9QTC | pdb_00009qtc

HINT1 complexed with GS-441524

• PDB DOI: https://doi.org/10.2210/pdb9QTC/pdb

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


• Deposited: 2025-04-08 Released: 2026-06-03 
• Deposition Author(s): Zimberger, C., Ferron, F.
• Funding Organization(s): Agence Nationale de la Recherche (ANR), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.188 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Impact of remdesivir modifications on human HINT1 binding - A structural and functional study in the remdesivir activation pathway.

Chazot, A., Zimberger, C., Fotopoulos, I., Canard, B., Alvarez, K., Ferron, F.

(2026) Structure 

• PubMed: 42184828 
• DOI: https://doi.org/10.1016/j.str.2026.04.015
• Primary Citation Related Structures: 
  9QRO, 9QTC


• PubMed Abstract: 
  

  Remdesivir is an antiviral ProTide-type nucleotide analog, which is activated into its 5'-triphosphate form by several cellular enzymes. The human histidine triad nucleotide-binding protein 1 (hHINT1) hydrolyzes the P-N bond to release the 5'-monophosphate. The nucleotide chemical structure consequently impacts the activation pathway efficacy. We report crystal structures of human HINT1 in complex with either the nucleoside GS-441524 or the monophosphate nucleoside GS-441524-MP-both metabolites of remdesivir at 1.30 Å and 1.58 Å resolution, respectively. Together with enzymatic data, these results disclose the main structural determinants governing activity, namely the steric hindrance of the phosphoramidate moiety as well as ribose modifications altering interactions with Asp43.

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Organizational Affiliation: 
• Aix Marseille Université, CNRS, AFMB, UMR 7257 Marseille, France.
Aix Marseille Université, CNRS, AFMB, UMR 7257 Marseille, France; European Virus Bioinformatics Center, Jena, Germany.
Aix Marseille Université, CNRS, AFMB, UMR 7257 Marseille, France. Electronic address: [e-mail].
Aix Marseille Université, CNRS, AFMB, UMR 7257 Marseille, France; European Virus Bioinformatics Center, Jena, Germany. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.13 kDa 
• Atom Count: 2,358 
• Modeled Residue Count: 227 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine triad nucleotide-binding protein 1	A, B	126	Homo sapiens	Mutation(s): 0  Gene Names: HINT1, HINT, PKCI1, PRKCNH1 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U08 (Subject of Investigation/LOI)	C [auth A]	(2~{R},3~{R},4~{S},5~{R})-2-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolane-2-carbonitrile C12 H13 N5 O4 BRDWIEOJOWJCLU-LTGWCKQJSA-N
MES	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.188 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.286	α = 90
b = 46.326	β = 94.66
c = 64.066	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-03 
Deposition Author(s): Zimberger, C., Ferron, F.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	IA-10-INBS-0005
Other private	France	XPLORE

Revision History  

• Version 1.0: 2026-06-03
  Type: Initial release