8CEQ

Crystal structure of monkeypox virus methyltransferase VP39 in complex with inhibitor TO427


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery and structural characterization of monkeypox virus methyltransferase VP39 inhibitors reveal similarities to SARS-CoV-2 nsp14 methyltransferase.

Silhan, J.Klima, M.Otava, T.Skvara, P.Chalupska, D.Chalupsky, K.Kozic, J.Nencka, R.Boura, E.

(2023) Nat Commun 14: 2259-2259

  • DOI: https://doi.org/10.1038/s41467-023-38019-1
  • Primary Citation of Related Structures:  
    8B07, 8CEQ, 8CER, 8CES, 8CET, 8CEV, 8CGB

  • PubMed Abstract: 

    Monkeypox is a disease with pandemic potential. It is caused by the monkeypox virus (MPXV), a double-stranded DNA virus from the Poxviridae family, that replicates in the cytoplasm and must encode for its own RNA processing machinery including the capping machinery. Here, we present crystal structures of its 2'-O-RNA methyltransferase (MTase) VP39 in complex with the pan-MTase inhibitor sinefungin and a series of inhibitors that were discovered based on it. A comparison of this 2'-O-RNA MTase with enzymes from unrelated single-stranded RNA viruses (SARS-CoV-2 and Zika) reveals a conserved sinefungin binding mode, implicating that a single inhibitor could be used against unrelated viral families. Indeed, several of our inhibitors such as TO507 also inhibit the coronaviral nsp14 MTase.


  • Organizational Affiliation

    Institute of Organic Chemistry and Biochemistry AS CR, Prague 6, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
A, B
307Monkeypox virusMutation(s): 0 
Gene Names: 
EC: 2.1.1.57
UniProt
Find proteins for A0A7H0DN74 (Monkeypox virus)
Explore A0A7H0DN74 
Go to UniProtKB:  A0A7H0DN74
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7H0DN74
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UF9 (Subject of Investigation/LOI)
Query on UF9

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2~{S})-2-azanyl-4-[[(2~{S},3~{S},4~{R},5~{R})-5-[4-azanyl-5-(2-phenylethynyl)pyrrolo[2,3-d]pyrimidin-7-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]butanoic acid
C23 H25 N5 O5 S
ARBIWWNISHROOL-XVZIYINBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.732α = 90
b = 83.904β = 90
c = 154.385γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2023-05-03
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection