6J10

Ciclopirox inhibits Hepatitis B Virus secretion by blocking capsid assembly


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.303 (Depositor), 0.310 (DCC) 
  • R-Value Work: 
    0.257 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.260 (Depositor) 

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Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

Ciclopirox inhibits Hepatitis B Virus secretion by blocking capsid assembly.

Kang, J.A.Kim, S.Park, M.Park, H.J.Kim, J.H.Park, S.Hwang, J.R.Kim, Y.C.Jun Kim, Y.Cho, Y.Sun Jin, M.Park, S.G.

(2019) Nat Commun 10: 2184-2184

  • DOI: https://doi.org/10.1038/s41467-019-10200-5
  • Primary Citation of Related Structures:  
    6J10

  • PubMed Abstract: 

    Chronic hepatitis B virus (HBV) infection can cause cirrhosis and hepatocellular carcinoma and is therefore a serious public health problem. Infected patients are currently treated with nucleoside/nucleotide analogs and interferon α, but this approach is not curative. Here, we screen 978 FDA-approved compounds for their ability to inhibit HBV replication in HBV-expressing HepG2.2.15 cells. We find that ciclopirox, a synthetic antifungal agent, strongly inhibits HBV replication in cells and in mice by blocking HBV capsid assembly. The crystal structure of the HBV core protein and ciclopirox complex reveals a unique binding mode at dimer-dimer interfaces. Ciclopirox synergizes with nucleoside/nucleotide analogs to prevent HBV replication in cells and in a humanized liver mouse model. Therefore, orally-administered ciclopirox may provide a novel opportunity to combat chronic HBV infection by blocking HBV capsid assembly.


  • Organizational Affiliation

    School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein
A, B, C, D, E
149Hepatitis B virus subtype adywMutation(s): 1 
UniProt
Find proteins for P03147 (Hepatitis B virus genotype D subtype adw (isolate United Kingdom/adyw/1979))
Explore P03147 
Go to UniProtKB:  P03147
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03147
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.303 (Depositor), 0.310 (DCC) 
  • R-Value Work:  0.257 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.260 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.924α = 90
b = 88.51β = 121.13
c = 99.162γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted B4OClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic OfNRF-2017R1A6A3A11035008
National Research Foundation (Korea)Korea, Republic OfNRF-2016R1A5A1007318
National Research Foundation (Korea)Korea, Republic OfNRF-2017R1E1A1A01074299
National Research Foundation (Korea)Korea, Republic OfNRF-2015M2A2A4A03044653

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-05-29
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Refinement description, Structure summary