4MK5

6-(3-methoxyphenyl)pyridine-2,3-diol bound to influenza 2009 pH1N1 endonuclease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystallographic fragment screening and structure-based optimization yields a new class of influenza endonuclease inhibitors.

Bauman, J.D.Patel, D.Baker, S.F.Vijayan, R.S.Xiang, A.Parhi, A.K.Martinez-Sobrido, L.Lavoie, E.J.Das, K.Arnold, E.

(2013) ACS Chem Biol 8: 2501-2508

  • DOI: https://doi.org/10.1021/cb400400j
  • Primary Citation of Related Structures:  
    4LN7, 4M4Q, 4M5O, 4M5Q, 4M5R, 4M5V, 4MK1, 4MK2, 4MK5

  • PubMed Abstract: 

    Seasonal and pandemic influenza viruses continue to be a leading global health concern. Emerging resistance to the current drugs and the variable efficacy of vaccines underscore the need for developing new flu drugs that will be broadly effective against wild-type and drug-resistant influenza strains. Here, we report the discovery and development of a class of inhibitors targeting the cap-snatching endonuclease activity of the viral polymerase. A high-resolution crystal form of pandemic 2009 H1N1 influenza polymerase acidic protein N-terminal endonuclease domain (PAN) was engineered and used for fragment screening leading to the identification of new chemical scaffolds binding to the PAN active site cleft. During the course of screening, binding of a third metal ion that is potentially relevant to endonuclease activity was detected in the active site cleft of PAN in the presence of a fragment. Using structure-based optimization, we developed a highly potent hydroxypyridinone series of compounds from a fragment hit that defines a new mode of chelation to the active site metal ions. A compound from the series demonstrating promising enzymatic inhibition in a fluorescence-based enzyme assay with an IC50 value of 11 nM was found to have an antiviral activity (EC50) of 11 μM against PR8 H1N1 influenza A in MDCK cells.


  • Organizational Affiliation

    Center for Advanced Biotechnology and Medicine, ‡Department of Chemistry and Chemical Biology, §Department of Medicinal Chemistry, Rutgers University , Piscataway, New Jersey 08854, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
POLYMERASE PA241Influenza A virus (A/Lima/WRAIR1695P/2009(H1N1))Mutation(s): 0 
Gene Names: PA
EC: 3.1
UniProt
Find proteins for M9V5A4 (Influenza A virus)
Explore M9V5A4 
Go to UniProtKB:  M9V5A4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM9V5A4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
28A
Query on 28A

Download Ideal Coordinates CCD File 
G [auth A]3-hydroxy-6-(3-methoxyphenyl)pyridin-2(5H)-one
C12 H11 N O3
UGMJNFNGAUVDRE-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
28A PDBBind:  4MK5 IC50: 450 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.195α = 90
b = 101.683β = 90
c = 66.206γ = 90
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-25
    Type: Initial release
  • Version 1.1: 2013-12-11
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations