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 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.260 

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Ligand Structure Quality Assessment 


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
  • 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 ...

    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. sgpark@gist.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid proteinA, B, C, D, E, F149Hepatitis B virus subtype adywMutation(s): 1 
Gene Names: C
UniProt
Find proteins for P03147 (Hepatitis B virus genotype D subtype adw (isolate United Kingdom/adyw/1979))
Explore P03147 
Go to UniProtKB:  P03147
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B4O (Subject of Investigation/LOI)
Query on B4O

Download Ideal Coordinates CCD File 
G [auth B], H [auth D], I [auth F]6-cyclohexyl-4-methyl-1-oxidanyl-pyridin-2-one
C12 H17 N O2
SCKYRAXSEDYPSA-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
B4O Binding MOAD:  6J10 Kd: 445 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.260 
  • 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  



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