8PIE

Crystal structure of the human nucleoside diphosphate kinase B domain in complex with the product AT-8500 formed by catalysis of compound AT-9010


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

The activation cascade of the broad-spectrum antiviral bemnifosbuvir characterized at atomic resolution.

Chazot, A.Zimberger, C.Feracci, M.Moussa, A.Good, S.Sommadossi, J.P.Alvarez, K.Ferron, F.Canard, B.

(2024) PLoS Biol 22: e3002743-e3002743

  • DOI: https://doi.org/10.1371/journal.pbio.3002743
  • Primary Citation of Related Structures:  
    8PIE, 8PTS, 8PWK, 8QCH

  • PubMed Abstract: 

    Bemnifosbuvir (AT-527) and AT-752 are guanosine analogues currently in clinical trials against several RNA viruses. Here, we show that these drugs require a minimal set of 5 cellular enzymes for activation to their common 5'-triphosphate AT-9010, with an obligate order of reactions. AT-9010 selectively inhibits essential viral enzymes, accounting for antiviral potency. Functional and structural data at atomic resolution decipher N6-purine deamination compatible with its metabolic activation. Crystal structures of human histidine triad nucleotide binding protein 1, adenosine deaminase-like protein 1, guanylate kinase 1, and nucleoside diphosphate kinase at 2.09, 2.44, 1.76, and 1.9 Å resolution, respectively, with cognate precursors of AT-9010 illuminate the activation pathway from the orally available bemnifosbuvir to AT-9010, pointing to key drug-protein contacts along the activation pathway. Our work provides a framework to integrate the design of antiviral nucleotide analogues, confronting requirements and constraints associated with activation enzymes along the 5'-triphosphate assembly line.


  • Organizational Affiliation

    Aix Marseille Université, CNRS, AFMB, UMR 7257, Marseille, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase B
A, B, C, D, E
A, B, C, D, E, F
171Homo sapiensMutation(s): 0 
Gene Names: NME2NM23B
EC: 2.7.4.6 (PDB Primary Data), 2.7.13.3 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P22392 (Homo sapiens)
Explore P22392 
Go to UniProtKB:  P22392
PHAROS:  P22392
GTEx:  ENSG00000243678 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22392
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HIP
Query on HIP
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC6 H11 N3 O5 PHIS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.19α = 90
b = 120.313β = 110.154
c = 71.918γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentFranceGrand Prix Scientifique de l'Institut de France -Fondation Simone et Cino Del Duca - 2022

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2024-09-04
    Changes: Database references