4NRT

Human Norovirus polymerase bound to Compound 6 (suramin derivative)

• PDB DOI: https://doi.org/10.2210/pdb4NRT/pdb

• Classification: VIRAL PROTEIN/TRANSCRIPTION INHIBITOR
• Organism(s): Norwalk-like virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-11-27 Released: 2014-10-15 
• Deposition Author(s): Croci, R., Pezzullo, M., Tarantino, D., Mastrangelo, E., Milani, M., Bolognesi, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.209 
• R-Value Work: 0.164 
• R-Value Observed: 0.164 

Literature

Structural bases of norovirus RNA dependent RNA polymerase inhibition by novel suramin-related compounds.

Croci, R., Pezzullo, M., Tarantino, D., Milani, M., Tsay, S.C., Sureshbabu, R., Tsai, Y.J., Mastrangelo, E., Rohayem, J., Bolognesi, M., Hwu, J.R.

(2014) PLoS One 9: e91765-e91765

• PubMed: 24622391 
• DOI: https://doi.org/10.1371/journal.pone.0091765
• Primary Citation of Related Structures:  
  4NRT, 4NRU


• PubMed Abstract: 
  

  Noroviruses (NV) are +ssRNA viruses responsible for severe gastroenteritis; no effective vaccines/antivirals are currently available. We previously identified Suramin (9) as a potent inhibitor of NV-RNA dependent RNA polymerase (NV-RdRp). Despite significant in vitro activities versus several pharmacological targets, Suramin clinical use is hampered by pharmacokinetics/toxicity problems. To improve Suramin access to NV-RdRp in vivo, a Suramin-derivative, 8, devoid of two sulphonate groups, was synthesized, achieving significant anti-human-NV-RdRp activity (IC50 = 28 nM); the compound inhibits also murine NV (mNV) RdRp. The synthesis process led to the isolation/characterization of lower molecular weight intermediates (3-7) hosting only one sulphonate head. The crystal structures of both hNV/mNV-RdRps in complex with 6, were analyzed, providing new knowledge on the interactions that a small fragment can establish with NV-RdRps, and establishing a platform for structure-guided optimization of potency, selectivity and drugability.

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Organizational Affiliation: 

Department of BioSciences, University of Milano, Milano, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.24 kDa 
• Atom Count: 4,469 
• Modelled Residue Count: 500 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hNV-RdRp	A	526	Norwalk-like virus	Mutation(s): 0
UniProt
Find proteins for A0ZNP5 (Norwalk-like virus) Explore A0ZNP5  Go to UniProtKB:  A0ZNP5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2NG	B [auth A]	4-({4-methyl-3-[(3-nitrobenzoyl)amino]benzoyl}amino)naphthalene-1,5-disulfonic acid C25 H19 N3 O10 S2 HRJXRQKWGJTVEE-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2NG	Binding MOAD:  4NRT	IC50: 1000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.209 
• R-Value Work: 0.164 
• R-Value Observed: 0.164 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.17	α = 90
b = 111.95	β = 90
c = 121.09	γ = 90

Software Package:

Software Name	Purpose
EDNA	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-15 
Deposition Author(s): Croci, R., Pezzullo, M., Tarantino, D., Mastrangelo, E., Milani, M., Bolognesi, M.

Revision History  

• Version 1.0: 2014-10-15
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description