7K5M

CRYSTAL STRUCTURE OF HBV CAPSID Y132A MUTANT IN COMPLEX WITH N-(3-chloro-4-fluorophenyl)-3-phenyl-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide AT 2.65A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb7K5M/pdb

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

Deposited: 2020-09-17 Released: 2021-07-28
Deposition Author(s): Kuduk, S.D., Stoops, B., Alexander, R., Lam, A.M., Espiritu, C., Vogel, R., Lau, V., Klumpp, K., Flores, O.A., Hartman, G.D., Lukacs, C.M., Abendroth, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.276
R-Value Work: 0.242
R-Value Observed: 0.244

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Identification of a new class of HBV capsid assembly modulator.

Kuduk, S.D., Stoops, B., Alexander, R., Lam, A.M., Espiritu, C., Vogel, R., Lau, V., Klumpp, K., Flores, O.A., Hartman, G.D.

(2021) Bioorg Med Chem Lett 39: 127848-127848

PubMed: 33610748 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2021.127848
Primary Citation of Related Structures:
7K5M

PubMed Abstract:
The HBV core protein is a druggable target of interest due to the multiple essential functions in the HBV life cycle to enable chronic HBV infection. The core protein oligomerizes to form the viral capsid, and modulation of the HBV capsid assembly has shown efficacy in clinical trials. Herein is described the identification and hit to lead SAR of a novel series of pyrazolo piperidine HBV capsid assembly modulators.

Organizational Affiliation

Novira Therapeutics, a Janssen Pharmaceuticals Company, 1400 McKean Road, Spring House, PA 19477, United States. Electronic address: skuduk@its.jnj.com.

Macromolecule Content

Total Structure Weight: 109.42 kDa
Atom Count: 6,216
Modelled Residue Count: 785
Deposited Residue Count: 948
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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	158	Hepatitis B virus subtype adyw	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03147
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VXJ (Subject of Investigation/LOI) Query on VXJ Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain N [auth E] SDF format, chain Q [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain N [auth E] MOL2 format, chain Q [auth F]	G [auth A] I [auth B] K [auth C] L [auth D] N [auth E] G [auth A], I [auth B], K [auth C], L [auth D], N [auth E], Q [auth F]	N-(3-chloro-4-fluorophenyl)-3-phenyl-2,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide C₁₉ H₁₆ Cl F N₄ O KJJIMZOASWDMDJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain N [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain N [auth E] Focus chain Q [auth F]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain P [auth E] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E]	H [auth A], J [auth B], M [auth D], O [auth E], P [auth E]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain M [auth D] Focus chain O [auth E] Focus chain P [auth E] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain M [auth D] Focus chain O [auth E] Focus chain P [auth E]