8PIE | pdb_00008pie

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

PDB DOI: https://doi.org/10.2210/pdb8PIE/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-06-21 Released: 2024-07-31
Deposition Author(s): Feracci, M., Chazot, A., Ferron, F., Alvarez, K., Canard, B.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.213 (Depositor), 0.218 (DCC)
R-Value Work:
0.172 (Depositor)

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

PubMed: 39190717 Search on PubMed
DOI: https://doi.org/10.1371/journal.pbio.3002743
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 120.13 kDa
Atom Count: 7,869
Modeled Residue Count: 906
Deposited Residue Count: 1,026
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase B	A, B, C, D, E A, B, C, D, E, F	171	Homo sapiens	Mutation(s): 0 Gene Names: NME2, NM23B 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22392
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7QT Query on 7QT Download:Ideal Coordinates CCD File SDF format, chain M [auth F] SDF format, chain L [auth E] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain M [auth F] MOL2 format, chain L [auth E] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain M [auth F] mmCIF format, chain L [auth E] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A] I [auth B] J [auth C] K [auth D] L [auth E] G [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F]	[(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 phosphono hydrogen phosphate C₁₁ H₁₆ F N₅ O₁₀ P₂ LEEQMJUVDQBILY-GITKWUPZSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]