8DDB

The N-terminal domain of PA endonuclease from the influenza H1N1 viral polymerase in complex with 4-(benzyloxy)-6-bromo-3-hydroxypicolinic acid

• PDB DOI: https://doi.org/10.2210/pdb8DDB/pdb

• Classification: VIRAL PROTEIN,HYDROLASE/INHIBITOR
• Organism(s): Influenza A virus (A/California/04/2009(H1N1))
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2022-06-17 Released: 2022-12-21 
• Deposition Author(s): Kohlbrand, A.J., Stokes, R.W., Karges, J., Seo, H., Sankaran, B., Cohen, S.M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.241 
• R-Value Work: 0.192 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

Carboxylic Acid Isostere Derivatives of Hydroxypyridinones as Core Scaffolds for Influenza Endonuclease Inhibitors.

Stokes, R.W., Kohlbrand, A.J., Seo, H., Sankaran, B., Karges, J., Cohen, S.M.

(2023) ACS Med Chem Lett 14: 75-82

• PubMed: 36655124 
• DOI: https://doi.org/10.1021/acsmedchemlett.2c00434
• Primary Citation of Related Structures:  
  7V04, 8CTF, 8DAL, 8DDB, 8DDE, 8DHN, 8DJV, 8DJY


• PubMed Abstract: 
  

  Among the most important influenza virus targets is the RNA-dependent RNA polymerase acidic N-terminal (PA _N ) endonuclease, which is a critical component of the viral replication machinery. To inhibit the activity of this metalloenzyme, small-molecule inhibitors employ metal-binding pharmacophores (MBPs) that coordinate to the dinuclear Mn ²⁺ active site. In this study, several metal-binding isosteres (MBIs) were examined where the carboxylic acid moiety of a hydroxypyridinone MBP is replaced with other groups to modulate the physicochemical properties of the compound. MBIs were evaluated for their ability to inhibit PA _N using a FRET-based enzymatic assay, and their mode of binding in PA _N was determined using X-ray crystallography.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, La Jolla, California 92093, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 22.87 kDa 
• Atom Count: 1,593 
• Modelled Residue Count: 179 
• Deposited Residue Count: 191 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase acidic protein	A	191	Influenza A virus (A/California/04/2009(H1N1))	Mutation(s): 0  Gene Names: PA EC: 3.1
UniProt
Find proteins for C3W5S0 (Influenza A virus (strain swl A/California/04/2009 H1N1)) Explore C3W5S0  Go to UniProtKB:  C3W5S0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R6X	E [auth A]	6-bromo-3-hydroxy-4-oxo-1,4-dihydropyridine-2-carboxylic acid C6 H4 Br N O4 PCMDXAXSHBWBAV-UHFFFAOYSA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.241 
• R-Value Work: 0.192 
• R-Value Observed: 0.197 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.228	α = 90
b = 76.228	β = 90
c = 121.608	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-12-21 
Deposition Author(s): Kohlbrand, A.J., Stokes, R.W., Karges, J., Seo, H., Sankaran, B., Cohen, S.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI149444

Revision History  

• Version 1.0: 2022-12-21
  Type: Initial release
  
• Version 1.1: 2023-02-01
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description