Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-2',3'-Vanadate

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.172 

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Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2.

Kim, Y.Wower, J.Maltseva, N.Chang, C.Jedrzejczak, R.Wilamowski, M.Kang, S.Nicolaescu, V.Randall, G.Michalska, K.Joachimiak, A.

(2021) Commun Biol 4: 193-193

  • DOI: https://doi.org/10.1038/s42003-021-01735-9
  • Primary Citation of Related Structures:  
    6WLC, 6WXC, 6X1B, 6X4I, 7K1L

  • PubMed Abstract: 

    SARS-CoV-2 Nsp15 is a uridine-specific endoribonuclease with C-terminal catalytic domain belonging to the EndoU family that is highly conserved in coronaviruses. As endoribonuclease activity seems to be responsible for the interference with the innate immune response, Nsp15 emerges as an attractive target for therapeutic intervention. Here we report the first structures with bound nucleotides and show how the enzyme specifically recognizes uridine moiety. In addition to a uridine site we present evidence for a second base binding site that can accommodate any base. The structure with a transition state analog, uridine vanadate, confirms interactions key to catalytic mechanisms. In the presence of manganese ions, the enzyme cleaves unpaired RNAs. This acquired knowledge was instrumental in identifying Tipiracil, an FDA approved drug that is used in the treatment of colorectal cancer, as a potential anti-COVID-19 drug. Using crystallography, biochemical, and whole-cell assays, we demonstrate that Tipiracil inhibits SARS-CoV-2 Nsp15 by interacting with the uridine binding pocket in the enzyme's active site. Our findings provide new insights for the development of uracil scaffold-based drugs.

  • Organizational Affiliation

    Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA. andrzejj@anl.gov.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uridylate-specific endoribonuclease
A, B
370Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.1 (PDB Primary Data), (UniProt), 3.4.22 (UniProt), (UniProt), (UniProt), (UniProt), (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), (UniProt)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UVC (Subject of Investigation/LOI)
Query on UVC

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
C9 H12 N2 O9 V
Query on SO4

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G [auth A],
I [auth B]
O4 S
Query on EDO

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F [auth A]1,2-ETHANEDIOL
C2 H6 O2
Query on ACT

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D [auth A],
E [auth A]
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.172 
  • Space Group: P 63
  • Diffraction Data: https://doi.org/10.18430/m37k1l
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.832α = 90
b = 150.832β = 90
c = 110.734γ = 120
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2021-02-24
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description