9N3H | pdb_00009n3h

Crystal structure of HBV capsid with compound 18


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 
    0.297 (Depositor), 0.299 (DCC) 
  • R-Value Work: 
    0.261 (Depositor), 0.270 (DCC) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Discovery of VNRX-9945, a Potent, Broadly Active Capsid Assembly Modulator as a Clinical Candidate for the Treatment of Chronic Hepatitis B Virus Infection.

Liu, B.Yao, J.Haimowitz, T.Benetatos, C.A.Boyd, S.A.Condon, S.M.Burns, C.J.White, A.Lakshminarasimhan, D.Suto, R.K.Cakici, O.Drager, A.S.Hart, S.G.E.Pevear, D.C.Coburn, G.A.

(2025) ACS Med Chem Lett 16: 1209-1216

  • DOI: https://doi.org/10.1021/acsmedchemlett.5c00315
  • Primary Citation of Related Structures:  
    9N3H

  • PubMed Abstract: 

    Targeting the capsid protein of the hepatitis B virus (HBV) has emerged as a promising strategy for developing new antiviral therapies. In this study, we report the discovery of a novel series of pyrrole oxo-carboxamide compounds as HBV capsid assembly modulators (CAMs) that block viral replication. Through a process of focused structure-activity relationship (SAR) optimization, we identified compound 12 (VNRX-9945), which exhibited excellent and broad antiviral activity against multiple HBV genotypes in vitro, along with favorable pharmacokinetic profiles across multiple species. Additionally, 12 demonstrated robust efficacy in the adeno-associated virus mouse model of HBV (AAV-HBV) infection. This compound has advanced into Phase 1 clinical trials to evaluate its safety and pharmacokinetics in healthy volunteers, to enable treatment of chronic HBV infections.


  • Organizational Affiliation
    • Venatorx Pharmaceuticals, Inc., 30 Spring Mill Drive, Malvern, Pennsylvania 19355, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein
A, B
160Hepatitis 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03147
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BVU (Subject of Investigation/LOI)
Query on A1BVU

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
N-[3-(difluoromethyl)phenyl]-5-[{[(1s,4s)-4-hydroxycyclohexyl]amino}(oxo)acetyl]-1,2,4-trimethyl-1H-pyrrole-3-carboxamide
C23 H27 F2 N3 O4
ZUNIWKRJDDBEPY-WOVMCDHWSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free:  0.297 (Depositor), 0.299 (DCC) 
  • R-Value Work:  0.261 (Depositor), 0.270 (DCC) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.152α = 90
b = 88.152β = 90
c = 290.557γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2025-07-30
    Changes: Database references