6J10

Ciclopirox inhibits Hepatitis B Virus secretion by blocking capsid assembly


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/s41467-019-10200-5

  • 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 approac ...

    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

    Department of Internal Medicine, CHA Gangnam Medical Center, CHA University School of Medicine, Seoul, 06125, Republic of Korea. yuricho@cha.ac.kr.,School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea.,School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea. sgpark@gist.ac.kr.,Department of Internal Medicine, CHA Gangnam Medical Center, CHA University School of Medicine, Seoul, 06125, Republic of Korea.,Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.,School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea. misunjin@gist.ac.kr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein
A, B, C, D, E, F
149Hepatitis B virus genotype D subtype adw (isolate United Kingdom/adyw/1979)Mutation(s): 1 
Gene Names: C
Find proteins for P03147 (Hepatitis B virus genotype D subtype adw (isolate United Kingdom/adyw/1979))
Go to UniProtKB:  P03147
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B4O
Query on B4O

Download SDF File 
Download CCD File 
B, D, F
6-cyclohexyl-4-methyl-1-oxidanyl-pyridin-2-one
C12 H17 N O2
SCKYRAXSEDYPSA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.257 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 153.924α = 90.00
b = 88.510β = 121.13
c = 99.162γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-05-29
    Type: Data collection, Database references