3HHK | pdb_00003hhk

HCV NS5b polymerase complex with a substituted benzothiadizine

PDB DOI: https://doi.org/10.2210/pdb3HHK/pdb

Classification: HYDROLASE/HYDROLASE Inhibitor
Organism(s): Hepatitis C virus subtype 1b
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-05-15 Released: 2009-09-08
Deposition Author(s): Concha, N.O., Singh, O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.250 (Depositor), 0.231 (DCC)
R-Value Work:
0.229 (Depositor), 0.228 (DCC)
R-Value Observed:
0.230 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Substituted benzothiadizine inhibitors of Hepatitis C virus polymerase.

Shaw, A.N., Tedesco, R., Bambal, R., Chai, D., Concha, N.O., Darcy, M.G., Dhanak, D., Duffy, K.J., Fitch, D.M., Gates, A., Johnston, V.K., Keenan, R.M., Lin-Goerke, J., Liu, N., Sarisky, R.T., Wiggall, K.J., Zimmerman, M.N.

(2009) Bioorg Med Chem Lett 19: 4350-4353

PubMed: 19515564 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2009.05.091
Primary Citation Related Structures:
3HHK

PubMed Abstract:
The synthesis and optimisation of HCV NS5B polymerase inhibitors with improved potency versus the existing compound 1 is described. Substitution in the benzothiadiazine portion of the molecule, furnishing improvement in potency in the high protein Replicon assay, is highlighted, culminating in the discovery of 12h, a highly potent oxyacetamide derivative.

Organizational Affiliation

Department of Medicinal Chemistry, GlaxoSmithKline, Collegeville, PA 19426, USA.

Macromolecule Content

Total Structure Weight: 125.84 kDa
Atom Count: 9,302
Modeled Residue Count: 1,126
Deposited Residue Count: 1,126
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HCV NS5 polymerase	A, B	563	Hepatitis C virus subtype 1b	Mutation(s): 0
UniProt
Find proteins for Q99AU2 (Hepatitis C virus genotype 1b) Explore Q99AU2 Go to UniProtKB: Q99AU2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99AU2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
77Z Query on 77Z 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-({(3R)-3-[(3S)-1-(3-methylbutyl)-2,4-dioxo-1,2,3,4-tetrahydroquinolin-3-yl]-1,1-dioxido-3,4-dihydro-2H-1,2,4-benzothiadiazin-7-yl}oxy)acetamide C₂₃ H₂₆ N₄ O₆ S BIRTVLIYTDXUDJ-IFMALSPDSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.250 (Depositor), 0.231 (DCC)
R-Value Work: 0.229 (Depositor), 0.228 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.74	α = 90
b = 107.442	β = 90
c = 126.807	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-09-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-09-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Advisory, Refinement description
Version 1.3: 2024-02-21
Changes: Advisory, Data collection, Database references, Derived calculations

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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.