8PWK

human HINT1 in complex with compound AT8003


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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
Histidine triad nucleotide-binding protein 1
A, B
126Homo sapiensMutation(s): 0 
Gene Names: HINT1HINTPKCI1PRKCNH1
EC: 3 (PDB Primary Data), 3.4.22 (UniProt), 3.9.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P49773 (Homo sapiens)
Explore P49773 
Go to UniProtKB:  P49773
PHAROS:  P49773
GTEx:  ENSG00000169567 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49773
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I0H (Subject of Investigation/LOI)
Query on I0H

Download Ideal Coordinates CCD File 
C [auth A][(2~{R},3~{R},4~{R},5~{R})-5-[2-azanyl-6-(methylamino)purin-9-yl]-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate
C12 H18 F N6 O6 P
SJCUNPMCBONQDJ-GSWPYSDESA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.961α = 90
b = 46.45β = 94.98
c = 63.771γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INBS-0005

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