Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 64.66 kDa 
• Atom Count: 4972 
• Modelled Residue Count: 563 
• Deposited Residue Count: 576 
• Unique protein chains: 1

1OS5

Crystal structure of HCV NS5B RNA polymerase complexed with a novel non-competitive inhibitor.

• PDB DOI: 10.2210/pdb1OS5/pdb

• Classification: TRANSFERASE
• Organism(s): Hepatitis C virus subtype 1b
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-03-18 Released: 2004-03-18 
• Deposition Author(s): Love, R.A., Parge, H.E., Yu, X., Hickey, M.J., Diehl, W., Gao, J., Wriggers, H., Ekker, A., Wang, L., Thomson, J.A., Dragovich, P.S., Fuhrman, S.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.251 
• R-Value Work: 0.207 
• R-Value Observed: 0.201 

Literature

Crystallographic identification of a noncompetitive inhibitor binding site on the hepatitis C virus NS5B RNA polymerase enzyme.

Love, R.A., Parge, H.E., Yu, X., Hickey, M.J., Diehl, W., Gao, J., Wriggers, H., Ekker, A., Wang, L., Thomson, J.A., Dragovich, P.S., Fuhrman, S.A.

(2003) J Virol 77: 7575-7581

• PubMed: 12805457 
• DOI: 10.1128/jvi.77.13.7575-7581.2003
• Primary Citation of Related Structures:  
  1OS5


• PubMed Abstract: 
  

The virus-encoded nonstructural protein 5B (NS5B) of hepatitis C virus (HCV) is an RNA-dependent RNA polymerase and is absolutely required for replication of the virus. NS5B exhibits significant differences from cellular polymerases and therefore has become an attractive target for anti-HCV therapy. Using a high-throughput screen, we discovered a novel NS5B inhibitor that binds to the enzyme noncompetitively with respect to nucleotide substrates. Here we report the crystal structure of NS5B complexed with this small molecule inhibitor. Unexpectedly, the inhibitor is bound within a narrow cleft on the protein's surface in the "thumb" domain, about 30 A from the enzyme's catalytic center. The interaction between this inhibitor and NS5B occurs without dramatic changes to the structure of the protein, and sequence analysis suggests that the binding site is conserved across known HCV genotypes. Possible mechanisms of inhibition include perturbation of protein dynamics, interference with RNA binding, and disruption of enzyme oligomerization.

---

Related Citations: 

• Hepatitis C Virus (HCV) NS5B RNA Polymerase and Mutants Thereof.
  Love, R.A., Parge, H.E., Hickey, M.J., Yu, X., Fuhrman, S.A., Diehl, W., Gao, J.
  (2002) Patent --: --

---

Organizational Affiliation: 

Pfizer Global Research and Development, La Jolla Laboratories, San Diego, California 92121, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatitis C virus NS5B RNA polymerase	A	576	Hepatitis C virus subtype 1b	Mutation(s): 3  Gene Names: NS5B EC: 3.4.22 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.7.7.48 (UniProt)
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
NH1	B [auth A]	3-(4-AMINO-2-TERT-BUTYL-5-METHYL-PHENYLSULFANYL)-6-CYCLOPENTYL-4-HYDROXY-6-[2-(4-HYDROXY-PHENYL)-ETHYL]-5,6-DIHYDRO-PYRAN-2-ONE C29 H37 N O4 S ZEBFKFGJWHOOST-LJAQVGFWSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NH1	Binding MOAD:  1OS5	Kd: 140 (nM) from 1 assay(s)
	PDBBind:  1OS5	Kd: 140 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.251 
• R-Value Work: 0.207 
• R-Value Observed: 0.201 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83	α = 90
b = 83	β = 90
c = 180	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-03-18 
• Released Date: 2004-03-18 
Deposition Author(s): Love, R.A., Parge, H.E., Yu, X., Hickey, M.J., Diehl, W., Gao, J., Wriggers, H., Ekker, A., Wang, L., Thomson, J.A., Dragovich, P.S., Fuhrman, S.A.

Revision History  

• Version 1.0: 2004-03-18
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations
• Version 1.4: 2021-10-27
  Changes: Database references