8GBU | pdb_00008gbu

Hepatitis B capsid Y132A mutant with compound AB-506

PDB DOI: https://doi.org/10.2210/pdb8GBU/pdb

Classification: VIRAL PROTEIN
Organism(s): Hepatitis B virus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-02-28 Released: 2023-09-06
Deposition Author(s): Horanyi, P.S., Mayclin, S.J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.285 (Depositor), 0.318 (DCC)
R-Value Work:
0.233 (Depositor), 0.283 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

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

PubMed: 37633618 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2023.129456
Primary Citation Related Structures:
8GBU

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.

Macromolecule Content

Total Structure Weight: 116.61 kDa
Atom Count: 6,984
Modeled Residue Count: 848
Deposited Residue Count: 1,002
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B, C, D, E A, B, C, D, E, F	167	Hepatitis B virus	Mutation(s): 1
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03147
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YWE (Subject of Investigation/LOI) Query on YWE Download:Ideal Coordinates CCD File SDF format, chain P [auth E] SDF format, chain O [auth E] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain P [auth E] MOL2 format, chain O [auth E] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain P [auth E] mmCIF format, chain O [auth E] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	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 DMJDVZSGLNPLSS-KRWDZBQOSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain O [auth E] Focus chain P [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain O [auth E] Focus chain P [auth E]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain T [auth F] SDF format, chain S [auth F] SDF format, chain R [auth E] SDF format, chain Q [auth E] SDF format, chain N [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain I [auth A] MOL2 format, chain T [auth F] MOL2 format, chain S [auth F] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain N [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain I [auth A] mmCIF format, chain T [auth F] mmCIF format, chain S [auth F] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth E] mmCIF format, chain N [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain I [auth A]	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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Interactions & Density Focus chain I [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F]