8BCR | pdb_00008bcr

DENV3 Methyltransferase in complexed with AT-9010 and SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.234 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AT9Click on this verticalbar to view detailsBest fitted SAMClick on this verticalbar to view detailsBest fitted SAHClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

AT-752 targets multiple sites and activities on the Dengue virus replication enzyme NS5.

Feracci, M.Eydoux, C.Fattorini, V.Lo Bello, L.Gauffre, P.Selisko, B.Sutto-Ortiz, P.Shannon, A.Xia, H.Shi, P.Y.Noel, M.Debart, F.Vasseur, J.J.Good, S.Lin, K.Moussa, A.Sommadossi, J.P.Chazot, A.Alvarez, K.Guillemot, J.C.Decroly, E.Ferron, F.Canard, B.

(2023) Antiviral Res 212: 105574-105574

  • DOI: https://doi.org/10.1016/j.antiviral.2023.105574
  • Primary Citation of Related Structures:  
    8BCR

  • PubMed Abstract: 

    AT-752 is a guanosine analogue prodrug active against dengue virus (DENV). In infected cells, it is metabolized into 2'-methyl-2'-fluoro guanosine 5'-triphosphate (AT-9010) which inhibits RNA synthesis in acting as a RNA chain terminator. Here we show that AT-9010 has several modes of action on DENV full-length NS5. AT-9010 does not inhibit the primer pppApG synthesis step significantly. However, AT-9010 targets two NS5-associated enzyme activities, the RNA 2'-O-MTase and the RNA-dependent RNA polymerase (RdRp) at its RNA elongation step. Crystal structure and RNA methyltransferase (MTase) activities of the DENV 2 MTase domain in complex with AT-9010 at 1.97 Å resolution shows the latter bound to the GTP/RNA-cap binding site, accounting for the observed inhibition of 2'-O but not N7-methylation activity. AT-9010 is discriminated ∼10 to 14-fold against GTP at the NS5 active site of all four DENV1-4 NS5 RdRps, arguing for significant inhibition through viral RNA synthesis termination. In Huh-7 cells, DENV1-4 are equally sensitive to AT-281, the free base of AT-752 (EC 50  ≈ 0.50 μM), suggesting broad spectrum antiviral properties of AT-752 against flaviviruses.


  • Organizational Affiliation

    AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyprotein
A, B
276dengue virus type 3Mutation(s): 0 
UniProt
Find proteins for A9LIE0 (dengue virus type 3)
Explore A9LIE0 
Go to UniProtKB:  A9LIE0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9LIE0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AT9 (Subject of Investigation/LOI)
Query on AT9

Download Ideal Coordinates CCD File 
D [auth B][[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
C11 H17 F N5 O13 P3
GFEXCNGIPRYQFE-GITKWUPZSA-N
SAM (Subject of Investigation/LOI)
Query on SAM

Download Ideal Coordinates CCD File 
C [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
E [auth B]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.234 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.26α = 90
b = 184.133β = 90
c = 52.149γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
Aimlessdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AT9Click on this verticalbar to view detailsBest fitted SAMClick on this verticalbar to view detailsBest fitted SAHClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-10-INSB-05-01

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description