8PYW

Crystal structure of the human Nucleoside-diphosphate kinase B domain bound to compound diphosphate form of AT-9052-Sp.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.170 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

An exonuclease-resistant chain-terminating nucleotide analogue targeting the SARS-CoV-2 replicase complex.

Shannon, A.Chazot, A.Feracci, M.Falcou, C.Fattorini, V.Selisko, B.Good, S.Moussa, A.Sommadossi, J.P.Ferron, F.Alvarez, K.Canard, B.

(2024) Nucleic Acids Res 52: 1325-1340

  • DOI: https://doi.org/10.1093/nar/gkad1194
  • Primary Citation of Related Structures:  
    8PYW

  • PubMed Abstract: 

    Nucleotide analogues (NA) are currently employed for treatment of several viral diseases, including COVID-19. NA prodrugs are intracellularly activated to the 5'-triphosphate form. They are incorporated into the viral RNA by the viral polymerase (SARS-CoV-2 nsp12), terminating or corrupting RNA synthesis. For Coronaviruses, natural resistance to NAs is provided by a viral 3'-to-5' exonuclease heterodimer nsp14/nsp10, which can remove terminal analogues. Here, we show that the replacement of the α-phosphate of Bemnifosbuvir 5'-triphosphate form (AT-9010) by an α-thiophosphate renders it resistant to excision. The resulting α-thiotriphosphate, AT-9052, exists as two epimers (RP/SP). Through co-crystallization and activity assays, we show that the Sp isomer is preferentially used as a substrate by nucleotide diphosphate kinase (NDPK), and by SARS-CoV-2 nsp12, where its incorporation causes immediate chain-termination. The same -Sp isomer, once incorporated by nsp12, is also totally resistant to the excision by nsp10/nsp14 complex. However, unlike AT-9010, AT-9052-RP/SP no longer inhibits the N-terminal nucleotidylation domain of nsp12. We conclude that AT-9052-Sp exhibits a unique mechanism of action against SARS-CoV-2. Moreover, the thio modification provides a general approach to rescue existing NAs whose activity is hampered by coronavirus proofreading capacity.


  • 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
Nucleoside diphosphate kinase B
A, B, C, D, E
A, B, C, D, E, F
152Homo 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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IF9 (Subject of Investigation/LOI)
Query on IF9

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
K [auth C]
M [auth D]
N [auth E]
H [auth A],
J [auth B],
K [auth C],
M [auth D],
N [auth E],
O [auth F]
[[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphoryl] dihydrogen phosphate
C11 H16 F N5 O9 P2 S
QCBAKKHBHHSVKS-VXAAHYPFSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
L [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.22α = 90
b = 121.06β = 107.135
c = 70.76γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Database references