2GC8

Structure of a Proline Sulfonamide Inhibitor Bound to HCV NS5b Polymerase

• PDB DOI: https://doi.org/10.2210/pdb2GC8/pdb

• Classification: TRANSFERASE
• Organism(s): Hepacivirus hominis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-03-13 Released: 2006-06-13 
• Deposition Author(s): Gopalsamy, A., Chopra, R., Lim, K., Ciszewski, G., Shi, M., Curran, K.J., Sukits, S.F., Svenson, K., Bard, J., Ellingboe, J.W., Agarwal, A., Krishnamurthy, G., Howe, A.Y., Orlowski, M., Feld, B., O'connell, J., Mansour, T.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.273 
• R-Value Work: 0.238 
• R-Value Observed: 0.216 

Starting Model: experimental

Literature

Discovery of Proline Sulfonamides as Potent and Selective Hepatitis C Virus NS5b Polymerase Inhibitors. Evidence for a New NS5b Polymerase Binding Site.

Gopalsamy, A., Chopra, R., Lim, K., Ciszewski, G., Shi, M., Curran, K.J., Sukits, S.F., Svenson, K., Bard, J., Ellingboe, J.W., Agarwal, A., Krishnamurthy, G., Howe, A.Y., Orlowski, M., Feld, B., O'connell, J., Mansour, T.S.

(2006) J Med Chem 49: 3052-3055

• PubMed: 16722622 
• DOI: https://doi.org/10.1021/jm060168g
• Primary Citation of Related Structures:  
  2GC8


• PubMed Abstract: 
  

  Through high throughput screening, substituted proline sulfonamide 6 was identified as HCV NS5b RNA-dependent RNA polymerase inhibitor. Optimization of various regions of the lead molecule resulted in compounds that displayed good potency and selectivity. The crystal structure of 6 and NS5b polymerase complex confirmed the binding near the active site region. The optimization approach and SAR are discussed in detail.

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Organizational Affiliation: 

Chemical and Screening Sciences, Wyeth Research, 401 N. Middletown Road, Pearl River, New York 10965, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 129.13 kDa 
• Atom Count: 9,167 
• Modelled Residue Count: 1,112 
• Deposited Residue Count: 1,156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase	A, B	578	Hepacivirus hominis	Mutation(s): 1  EC: 2.7.7.48
UniProt
Find proteins for Q99AU2 (Hepatitis C virus subtype 1b) Explore Q99AU2  Go to UniProtKB:  Q99AU2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
885	C [auth A], D [auth B]	1-[(2-AMINO-4-CHLORO-5-METHYLPHENYL)SULFONYL]-L-PROLINE C12 H15 Cl N2 O4 S OWYKAFABUYXQLE-JTQLQIEISA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
885	BindingDB:  2GC8	IC50: 3100 (nM) from 1 assay(s)
	PDBBind:  2GC8	IC50: 3100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.273 
• R-Value Work: 0.238 
• R-Value Observed: 0.216 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.809	α = 90
b = 105.91	β = 90
c = 126.624	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-13 
Deposition Author(s): Gopalsamy, A., Chopra, R., Lim, K., Ciszewski, G., Shi, M., Curran, K.J., Sukits, S.F., Svenson, K., Bard, J., Ellingboe, J.W., Agarwal, A., Krishnamurthy, G., Howe, A.Y., Orlowski, M., Feld, B., O'connell, J., Mansour, T.S.

Revision History  

• Version 1.0: 2006-06-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description