Hepatitis B capsid Y132A mutant with compound AB-506

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Design, synthesis, and structure-activity relationship of a bicyclic HBV capsid assembly modulator chemotype leading to the identification of clinical candidate AB-506.

Cole, A.G.Kultgen, S.G.Mani, N.Quintero, J.G.Yi Fan, K.Ardzinski, A.Stever, K.Dorsey, B.D.Phelps, J.R.Lee, A.C.H.Thi, E.P.Chiu, T.Tang, S.Horanyi, P.S.Mayclin, S.J.Harasym, T.O.Sofia, M.J.

(2023) Bioorg Med Chem Lett 94: 129456-129456

  • DOI: https://doi.org/10.1016/j.bmcl.2023.129456
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Disruption of the HBV capsid assembly process through small-molecule interaction with HBV core protein is a validated target for the suppression of hepatitis B viral replication and the development of new antivirals. Through combination of key structural features associated with two distinct series of capsid assembly modulators, a novel aminochroman-based chemotype was identified. Optimization of anti-HBV potency through generation of SAR in addition to further core modifications provided a series of related functionalized aminoindanes. Key compounds demonstrated excellent cellular potency in addition to favorable ADME and pharmacokinetic profiles and were shown to be highly efficacious in a mouse model of HBV replication. Aminoindane derivative AB-506 was subsequently advanced into clinical development.

  • Organizational Affiliation

    Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA. Electronic address: acole@arbutusbio.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein
A, B, C, D, E
A, B, C, D, E, F
167Hepatitis B virusMutation(s): 1 
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YWE (Subject of Investigation/LOI)
Query on YWE

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
J [auth B]
K [auth C]
O [auth E]
G [auth A],
H [auth A],
J [auth B],
K [auth C],
O [auth E],
P [auth E]
(1-methyl-1H-1,2,4-triazol-3-yl)methyl {(1S)-4-[(3-chloro-4-fluorophenyl)carbamoyl]-7-fluoro-2,3-dihydro-1H-inden-1-yl}carbamate
C21 H18 Cl F2 N5 O3
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A]
L [auth C]
M [auth C]
N [auth D]
Q [auth E]
I [auth A],
L [auth C],
M [auth C],
N [auth D],
Q [auth E],
R [auth E],
S [auth F],
T [auth F]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.936α = 90
b = 87.879β = 104.12
c = 100.827γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-06
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Database references