3HVO

Structure of the genotype 2B HCV polymerase bound to a NNI

• PDB DOI: https://doi.org/10.2210/pdb3HVO/pdb

• Classification: TRANSFERASE
• Organism(s): Hepatitis C virus isolate HC-J8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-06-16 Released: 2009-08-04 
• Deposition Author(s): Rydberg, E.H., Carfi, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.218 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Identification and Biological Evaluation of a Series of 1H-Benzo[de]isoquinoline-1,3(2H)-diones as Hepatitis C Virus NS5B Polymerase Inhibitors

Ontoria, J.M., Rydberg, E.H., Di-Marco, S., Tomei, L., Antenni, B., Melancona, S., Martin-Hernando, J.I., Gennari, N., Koch, U., Narjes, F., Rowley, M., Summa, V., Carroll, S.S., Olsen, D.B., De-Francesco, R., Altamura, S., Migliaccio, G., Carfi, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 126.36 kDa 
• Atom Count: 9,652 
• Modelled Residue Count: 1,117 
• Deposited Residue Count: 1,126 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A, B	563	Hepatitis C virus isolate HC-J8	Mutation(s): 1  EC: 2.7.7.48
UniProt
Find proteins for P26661 (Hepatitis C virus genotype 2b (isolate HC-J8)) Explore P26661  Go to UniProtKB:  P26661

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VGI	C [auth A], D [auth B]	2-(3-bromophenyl)-6-[(2-hydroxyethyl)amino]-1h-benzo[de]isoquinoline-1,3(2h)-dione C20 H15 Br N2 O3 JZCUVYNOSDWORZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
VGI	BindingDB:  3HVO	IC50: min: 180, max: 770 (nM) from 2 assay(s)
		EC50: 1.10e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.218 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.293	α = 90
b = 64.648	β = 89.73
c = 135.714	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-04 
Deposition Author(s): Rydberg, E.H., Carfi, A.

Revision History  

• Version 1.0: 2009-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2019-01-23
  Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2021-11-10
  Changes: Database references, Derived calculations
• Version 2.2: 2023-11-01
  Changes: Data collection, Refinement description