2AX1

Hepatitis C Virus NS5b RNA Polymerase in complex with a covalent inhibitor (5ee)

• PDB DOI: https://doi.org/10.2210/pdb2AX1/pdb

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


• Deposited: 2005-09-02 Released: 2006-01-24 
• Deposition Author(s): Powers, J.P., Piper, D.E., Li, Y., Mayorga, V., Anzola, J., Chen, J.M., Jaen, J.C., Lee, G., Liu, J., Peterson, M.G., Tonn, G.R., Ye, Q., Walker, N.P., Wang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.229 
• R-Value Work: 0.202 
• R-Value Observed: 0.217 

Literature

SAR and Mode of Action of Novel Non-Nucleoside Inhibitors of Hepatitis C NS5b RNA Polymerase.

Powers, J.P., Piper, D.E., Li, Y., Mayorga, V., Anzola, J., Chen, J.M., Jaen, J.C., Lee, G., Liu, J., Peterson, M.G., Tonn, G.R., Ye, Q., Walker, N.P., Wang, Z.

(2006) J Med Chem 49: 1034-1046

• PubMed: 16451069 
• DOI: https://doi.org/10.1021/jm050859x
• Primary Citation of Related Structures:  
  2AWZ, 2AX0, 2AX1


• PubMed Abstract: 
  

  Novel non-nucleoside inhibitors of the HCV RNA polymerase (NS5b) with sub-micromolar biochemical potency have been identified which are selective for the inhibition of HCV NS5b over other polymerases. The structures of the complexes formed between several of these inhibitors and HCV NS5b were determined by X-ray crystallography, and the inhibitors were found to bind in an allosteric binding site separate from the active site. Structure-activity relationships and structural studies have identified the mechanism of action for compounds in this series, several of which possess drug-like properties, as unique, reversible, covalent inhibitors of HCV NS5b.

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Organizational Affiliation: 

Amgen Inc., 1120 Veterans Boulevard, South San Francisco, CA 94080, 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: 130.95 kDa 
• Atom Count: 9,587 
• Modelled Residue Count: 1,115 
• Deposited Residue Count: 1,160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A, B	580	Hepacivirus hominis	Mutation(s): 11  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5EE	G [auth A], L [auth B]	5R-(3,4-DICHLOROPHENYLMETHYL)-3-(2-THIOPHENESULFONYLAMINO)-4-OXO-2-THIONOTHIAZOLIDINE C14 H10 Cl2 N2 O3 S4 GAOOBYJHWAKZKU-LLVKDONJSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.229 
• R-Value Work: 0.202 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.009	α = 90
b = 86.77	β = 90
c = 162.739	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
CNS	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-24 
Deposition Author(s): Powers, J.P., Piper, D.E., Li, Y., Mayorga, V., Anzola, J., Chen, J.M., Jaen, J.C., Lee, G., Liu, J., Peterson, M.G., Tonn, G.R., Ye, Q., Walker, N.P., Wang, Z.

Revision History  

• Version 1.0: 2006-01-24
  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: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-16
  Changes: Data collection, Structure summary