8QCH | pdb_00008qch

Human Adenosine deaminase-like protein in complex with compound AT8001

PDB DOI: https://doi.org/10.2210/pdb8QCH/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2023-08-26 Released: 2024-07-31
Deposition Author(s): Zimberger, C., canard, B., Ferron, F.
Funding Organization(s): Agence Nationale de la Recherche (ANR), Fondation pour la Recherche Medicale (FRM)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free:
0.243 (Depositor), 0.233 (DCC)
R-Value Work:
0.214 (Depositor), 0.202 (DCC)
R-Value Observed:
0.216 (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: 328.2 kDa
Atom Count: 23,207
Modeled Residue Count: 2,765
Deposited Residue Count: 2,840
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine deaminase-like protein	A, B, C, D, E A, B, C, D, E, F, G, H	355	Homo sapiens	Mutation(s): 0 Gene Names: ADAL, ADAL1 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6DHV7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EIF (Subject of Investigation/LOI) Query on EIF Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain X [auth D] SDF format, chain QA [auth H] SDF format, chain NA [auth G] SDF format, chain N [auth B] SDF format, chain I [auth A] SDF format, chain GA [auth F] SDF format, chain CA [auth E] MOL2 format, chain R [auth C] MOL2 format, chain X [auth D] MOL2 format, chain QA [auth H] MOL2 format, chain NA [auth G] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain GA [auth F] MOL2 format, chain CA [auth E] mmCIF format, chain R [auth C] mmCIF format, chain X [auth D] mmCIF format, chain QA [auth H] mmCIF format, chain NA [auth G] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain GA [auth F] mmCIF format, chain CA [auth E]	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		Interactions Focus chain CA [auth E] Focus chain GA [auth F] Focus chain I [auth A] Focus chain N [auth B] Focus chain NA [auth G] Focus chain QA [auth H] Focus chain R [auth C] Focus chain X [auth D] Interactions & Density Focus chain CA [auth E] Focus chain GA [auth F] Focus chain I [auth A] Focus chain N [auth B] Focus chain NA [auth G] Focus chain QA [auth H] Focus chain R [auth C] Focus chain X [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain MA [auth G] MOL2 format, chain BA [auth E] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain MA [auth G] mmCIF format, chain BA [auth E] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain MA [auth G]	BA [auth E], MA [auth G], V [auth D], W [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain MA [auth G] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain BA [auth E] Focus chain MA [auth G] Focus chain V [auth D] Focus chain W [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain P [auth B] SDF format, chain Z [auth D] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain SA [auth H] SDF format, chain Q [auth B] SDF format, chain PA [auth G] SDF format, chain M [auth A] SDF format, chain LA [auth F] SDF format, chain L [auth A] SDF format, chain KA [auth F] SDF format, chain K [auth A] SDF format, chain JA [auth F] SDF format, chain IA [auth F] SDF format, chain FA [auth E] SDF format, chain EA [auth E] MOL2 format, chain AA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Z [auth D] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain SA [auth H] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain FA [auth E] MOL2 format, chain EA [auth E] mmCIF format, chain AA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain Z [auth D] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain SA [auth H] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth G] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain IA [auth F] mmCIF format, chain FA [auth E] mmCIF format, chain EA [auth E]	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		Interactions Focus chain AA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain P [auth B] Focus chain PA [auth G] Focus chain Q [auth B] Focus chain SA [auth H] Focus chain T [auth C] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain P [auth B] Focus chain PA [auth G] Focus chain Q [auth B] Focus chain SA [auth H] Focus chain T [auth C] Focus chain U [auth C] Focus chain Z [auth D]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain Y [auth D] SDF format, chain RA [auth H] SDF format, chain OA [auth G] SDF format, chain O [auth B] SDF format, chain J [auth A] SDF format, chain HA [auth F] SDF format, chain DA [auth E] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain RA [auth H] MOL2 format, chain OA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain J [auth A] MOL2 format, chain HA [auth F] MOL2 format, chain DA [auth E] mmCIF format, chain S [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain RA [auth H] mmCIF format, chain OA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain J [auth A] mmCIF format, chain HA [auth F] mmCIF format, chain DA [auth E]	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		Interactions Focus chain DA [auth E] Focus chain HA [auth F] Focus chain J [auth A] Focus chain O [auth B] Focus chain OA [auth G] Focus chain RA [auth H] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain DA [auth E] Focus chain HA [auth F] Focus chain J [auth A] Focus chain O [auth B] Focus chain OA [auth G] Focus chain RA [auth H] Focus chain S [auth C] Focus chain Y [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain TA [auth H] MOL2 format, chain TA [auth H] mmCIF format, chain TA [auth H]	TA [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain TA [auth H] Interactions & Density Focus chain TA [auth H]