5E0I | pdb_00005e0i

Crystal structure of the HBV capsid Y132A mutant (VCID 8772) in complex with NVR10-001E2 at 1.95A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.252 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

High-resolution crystal structure of a hepatitis B virus replication inhibitor bound to the viral core protein.

Klumpp, K.Lam, A.M.Lukacs, C.Vogel, R.Ren, S.Espiritu, C.Baydo, R.Atkins, K.Abendroth, J.Liao, G.Efimov, A.Hartman, G.Flores, O.A.

(2015) Proc Natl Acad Sci U S A 112: 15196-15201

  • DOI: https://doi.org/10.1073/pnas.1513803112
  • Primary Citation Related Structures: 
    5E0I

  • PubMed Abstract: 

    The hepatitis B virus (HBV) core protein is essential for HBV replication and an important target for antiviral drug discovery. We report the first, to our knowledge, high-resolution crystal structure of an antiviral compound bound to the HBV core protein. The compound NVR-010-001-E2 can induce assembly of the HBV core wild-type and Y132A mutant proteins and thermostabilize the proteins with a Tm increase of more than 10 °C. NVR-010-001-E2 binds at the dimer-dimer interface of the core proteins, forms a new interaction surface promoting protein-protein interaction, induces protein assembly, and increases stability. The impact of naturally occurring core protein mutations on antiviral activity correlates with NVR-010-001-E2 binding interactions determined by crystallography. The crystal structure provides understanding of a drug efficacy mechanism related to the induction and stabilization of protein-protein interactions and enables structure-guided design to improve antiviral potency and drug-like properties.


  • Organizational Affiliation
    • Novira Therapeutics, Doylestown, PA 18902; kklumpp@noviratherapeutics.com.

Macromolecule Content 

  • Total Structure Weight: 109.09 kDa 
  • Atom Count: 7,532 
  • Modeled Residue Count: 880 
  • Deposited Residue Count: 942 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid protein
A, B, C, D, E
A, B, C, D, E, F
157Hepatitis B virus subtype adywMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03147
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.252 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.6α = 90
b = 88.17β = 103.47
c = 102.25γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
Cootmodel building
PHASERphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-09
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary