8GIH | pdb_00008gih

Structure of Hepatitis B Virus Capsid Y132A mutant in complex with Compound 24

PDB DOI: https://doi.org/10.2210/pdb8GIH/pdb

Classification: VIRAL PROTEIN/INHIBITOR
Organism(s): Hepatitis B virus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-03-14 Released: 2023-04-12
Deposition Author(s): Shaffer, P.L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.253 (Depositor), 0.253 (DCC)
R-Value Work:
0.205 (Depositor), 0.206 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Diazepinone HBV capsid assembly modulators.

Kuduk, S.D., DeRatt, L.G., Stoops, B., Shaffer, P., Lam, A.M., Espiritu, C., Vogel, R., Lau, V., Flores, O.A., Hartman, G.D.

(2022) Bioorg Med Chem Lett 72: 128823

PubMed: 35644301 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2022.128823
Primary Citation Related Structures:
8GIH

PubMed Abstract:
The HBV capsid core protein serves a number of important functions in the viral life cycle enabling chronic HBV infection to persist, and therefore is a promising drug target. Interfering with capsid assembly has shown efficacy in clinical trials with small molecule capsid assembly modulators (CAMs). Herein is described the further optimization of a progressive series of diazepinone HBV CAMs.

Organizational Affiliation

Janssen Research and Development, 1400 McKean Road, Spring House, PA 19477, United States. Electronic address: skuduk@its.jnj.com.

Macromolecule Content

Total Structure Weight: 111.18 kDa
Atom Count: 6,413
Modeled Residue Count: 809
Deposited Residue Count: 960
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	160	Hepatitis B virus	Mutation(s): 1 Gene Names: C
UniProt
Find proteins for L7R9I1 (Hepatitis B virus) Explore L7R9I1 Go to UniProtKB: L7R9I1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	L7R9I1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZMH (Subject of Investigation/LOI) Query on ZMH Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain X [auth F] SDF format, chain U [auth E] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain X [auth F] MOL2 format, chain U [auth E] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain X [auth F] mmCIF format, chain U [auth E] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain I [auth A]	I [auth A] K [auth B] O [auth C] R [auth D] U [auth E] I [auth A], K [auth B], O [auth C], R [auth D], U [auth E], X [auth F]	(6S,8R)-N-(3-bromo-4-fluorophenyl)-8-fluoro-10-methyl-11-oxo-1,3,4,7,8,9,10,11-octahydro-2H-pyrido[4',3':3,4]pyrazolo[1,5-a][1,4]diazepine-2-carboxamide C₁₈ H₁₈ Br F₂ N₅ O₂ HKVGNSIAARSCKF-SNVBAGLBSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain W [auth F] SDF format, chain V [auth F] SDF format, chain T [auth E] SDF format, chain S [auth E] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain W [auth F] MOL2 format, chain V [auth F] MOL2 format, chain T [auth E] MOL2 format, chain S [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain W [auth F] mmCIF format, chain V [auth F] mmCIF format, chain T [auth E] mmCIF format, chain S [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [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] L [auth C] M [auth C] G [auth A], H [auth A], J [auth B], L [auth C], M [auth C], N [auth C], P [auth D], Q [auth D], S [auth E], T [auth E], V [auth F], W [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth F]