The RNA-dependent RNA polymerase domain of dengue 2 NS5, bound with RK-0404678

Experimental Data Snapshot

  • Resolution: 2.43 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Discovery of a small molecule inhibitor targeting dengue virus NS5 RNA-dependent RNA polymerase.

Shimizu, H.Saito, A.Mikuni, J.Nakayama, E.E.Koyama, H.Honma, T.Shirouzu, M.Sekine, S.I.Shioda, T.

(2019) PLoS Negl Trop Dis 13: e0007894-e0007894

  • DOI: https://doi.org/10.1371/journal.pntd.0007894
  • Primary Citation of Related Structures:  
    6IZX, 6IZY, 6IZZ, 6J00

  • PubMed Abstract: 

    Dengue is a mosquito-borne viral infection that has spread globally in recent years. Around half of the world's population, especially in the tropics and subtropics, is at risk of infection. Every year, 50-100 million clinical cases are reported, and more than 500,000 patients develop the symptoms of severe dengue infection: dengue haemorrhagic fever and dengue shock syndrome, which threaten life in Asia and Latin America. No antiviral drug for dengue is available. The dengue virus (DENV) non-structural protein 5 (NS5), which possesses the RNA-dependent RNA polymerase (RdRp) activity and is responsible for viral replication and transcription, is an attractive target for anti-dengue drug development. In the present study, 16,240 small-molecule compounds in a fragment library were screened for their capabilities to inhibit the DENV type 2 (DENV2) RdRp activities in vitro. Based on in cellulo antiviral and cytotoxity assays, we selected the compound RK-0404678 with the EC50 value of 6.0 μM for DENV2. Crystallographic analyses revealed two unique binding sites for RK-0404678 within the RdRp, which are conserved in flavivirus NS5 proteins. No resistant viruses emerged after nine rounds of serial passage of DENV2 in the presence of RK-0404678, suggesting the high genetic barrier of this compound to the emergence of a resistant virus. Collectively, RK-0404678 and its binding sites provide a new framework for antiviral drug development.

  • Organizational Affiliation

    Drug Discovery Chemistry Platform Unit, RIKEN Center for Sustainable Resource Science, Hirosawa, Wako, Saitama, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyprotein686dengue virus type 2Mutation(s): 0 
Find proteins for P14340 (Dengue virus type 2 (strain Thailand/NGS-C/1944))
Explore P14340 
Go to UniProtKB:  P14340
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14340
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B5C (Subject of Investigation/LOI)
Query on B5C

Download Ideal Coordinates CCD File 
M [auth A],
N [auth A]
2-oxo-2H-1,3-benzoxathiol-5-yl acetate
C9 H6 O4 S
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
Query on CO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.43 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 236.5α = 90
b = 236.5β = 90
c = 236.5γ = 90
Software Package:
Software NamePurpose
xia2data scaling
Cootmodel building
xia2data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)Japan--
Japan Society for the Promotion of ScienceJapan17K07322

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description