9RHN | pdb_00009rhn

Structure of SARS-coV-2 NSP3 macrodomain in complex with ligand

• PDB DOI: https://doi.org/10.2210/pdb9RHN/pdb

• Classification: VIRUS
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-06-09 Released: 2026-06-24 
• Deposition Author(s): Ruiz Carrillo, D., Sander, S., Tidow, H., Garcia-Alai, M., Fliegert, R., Sandmann, M.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.209 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Design, structure-based optimization and antiviral evaluation of potent inhibitors for the macrodomain Mac1 of SARS-CoV-2.

Sandmann, M., Tajdar, S., Sander, S., Ruiz Carrillo, D., Ganter, B., Fischer, C., Ocenas, M., Etzold, S., Pekarek, N., Berger, J., Meister, T.L., Selisko, B., Canard, B., Watt, J.M., Baszczynski, O., Potter, B.V., Garcia Alai, M., Henning, T., Susanne, P., Meier, C., Fliegert, R.

(2026) Nat Commun 17

• PubMed: 42509248 
• DOI: https://doi.org/10.1038/s41467-026-75835-7
• Primary Citation Related Structures: 
  9RHN, 9RHO


• PubMed Abstract: 
  

  Enzymatically active macrodomains of (+)ss-RNA viruses mediate immune evasion by countering ADP-ribosylation and are therefore promising druggable targets. Here we report testing of ADP / ADP-ribose analogues for their ability to inhibit Mac1 of SARS-CoV-2, measurement of the affinity of active compounds and characterization of their binding mode by cocrystallization, uncovering critical molecular determinants of protein-ligand interaction. Key findings of the resulting structure-activity relationship (SAR) include that inhibitory potency is improved by either replacing the distal ribose of ADP-ribose by a small alkyl group or the adenine N7 by carbon. Based on insights from the SAR, we show β-methyl-GS-441524-diphosphate as nanomolar inhibitor that exhibits >1000-fold selectivity over human MacroD1 and MacroD2. Addition of C ₁₁ -acyloxybenzyl (AB)-masking groups yields a membrane permeable, lipophilic prodrug that inhibits SARS-CoV-2 in cell culture (EC ₅₀ 0.06 µM) while exhibiting low cytotoxicity (CC ₅₀  > 50 µM). Replacement of the terminal methyl phosphate with an ethyl phosphonate increases stability of the prodrug with little effect on toxicity and antiviral potency (EC ₅₀  = 0.03 µM), making it a membrane-permeable nucleotide-based prodrug against viral macrodomains.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
Organic Chemistry, Department of Chemistry, University of Hamburg, Hamburg, Germany.
The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR) & Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
European Molecular Biology Laboratory Hamburg, Hamburg, Germany.
Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
Bernhard Nocht Institute, Leibniz Institute for Tropical Medicine, Hamburg, Germany.
Institute for Infection Research and Vaccine Development (IIRVD), Centre for Internal Medicine, University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany.
German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.
Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Université, UMR7257, Marseille, France.
Department of Life Sciences, University of Bath, Bath, UK.
Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Oxford, UK.
Centre for Structural Systems Biology (CSSB), DESY Campus, Hamburg, Germany.
Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. [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: 37.36 kDa 
• Atom Count: 2,973 
• Modeled Residue Count: 338 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A, B	169	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1  Go to UniProtKB:  P0DTC1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1JF9 (Subject of Investigation/LOI)	C [auth A], D [auth B]	[[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-ethyl-phosphinic acid C14 H19 N5 O9 P2 RPMCXDPZZYWVEM-LHMODEAPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.209 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.501	α = 90
b = 83.501	β = 90
c = 41.426	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing
PDB-REDO	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-24 
Deposition Author(s): Ruiz Carrillo, D., Sander, S., Tidow, H., Garcia-Alai, M., Fliegert, R., Sandmann, M.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB 1328

Revision History  

• Version 1.0: 2026-06-24
  Type: Initial release
  
• Version 1.1: 2026-07-01
  Changes: Database references
• Version 1.2: 2026-08-19
  Changes: Database references