9B19 | pdb_00009b19

EV-D68 in complex with inhibitor Jun11-54-1

• PDB DOI: https://doi.org/10.2210/pdb9B19/pdb
• EM Map EMD-44071: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): enterovirus D68
• Mutation(s): No 


• Deposited: 2024-03-13 Released: 2025-03-19 
• Deposition Author(s): Klose, T., Kuhn, R.J., Jun, W., Center for Structural Biology of Infectious Diseases (CSBID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Design of enterovirus D68 capsid inhibitors with in vivo antiviral efficacy

Li, K., Rudy, M.J., Klose, T., Tan, H., Wu, X., Anderson, J.S., Yu, W., Jadhav, P., Zhang, Q., Clarke, P., Kuhn, R.J., Tyler, K.L., Wang, J.

To be published.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 240-mer - A60B60C60D60 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
Pseudo Stoichiometry: Hetero 240-mer - A120B60C60 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 96.81 kDa 
• Atom Count: 6,352 
• Modeled Residue Count: 812 
• Deposited Residue Count: 873 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A	309	enterovirus D68	Mutation(s): 0  EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for A0A097BW12 (Human enterovirus D68) Explore A0A097BW12  Go to UniProtKB:  A0A097BW12

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
viral protein 3	B	247	enterovirus D68	Mutation(s): 0
UniProt
Find proteins for A0A097BW12 (Human enterovirus D68) Explore A0A097BW12  Go to UniProtKB:  A0A097BW12

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
viral protein 2	C	248	enterovirus D68	Mutation(s): 0
UniProt
Find proteins for A0A0K1NYJ9 (Human enterovirus D68) Explore A0A0K1NYJ9  Go to UniProtKB:  A0A0K1NYJ9

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP4	D	69	enterovirus D68	Mutation(s): 0
UniProt
Find proteins for Q68T42 (Human enterovirus D68) Explore Q68T42  Go to UniProtKB:  Q68T42

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AIE (Subject of Investigation/LOI)	E [auth A]	N-{(4M)-4-[5-(aminomethyl)thiophen-2-yl]quinolin-8-yl}-4-[(propan-2-yl)oxy]benzamide C24 H23 N3 O2 S ZHPRIQJGWCNUFC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Klose, T., Kuhn, R.J., Jun, W., Center for Structural Biology of Infectious Diseases (CSBID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI157046
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI147325

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release
  
• Version 1.1: 2025-03-26
  Changes: Data collection, Other, Structure summary
• Version 1.2: 2025-07-30
  Changes: Data collection, Other, Structure summary