7M0N

The crystal structure of wild type PA endonuclease (A/Vietnam/1203/2004) in complex with Raltegravir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Chemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential.

Slavish, P.J.Cuypers, M.G.Rimmer, M.A.Abdolvahabi, A.Jeevan, T.Kumar, G.Jarusiewicz, J.A.Vaithiyalingam, S.Jones, J.C.Bowling, J.J.Price, J.E.DuBois, R.M.Min, J.Webby, R.J.Rankovic, Z.White, S.W.

(2023) Eur J Med Chem 247: 115035-115035

  • DOI: https://doi.org/10.1016/j.ejmech.2022.115035
  • Primary Citation of Related Structures:  
    6V6X, 6V9E, 6VBR, 6VG9, 6VIV, 6VJH, 6VL3, 6WIJ, 6WJ4, 7K87, 7LM4, 7LW6, 7M0N, 7MPF, 7MTY, 7N47, 7N55, 7N68, 7N8F, 7RKP, 7UMR, 7UUH, 8DIP, 8DPJ, 8DTW, 8E4S

  • PubMed Abstract: 

    Influenza is one of the leading causes of disease-related mortalities worldwide. Several strategies have been implemented during the past decades to hinder the replication cycle of influenza viruses, all of which have resulted in the emergence of resistant virus strains. The most recent example is baloxavir marboxil, where a single mutation in the active site of the target endonuclease domain of the RNA-dependent-RNA polymerase renders the recent FDA approved compound ∼1000-fold less effective. Raltegravir is a first-in-class HIV inhibitor that shows modest activity to the endonuclease. Here, we have used structure-guided approaches to create rationally designed derivative molecules that efficiently engage the endonuclease active site. The design strategy was driven by our previously published structures of endonuclease-substrate complexes, which allowed us to target functionally conserved residues and reduce the likelihood of resistance mutations. We succeeded in developing low nanomolar equipotent inhibitors of both wild-type and baloxavir-resistant endonuclease. We also developed macrocyclic versions of these inhibitors that engage the active site in the same manner as their 'open' counterparts but with reduced affinity. Structural analyses provide clear avenues for how to increase the affinity of these cyclic compounds.


  • Organizational Affiliation

    Departments of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein PA-X
A, B, C, D
187Influenza A virus (A/ruddy turnstone/New Jersey/Sg-00524/2008(H4N6))Mutation(s): 0 
Gene Names: PA
UniProt
Find proteins for C6Y633 (Influenza A virus)
Explore C6Y633 
Go to UniProtKB:  C6Y633
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6Y633
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RLT (Subject of Investigation/LOI)
Query on RLT

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
Q [auth C],
V [auth D]
N-(4-fluorobenzyl)-5-hydroxy-1-methyl-2-(1-methyl-1-{[(5-methyl-1,3,4-oxadiazol-2-yl)carbonyl]amino}ethyl)-6-oxo-1,6-di hydropyrimidine-4-carboxamide
C20 H21 F N6 O5
CZFFBEXEKNGXKS-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
H [auth A]
I [auth A]
O [auth B]
BA [auth D],
CA [auth D],
H [auth A],
I [auth A],
O [auth B],
P [auth B],
T [auth C],
U [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth B],
L [auth B],
W [auth D],
X [auth D],
Y [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
AA [auth D]
F [auth A]
G [auth A]
M [auth B]
N [auth B]
AA [auth D],
F [auth A],
G [auth A],
M [auth B],
N [auth B],
R [auth C],
S [auth C],
Z [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.702α = 90
b = 135.126β = 90
c = 126.751γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references, Structure summary
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description