9N3H | pdb_00009n3h

Crystal structure of HBV capsid with compound 18

• PDB DOI: https://doi.org/10.2210/pdb9N3H/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Hepatitis B virus subtype adyw
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-01-31 Released: 2025-07-02 
• Deposition Author(s): White, A., Lakshminarasimhan, D., Cakici, O., Suto, R.
• Funding Organization(s): Other private

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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

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

• PubMed: 40666476 
• DOI: https://doi.org/10.1021/acsmedchemlett.5c00315
• Primary Citation 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.

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Organizational Affiliation: 
• Venatorx Pharmaceuticals, Inc., 30 Spring Mill Drive, Malvern, Pennsylvania 19355, United States.
Xtal Biostructures, Inc., 12 Michigan Drive, Natick, Massachusetts 01760, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.9 kDa 
• Atom Count: 2,188 
• Modeled Residue Count: 268 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B	160	Hepatitis B virus subtype adyw	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BVU (Subject of Investigation/LOI)	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 = 88.152	α = 90
b = 88.152	β = 90
c = 290.557	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): White, A., Lakshminarasimhan, D., Cakici, O., Suto, R.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

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