMS4  Go to UniProtKB:  Q6YMS4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6CJ	D [auth A]	N-[8-(cyclohexyloxy)-1-oxo-2-phenyl-1H-pyrido[2,1-b][1,3]benzothiazole-4-carbonyl]-L-tyrosine C33 H30 N2 O6 S PTUWWNGMUPSKDC-MHZLTWQESA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162	α = 90
b = 180.9	β = 90
c = 58.1	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-10-05 
Deposition Author(s): Tarantino, D., Mastrangelo, E., Milani, M.

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Funding Organization	Location	Grant Number
European Commission	Ecuador	SILVER project 2606444

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2016-10-12
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references