4YYL

Phenolic acid derivative bound to influenza strain H1N1 polymerase subunit PA endonuclease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.905 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and computational study on inhibitory compounds for endonuclease activity of influenza virus polymerase

Fudo, S.Yamamoto, N.Nukaga, M.Odagiri, T.Tashiro, M.Neya, S.Hoshino, T.

(2015) Bioorg.Med.Chem. 23: 5466-5475

  • DOI: 10.1016/j.bmc.2015.07.046

  • PubMed Abstract: 
  • Seasonal epidemics and occasional pandemics caused by influenza viruses are global threats to humans. Since the efficacy of currently approved drugs is limited by the emerging resistance of the viruses, the development of new antiviral drugs is still ...

    Seasonal epidemics and occasional pandemics caused by influenza viruses are global threats to humans. Since the efficacy of currently approved drugs is limited by the emerging resistance of the viruses, the development of new antiviral drugs is still demanded. Endonuclease activity, which lies in the influenza polymerase acidic protein N-terminal domain (PA(N)), is a potent target for novel antiviral agents. Here, we report the identification of some novel inhibitors for PA(N) endonuclease activity. The binding mode of one of the inhibitory compounds to PA(N) was investigated in detail by means of X-ray crystal structure analysis and molecular dynamics (MD) simulation. It was observed in the crystal structure that three molecules of the same kind of inhibitor were bound to one PA(N). One of the three molecules is located at the active site and makes a chelation to metal ions. Another molecule is positioned at the space adjacent to the metal-chelated site. The other molecule is located at a site slightly apart from the metal-chelated site, causing a conformational change of Arg124. The last binding site was not observed in previous crystallographic studies. Hence, the stability of inhibitor binding was examined by performing 100-ns MD simulation. During the MD simulation, the three inhibitor molecules fluctuated at the respective binding sites at different amplitudes, while all of the molecules maintained interactions with the protein. Molecular mechanics/generalized Born surface area (MM/GBSA) analysis suggested that the molecule in the last binding site has a higher affinity than the others. Structural information obtained in this study will provide a hint for designing and developing novel potent agents against influenza viruses.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase acidic protein
A
191Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)Mutation(s): 0 
Gene Names: PA
EC: 3.1.-.-
Find proteins for P03433 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Go to UniProtKB:  P03433
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
4KN
Query on 4KN

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Download CCD File 
A
2-(4-fluorophenoxy)-1-(2,3,4-trihydroxyphenyl)ethanone
C14 H11 F O5
USPMIJCAMCULDC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4KNIC50: 9700 nM (88) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.905 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 66.766α = 90.00
b = 66.766β = 90.00
c = 126.251γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
MOLREPphasing
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan24590548

Revision History 

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2015-09-09
    Type: Database references