2JC0 | pdb_00002jc0

CRYSTAL STRUCTURE OF HEPATITIS C VIRUS POLYMERASE IN COMPLEX WITH INHIBITOR SB655264

• PDB DOI: https://doi.org/10.2210/pdb2JC0/pdb

• Classification: HYDROLASE
• Organism(s): Hepacivirus hominis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-12-18 Released: 2007-02-13 
• Deposition Author(s): Wonacott, A., Skarzynski, T., Singh, O.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.248 (Depositor) 
• R-Value Work: 
  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Optimization of Novel Acyl Pyrrolidine Inhibitors of Hepatitis C Virus RNA-Dependent RNA Polymerase Leading to a Development Candidate.

Slater, M.J., Amphlett, E.M., Andrews, D.M., Bravi, G., Burton, G., Cheasty, A.G., Corfield, J.A., Ellis, M.R., Fenwick, R.H., Fernandes, S., Guidetti, R., Haigh, D., Hartley, C.D., Howes, P.D., Jackson, D.L., Jarvest, R.L., Lovegrove, V.L., Medhurst, K.J., Parry, N.R., Price, H., Shah, P., Singh, O.M., Stocker, R., Thommes, P., Wilkinson, C., Wonacott, A.

(2007) J Med Chem 50: 897

• PubMed: 17269759 
• DOI: https://doi.org/10.1021/jm061207r
• Primary Citation of Related Structures:  
  2JC0, 2JC1


• PubMed Abstract: 
  

  Optimization of a pyrrolidine-based template using structure-based design and physicochemical considerations has provided a development candidate 20b (3082) with submicromolar potency in the HCV replicon and good pharmacokinetic properties.

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Organizational Affiliation: 
• Infectious Diseases CEDD and Medicinal Discovery Research, GlaxoSmithKline, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, United Kingdom. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 128.54 kDa 
• Atom Count: 9,423 
• Modeled Residue Count: 1,113 
• Deposited Residue Count: 1,140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-DEPENDENT RNA-POLYMERASE	A, B	570	Hepacivirus hominis	Mutation(s): 0
UniProt
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK)) Explore P26663  Go to UniProtKB:  P26663

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
699	C [auth A], D [auth A], E [auth B], F [auth B]	(2S,4S,5R)-2-ISOBUTYL-5-(2-THIENYL)-1-[4-(TRIFLUOROMETHYL)BENZOYL]PYRROLIDINE-2,4-DICARBOXYLIC ACID C22 H22 F3 N O5 S ZNCZVHCYBGHCHA-XPIZARPCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
699	BindingDB:  2JC0	IC50: 300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.248 (Depositor) 
• R-Value Work:  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.74	α = 90
b = 105.893	β = 90
c = 126.12	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-13 
Deposition Author(s): Wonacott, A., Skarzynski, T., Singh, O.M.

Revision History  

• Version 1.0: 2007-02-13
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Other