6DCZ | pdb_00006dcz

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 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acs.jmedchem.8b01363
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 22.73 kDa 
  • Atom Count: 1,513 
  • Modeled Residue Count: 180 
  • Deposited Residue Count: 192 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Polymerase acidic protein192Influenza 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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC3W5S0
Sequence Annotations
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
G5Y BindingDB:  6DCZ IC50: min: 1.97e+4, max: 2.00e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free:  0.276 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
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

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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
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description