5MRK

Structural basis of Zika virus methyltransferase inhibition by sinefungin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

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Literature

Structural basis of Zika virus methyltransferase inhibition by sinefungin.

Hercik, K., Brynda, J., Nencka, R., Boura, E.

(2017) Arch Virol 162: 2091-2096

  • DOI: 10.1007/s00705-017-3345-x
  • Primary Citation of Related Structures:  
    5MRK

  • PubMed Abstract: 

    • Zika virus is considered a major global threat to human kind. Here, we present a crystal structure of one of its essential enzymes, the methyltransferase, with the inhibitor sinefungin. This structure, together with previously solved structures with bound substrates, will provide the information needed for rational inhibitor design ...

    Zika virus is considered a major global threat to human kind. Here, we present a crystal structure of one of its essential enzymes, the methyltransferase, with the inhibitor sinefungin. This structure, together with previously solved structures with bound substrates, will provide the information needed for rational inhibitor design. Based on the structural data we suggest the modification of the adenine moiety of sinefungin to increase selectivity and to covalently link it to a GTP analogue, to increase the affinity of the synthesized compounds.

    Organizational Affiliation: 

    Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10, Prague 6, Czech Republic. boura@uochb.cas.cz.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
methyltransferaseA, B265Zika virusMutation(s): 0 
EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013))
Explore A0A024B7W1 
Go to UniProtKB:  A0A024B7W1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A024B7W1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SFG
Query on SFG
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		SINEFUNGIN
C15 H23 N7 O5
LMXOHSDXUQEUSF-YECHIGJVSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.84α = 90
b = 52.01β = 107.56
c = 84.17γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2016-12-23 
  • Released Date: 2017-01-25 
    • Deposition Author(s): Hercik, K., Boura, E.

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-05-17
    Changes: Database references
  • Version 1.2: 2017-06-28
    Changes: Database references