3HVO | pdb_00003hvo

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.218 (Depositor), 0.228 (DCC)
R-Value Work:
0.182 (Depositor), 0.192 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P26661
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VGI Query on VGI Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
VGI	BindingDB: 3HVO	IC50: min: 180, max: 770 (nM) from 2 assay(s)
VGI	BindingDB: 3HVO	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 (Depositor), 0.228 (DCC)
R-Value Work: 0.182 (Depositor), 0.192 (DCC)
R-Value Observed: 0.184 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-08-04

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.