7K5M | pdb_00007k5m

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.276 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Starting Model: other

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 
• 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.

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Organizational Affiliation: 

Novira Therapeutics, a Janssen Pharmaceuticals Company, 1400 McKean Road, Spring House, PA 19477, United States. Electronic address: [e-mail].

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VXJ (Subject of Investigation/LOI)	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
IPA	H [auth A], J [auth B], M [auth D], O [auth E], P [auth E]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.276 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.58	α = 90
b = 87.96	β = 103.53
c = 106.71	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 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.

Revision History  

• Version 1.0: 2021-07-28
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary