3FRZ

Crystal Structure of HCV NS5B RNA polymerase in complex with PF868554

• PDB DOI: https://doi.org/10.2210/pdb3FRZ/pdb

• Classification: TRANSFERASE
• Organism(s): Hepatitis C virus (isolate BK)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-01-08 Released: 2009-03-10 
• Deposition Author(s): Parge, H.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.221 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Literature

Discovery of (R)-6-cyclopentyl-6-(2-(2,6-diethylpyridin-4-yl)ethyl)-3-((5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)methyl)-4-hydroxy-5,6-dihydropyran-2-one (PF-00868554) as a potent and orally available hepatitis C virus polymerase inhibitor.

Li, H., Tatlock, J., Linton, A., Gonzalez, J., Jewell, T., Patel, L., Ludlum, S., Drowns, M., Rahavendran, S.V., Skor, H., Hunter, R., Shi, S.T., Herlihy, K.J., Parge, H., Hickey, M., Yu, X., Chau, F., Nonomiya, J., Lewis, C.

(2009) J Med Chem 52: 1255-1258

• PubMed: 19209845 
• DOI: https://doi.org/10.1021/jm8014537
• Primary Citation of Related Structures:  
  3FRZ


• PubMed Abstract: 
  

  The HCV RNA-dependent RNA polymerase has emerged as one of the key targets for novel anti-HCV therapy development. Herein, we report the optimization of the dihydropyrone series inhibitors to improve compound aqueous solubility and reduce CYP2D6 inhibition, which led to the discovery of compound 24 (PF-00868554). Compound 24 is a potent and selective HCV polymerase inhibitor with a favorable pharmacokinetic profile and has recently entered a phase II clinical evaluation in patients with genotype 1 HCV.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 65.37 kDa 
• Atom Count: 5,060 
• Modelled Residue Count: 562 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase	A	576	Hepatitis C virus (isolate BK)	Mutation(s): 5  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AG6	C [auth A]	N-[(benzyloxy)carbonyl]-L-alpha-glutamyl-N-[(1S)-4-oxo-4-phenyl-1-propylbut-2-en-1-yl]-L-phenylalaninamide C35 H39 N3 O7 LKWUEIKYVLZLJI-DTXPUJKBSA-N
AG0	B [auth A]	(6R)-6-cyclopentyl-6-[2-(2,6-diethylpyridin-4-yl)ethyl]-3-[(5,7-dimethyl[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)methyl]-4-hydroxy-5,6-dihydro-2H-pyran-2-one C29 H37 N5 O3 SLVAPEZTBDBAPI-GDLZYMKVSA-N
BME	D [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AG0	PDBBind:  3FRZ	IC50: 7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.221 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.2	α = 90
b = 83.2	β = 90
c = 180.263	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
ARP/wARP	model building
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-10 
Deposition Author(s): Parge, H.E.

Revision History  

• Version 1.0: 2009-03-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations