Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 23.34 kDa 
• Atom Count: 1730 
• Modelled Residue Count: 181 
• Deposited Residue Count: 191 
• Unique protein chains: 1

4YYL

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

• PDB DOI: 10.2210/pdb4YYL/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Influenza A virus (A/Puerto Rico/8/1934(H1N1))
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-03-24 Released: 2015-04-29 
• Deposition Author(s): Fudo, S., Yamamoto, N., Nukaga, M., Odagiri, T., Tashiro, M., Neya, S., Hoshino, T.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.234 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

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

• PubMed: 26252962 
• DOI: 10.1016/j.bmc.2015.07.046
• Primary Citation of Related Structures:  
  4YYL


• 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 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.

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Organizational Affiliation: 

Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase acidic protein	A	191	Influenza A virus (A/Puerto Rico/8/1934(H1N1))	Mutation(s): 0  Gene Names: PA EC: 3.1
UniProt
Find proteins for P03433 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)) Explore P03433  Go to UniProtKB:  P03433

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4KN	B [auth A], C [auth A], D [auth A]	2-(4-fluorophenoxy)-1-(2,3,4-trihydroxyphenyl)ethanone C14 H11 F O5 USPMIJCAMCULDC-UHFFFAOYSA-N
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	E [auth A], F [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4KN	Binding MOAD:  4YYL	IC50: 9700 (nM) from 1 assay(s)
	BindingDB:  4YYL	IC50: 9700 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.234 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.766	α = 90
b = 66.766	β = 90
c = 126.251	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-03-24 
• Released Date: 2015-04-29 
Deposition Author(s): Fudo, S., Yamamoto, N., Nukaga, M., Odagiri, T., Tashiro, M., Neya, S., Hoshino, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	24590548

Revision History  

• Version 1.0: 2015-04-29
  Type: Initial release
  
• Version 1.1: 2015-09-09
  Changes: Database references
• Version 1.2: 2020-02-19
  Changes: Data collection, Database references, Derived calculations