9FA9

Coxsackievirus A9 bound with compound 16 (CL298)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

SAR Analysis of Novel Coxsackie virus A9 Capsid Binders.

Tammaro, C.Plavec, Z.Myllymaki, L.Mitchell, C.Consalvi, S.Biava, M.Ciogli, A.Domanska, A.Leppilampi, V.Buckner, C.Manetto, S.Scio, P.Coluccia, A.Laajala, M.Dondio, G.M.Bigogno, C.Marjomaki, V.Butcher, S.J.Poce, G.

(2024) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00701
  • Primary Citation of Related Structures:  
    8S7J, 9EXI, 9FA9, 9FCZ, 9FGN, 9FO2, 9FO5, 9FP5

  • PubMed Abstract: 

    Enterovirus infections are common in humans, yet there are no approved antiviral treatments. In this study we concentrated on inhibition of one of the Enterovirus B (EV-B), namely Coxsackievirus A9 (CVA9), using a combination of medicinal chemistry, virus inhibition assays, structure determination from cryogenic electron microscopy and molecular modeling, to determine the structure activity relationships for a promising class of novel N -phenylbenzylamines. Of the new 29 compounds synthesized, 10 had half maximal effective concentration (EC 50 ) values between 0.64-10.46 μM, and of these, 7 had 50% cytotoxicity concentration (CC 50 ) values higher than 200 μM. In addition, this new series of compounds showed promising physicochemical properties and act through capsid stabilization, preventing capsid expansion and subsequent release of the genome.


  • Organizational Affiliation

    Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP1283Human coxsackievirus A9 (strain Griggs)Mutation(s): 7 
UniProt
Find proteins for P21404 (Coxsackievirus A9 (strain Griggs))
Explore P21404 
Go to UniProtKB:  P21404
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21404
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP2261Human coxsackievirus A9 (strain Griggs)Mutation(s): 1 
UniProt
Find proteins for P21404 (Coxsackievirus A9 (strain Griggs))
Explore P21404 
Go to UniProtKB:  P21404
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21404
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP3238Human coxsackievirus A9 (strain Griggs)Mutation(s): 0 
UniProt
Find proteins for P21404 (Coxsackievirus A9 (strain Griggs))
Explore P21404 
Go to UniProtKB:  P21404
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21404
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP468Human coxsackievirus A9 (strain Griggs)Mutation(s): 0 
UniProt
Find proteins for P21404 (Coxsackievirus A9 (strain Griggs))
Explore P21404 
Go to UniProtKB:  P21404
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21404
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IBS (Subject of Investigation/LOI)
Query on A1IBS

Download Ideal Coordinates CCD File 
E [auth A]~{N}-[(2-fluorophenyl)methyl]-4-[(4-methylpiperazin-1-yl)methyl]aniline
C19 H24 F N3
GFWGMYAJMIQTFM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2.0
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland315950
Sigrid Juselius FoundationFinland95-7202-38
Jane and Aatos Erkko FoundationFinland--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release