6DCZ

The N-terminal domain of PA endonuclease from the influenza H1N1 virus in complex with 3-hydroxy-4-oxo-4H-pyran-2-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure-Activity Relationships in Metal-Binding Pharmacophores for Influenza Endonuclease.

Credille, C.V.Dick, B.L.Morrison, C.N.Stokes, R.W.Adamek, R.N.Wu, N.C.Wilson, I.A.Cohen, S.M.

(2018) J Med Chem 61: 10206-10217

  • DOI: 10.1021/acs.jmedchem.8b01363
  • Primary Citation of Related Structures:  
    6DCY, 6DCZ, 6DZQ, 6E0Q

  • PubMed Abstract: 
  • Metalloenzymes represent an important target space for drug discovery. A limitation to the early development of metalloenzyme inhibitors has been the lack of established structure-activity relationships (SARs) for molecules that bind the metal ion cofactor(s) of a metalloenzyme ...

    Metalloenzymes represent an important target space for drug discovery. A limitation to the early development of metalloenzyme inhibitors has been the lack of established structure-activity relationships (SARs) for molecules that bind the metal ion cofactor(s) of a metalloenzyme. Herein, we employed a bioinorganic perspective to develop an SAR for inhibition of the metalloenzyme influenza RNA polymerase PA N endonuclease. The identified trends highlight the importance of the electronics of the metal-binding pharmacophore (MBP), in addition to MBP sterics, for achieving improved inhibition and selectivity. By optimization of the MBPs for PA N endonuclease, a class of highly active and selective fragments was developed that displays IC 50 values <50 nM. This SAR led to structurally distinct molecules that also displayed IC 50 values of ∼10 nM, illustrating the utility of a metal-centric development campaign in generating highly active and selective metalloenzyme inhibitors.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase acidic proteinA192Influenza 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G5Y (Subject of Investigation/LOI)
Query on G5Y

Download Ideal Coordinates CCD File 
B [auth A]3-hydroxy-4-oxo-4H-pyran-2-carboxylic acid
C6 H4 O5
XZUDOWCTKOXYCZ-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.207 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.84α = 90
b = 75.84β = 90
c = 121.3γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM098435

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-12-05
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence