SARS-CoV-2 Macrodomain in complex with ADP-HPD

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.0 of the entry. See complete history


Viral macrodomains: a structural and evolutionary assessment of the pharmacological potential.

Rack, J.G.M.Zorzini, V.Zhu, Z.Schuller, M.Ahel, D.Ahel, I.

(2020) Open Biol 10: 200237-200237

  • DOI: https://doi.org/10.1098/rsob.200237
  • Primary Citation of Related Structures:  
    6Z5T, 6Z6I, 6Z72

  • PubMed Abstract: 

    Viral macrodomains possess the ability to counteract host ADP-ribosylation, a post-translational modification implicated in the creation of an antiviral environment via immune response regulation. This brought them into focus as promising therapeutic targets, albeit the close homology to some of the human macrodomains raised concerns regarding potential cross-reactivity and adverse effects for the host. Here, we evaluate the structure and function of the macrodomain of SARS-CoV-2, the causative agent of COVID-19. We show that it can antagonize ADP-ribosylation by PARP14, a cellular (ADP-ribosyl)transferase necessary for the restriction of coronaviral infections. Furthermore, our structural studies together with ligand modelling revealed the structural basis for poly(ADP-ribose) binding and hydrolysis, an emerging new aspect of viral macrodomain biology. These new insights were used in an extensive evolutionary analysis aimed at evaluating the druggability of viral macrodomains not only from the Coronaviridae but also Togaviridae and Iridoviridae genera (causing diseases such as Chikungunya and infectious spleen and kidney necrosis virus disease, respectively). We found that they contain conserved features, distinct from their human counterparts, which may be exploited during drug design.

  • Organizational Affiliation

    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Replicase polyprotein 1ab
A, B, C, D
176Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: (PDB Primary Data), 3.4.22 (PDB Primary Data), (PDB Primary Data), (PDB Primary Data), (PDB Primary Data), (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.1 (PDB Primary Data), 2.1.1 (PDB Primary Data), 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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1R (Subject of Investigation/LOI)
Query on A1R

Download Ideal Coordinates CCD File 
CA [auth D]
E [auth A]
J [auth A]
M [auth B]
R [auth C]
CA [auth D],
E [auth A],
J [auth A],
M [auth B],
R [auth C],
X [auth C]
C15 H24 N6 O12 P2
Query on MPO

Download Ideal Coordinates CCD File 
C7 H15 N O4 S
Query on GOL

Download Ideal Coordinates CCD File 
DA [auth D],
H [auth A],
N [auth B],
S [auth C],
W [auth C]
C3 H8 O3
Query on EDO

Download Ideal Coordinates CCD File 
EA [auth D]
F [auth A]
FA [auth D]
G [auth A]
GA [auth D]
EA [auth D],
F [auth A],
FA [auth D],
G [auth A],
GA [auth D],
HA [auth D],
I [auth A],
IA [auth D],
JA [auth D],
P [auth B],
T [auth C],
U [auth C],
V [auth C]
C2 H6 O2
Query on NA

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
K [auth A]
KA [auth D]
L [auth A]
AA [auth C],
BA [auth C],
K [auth A],
KA [auth D],
L [auth A],
LA [auth D],
Q [auth B],
Y [auth C],
Z [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.816α = 90
b = 83.096β = 94.51
c = 84.363γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom101794 and 210634

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release