3H98 | pdb_00003h98

Crystal structure of HCV NS5b 1b with (1,1-dioxo-2H-[1,2,4]benzothiadiazin-3-yl) azolo[1,5-a]pyrimidine derivative

PDB DOI: https://doi.org/10.2210/pdb3H98/pdb

Classification: TRANSFERASE
Organism(s): Hepatitis C virus (isolate BK)
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-04-30 Released: 2009-10-13
Deposition Author(s): Wang, G., Lei, H., Wang, X., Das, D., Mackinnon, C., Montalbetti, C.A.G., Mears, R., Gai, X., Bailey, S., Ruhrmund, D., Hooi, L., Misialek, S., Rajagopalan, R., Cheng, R.K.Y., Barker, J.L., Felicetti, B., Stoycheva, A., Buckman, B., Kossen, K., Seiwert, S., Beigelmana, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.274 (Depositor), 0.273 (DCC)
R-Value Work:
0.208 (Depositor), 0.206 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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Literature

HCV NS5B polymerase inhibitors 2: Synthesis and in vitro activity of (1,1-dioxo-2H-[1,2,4]benzothiadiazin-3-yl) azolo[1,5-a]pyridine and azolo[1,5-a]pyrimidine derivatives.

Wang, G., Lei, H., Wang, X., Das, D., Hong, J., Mackinnon, C.H., Coulter, T.S., Montalbetti, C.A., Mears, R., Gai, X., Bailey, S.E., Ruhrmund, D., Hooi, L., Misialek, S., Rajagopalan, P.T., Cheng, R.K., Barker, J.J., Felicetti, B., Schonfeld, D.L., Stoycheva, A., Buckman, B.O., Kossen, K., Seiwert, S.D., Beigelman, L.

(2009) Bioorg Med Chem Lett 19: 4480-4483

PubMed: 19500983 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2009.05.022
Primary Citation Related Structures:
3H98

PubMed Abstract:
(1,1-Dioxo-2H-[1,2,4]benzothiadiazin-3-yl) azolo[1,5-a]pyridine and azolo[1,5-a]pyrimidine derivatives have been investigated as potential anti-HCV drugs. Their synthesis, HCV NS5B polymerase inhibition, and replicon activity are discussed.

Organizational Affiliation

Discovery Research, InterMune, Inc., Brisbane, CA 94005, USA. gyiwang@yahoo.com

Macromolecule Content

Total Structure Weight: 129.53 kDa
Atom Count: 9,544
Modeled Residue Count: 1,110
Deposited Residue Count: 1,152
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase	A, B	576	Hepatitis C virus (isolate BK)	Mutation(s): 0 EC: 2.7.7.48
UniProt
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK)) Explore P26663 Go to UniProtKB: P26663
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P26663
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B5P Query on B5P Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	N-{3-[5-hydroxy-8-(3-methylbutyl)-7-oxo-7,8-dihydroimidazo[1,2-a]pyrimidin-6-yl]-1,1-dioxido-4H-1,2,4-benzothiadiazin-7-yl}methanesulfonamide C₁₉ H₂₂ N₆ O₆ S₂ HJSHQVOBZCLIRI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.274 (Depositor), 0.273 (DCC)
R-Value Work: 0.208 (Depositor), 0.206 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.931	α = 90
b = 106.196	β = 90
c = 126.417	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-10-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-10-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description