8QCH

Human Adenosine deaminase-like protein in complex with compound AT8001


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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
Adenosine deaminase-like protein
A, B, C, D, E
A, B, C, D, E, F, G, H
355Homo sapiensMutation(s): 0 
Gene Names: ADALADAL1
EC: 3.5.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q6DHV7 (Homo sapiens)
Explore Q6DHV7 
Go to UniProtKB:  Q6DHV7
PHAROS:  Q6DHV7
GTEx:  ENSG00000168803 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DHV7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EIF (Subject of Investigation/LOI)
Query on EIF

Download Ideal Coordinates CCD File 
CA [auth E]
GA [auth F]
I [auth A]
N [auth B]
NA [auth G]
CA [auth E],
GA [auth F],
I [auth A],
N [auth B],
NA [auth G],
QA [auth H],
R [auth C],
X [auth D]
[(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate
C11 H15 F N5 O7 P
BOEZKCHYGLAVGV-GITKWUPZSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
BA [auth E],
MA [auth G],
V [auth D],
W [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
EA [auth E]
FA [auth E]
IA [auth F]
JA [auth F]
AA [auth D],
EA [auth E],
FA [auth E],
IA [auth F],
JA [auth F],
K [auth A],
KA [auth F],
L [auth A],
LA [auth F],
M [auth A],
P [auth B],
PA [auth G],
Q [auth B],
SA [auth H],
T [auth C],
U [auth C],
Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
DA [auth E]
HA [auth F]
J [auth A]
O [auth B]
OA [auth G]
DA [auth E],
HA [auth F],
J [auth A],
O [auth B],
OA [auth G],
RA [auth H],
S [auth C],
Y [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA
Query on NA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.757α = 90
b = 142.983β = 90
c = 156.399γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
Aimlessdata scaling
MoRDaphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-10-INBS-0005
Fondation pour la Recherche Medicale (FRM)FranceSoutien aux equipes

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