4O4R

Murine Norovirus RdRp in complex with PPNDS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

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Ligand Structure Quality Assessment 


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Literature

PPNDS inhibits murine Norovirus RNA-dependent RNA-polymerase mimicking two RNA stacking bases.

Croci, R., Tarantino, D., Milani, M., Pezzullo, M., Rohayem, J., Bolognesi, M., Mastrangelo, E.

(2014) FEBS Lett 588: 1720-1725

  • DOI: https://doi.org/10.1016/j.febslet.2014.03.021
  • Primary Citation of Related Structures:  
    4O4R

  • PubMed Abstract: 

    Norovirus (NV) is a major cause of gastroenteritis worldwide. Antivirals against such important pathogens are on demand. Among the viral proteins that orchestrate viral replication, RNA-dependent-RNA-polymerase (RdRp) is a promising drug development target. From an in silico-docking search focused on the RdRp active site, we selected the compound PPNDS, which showed low micromolar IC50vs. murine NV-RdRp in vitro. We report the crystal structure of the murine NV-RdRp/PPNDS complex showing that two molecules of the inhibitor bind in antiparallel stacking interaction, properly oriented to block exit of the newly synthesized RNA. Such inhibitor-binding mode mimics two stacked nucleotide-bases of the RdRp/ssRNA complex.

    • Organizational Affiliation: 

    Department of Biosciences, University of Milano, Via Celoria 26, I-20133 Milano, Italy.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-dependent-RNA-polymerase
A, B, C
515Murine norovirus 1Mutation(s): 0 
UniProt
Find proteins for Q80J95 (Norovirus (isolate Mouse/NoV/United States/MNV1/2002/GV))
Explore Q80J95 
Go to UniProtKB:  Q80J95
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ80J95
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
20V
Query on 20V
Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
L [auth B]
M [auth B]
R [auth C]
D [auth A],
E [auth A],
L [auth B],
M [auth B],
R [auth C],
S [auth C]
3-[(E)-{4-formyl-5-hydroxy-6-methyl-3-[(phosphonooxy)methyl]pyridin-2-yl}diazenyl]-7-nitronaphthalene-1,5-disulfonic acid
C18 H15 N4 O14 P S2
CMVLDSZYDWJTCG-QZQOTICOSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
20V Binding MOAD:  4O4R IC50: 880 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.71α = 90
b = 197.43β = 114.06
c = 109.57γ = 90
Software Package:
Software NamePurpose
PXSOFTdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description