5IQ6

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.261
R-Value Work: 0.191
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/j.antiviral.2016.09.007
Primary Citation of 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.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6YMS4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6CJ Query on 6CJ Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	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		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]