3CJ0 | pdb_00003cj0

Crystal structure of hepatitis c virus rna-dependent rna polymerase ns5b in complex with small molecule fragments

• PDB DOI: https://doi.org/10.2210/pdb3CJ0/pdb

• Classification: TRANSFERASE
• Organism(s): Hepatitis C virus subtype 1b
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-12 Released: 2008-04-15 
• Deposition Author(s): Kissinger, c.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.230 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Fragment-based discovery of hepatitis C virus NS5b RNA polymerase inhibitors.

Antonysamy, S.S., Aubol, B., Blaney, J., Browner, M.F., Giannetti, A.M., Harris, S.F., Hebert, N., Hendle, J., Hopkins, S., Jefferson, E., Kissinger, C., Leveque, V., Marciano, D., McGee, E., Najera, I., Nolan, B., Tomimoto, M., Torres, E., Wright, T.

(2008) Bioorg Med Chem Lett 18: 2990-2995

• PubMed: 18400495 
• DOI: https://doi.org/10.1016/j.bmcl.2008.03.056
• Primary Citation Related Structures: 
  3CIZ, 3CJ0, 3CJ2, 3CJ3, 3CJ4, 3CJ5


• PubMed Abstract: 
  

  Non-nucleoside inhibitors of HCV NS5b RNA polymerase were discovered by a fragment-based lead discovery approach, beginning with crystallographic fragment screening. The NS5b binding affinity and biochemical activity of fragment hits and inhibitors was determined by surface plasmon resonance (Biacore) and an enzyme inhibition assay, respectively. Crystallographic fragment screening hits with approximately 1-10mM binding affinity (K(D)) were iteratively optimized to give leads with approximately 200nM biochemical activity and low microM cellular activity in a Replicon assay.

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Organizational Affiliation: 
• Medicinal Chemistry, SGX Pharmaceuticals, Inc., 10505 Roselle Street, San Diego, CA 92121, USA.

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: 128.9 kDa 
• Atom Count: 9,153 
• Modeled Residue Count: 1,124 
• Deposited Residue Count: 1,152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase	A, B	576	Hepatitis C virus subtype 1b	Mutation(s): 0  Gene Names: NS5B EC: 2.7.7.48
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
SX2	C [auth A], D [auth B]	4-[(5-bromopyridin-2-yl)amino]-4-oxobutanoic acid C9 H9 Br N2 O3 XFYYQDHEDOXWGA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.230 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.961	α = 90
b = 105.802	β = 90
c = 126.484	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-15 
Deposition Author(s): Kissinger, c.

Revision History  

• Version 1.0: 2008-04-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations