7BF6

Crystal structure of SARS-CoV-2 macrodomain in complex with remdesivir metabolite GS-441524

• PDB DOI: https://doi.org/10.2210/pdb7BF6/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-12-31 Released: 2021-01-13 
• Deposition Author(s): Ni, X., Knapp, S., Chaikuad, A., Structural Genomics Consortium, Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.226 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

Structural Insights into Plasticity and Discovery of Remdesivir Metabolite GS-441524 Binding in SARS-CoV-2 Macrodomain.

Ni, X., Schroder, M., Olieric, V., Sharpe, M.E., Hernandez-Olmos, V., Proschak, E., Merk, D., Knapp, S., Chaikuad, A.

(2021) ACS Med Chem Lett 12: 603-609

• PubMed: 33850605 
• DOI: https://doi.org/10.1021/acsmedchemlett.0c00684
• Primary Citation of Related Structures:  
  6YWK, 6YWL, 6YWM, 7BF3, 7BF4, 7BF5, 7BF6


• PubMed Abstract: 
  

  The nsP3 macrodomain is a conserved protein interaction module that plays essential regulatory roles in the host immune response by recognizing and removing posttranslational ADP-ribosylation sites during SARS-CoV-2 infection. Thus targeting this protein domain may offer a therapeutic strategy to combat current and future virus pandemics. To assist inhibitor development efforts, we report here a comprehensive set of macrodomain crystal structures complexed with diverse naturally occurring nucleotides, small molecules, and nucleotide analogues including GS-441524 and its phosphorylated analogue, active metabolites of remdesivir. The presented data strengthen our understanding of the SARS-CoV-2 macrodomain structural plasticity and provide chemical starting points for future inhibitor development.

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Organizational Affiliation: 

Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, 60438 Frankfurt am Main, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 57.21 kDa 
• Atom Count: 4,069 
• Modelled Residue Count: 507 
• Deposited Residue Count: 519 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A, B, C	173	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U08 (Subject of Investigation/LOI)	D [auth A], H [auth B], I [auth C]	(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
EDO	E [auth A], F [auth A], G [auth A], J [auth C], K [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.226 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.238	α = 90
b = 30.476	β = 119.87
c = 111.685	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Ni, X., Knapp, S., Chaikuad, A., Structural Genomics Consortium, Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2021-01-13
  Type: Initial release
  
• Version 2.0: 2021-01-27
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2021-07-07
  Changes: Database references
• Version 2.2: 2022-07-27
  Changes: Database references, Source and taxonomy, Structure summary
• Version 2.3: 2024-01-31
  Changes: Data collection, Refinement description