2HAI

Crystal structure of HCV NS5B RNA polymerase in complex with novel class of dihydropyrone-containing inhibitor.

• PDB DOI: https://doi.org/10.2210/pdb2HAI/pdb

• Classification: TRANSFERASE
• Organism(s): Hepacivirus hominis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-06-12 Released: 2006-09-05 
• Deposition Author(s): Li, H., Love, R.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.236 
• R-Value Work: 0.215 
• R-Value Observed: 0.215 

Starting Model: other

Literature

Identification and structure-based optimization of novel dihydropyrones as potent HCV RNA polymerase inhibitors.

Li, H., Tatlock, J., Linton, A., Gonzalez, J., Borchardt, A., Dragovich, P., Jewell, T., Prins, T., Zhou, R., Blazel, J., Parge, H., Love, R., Hickey, M., Doan, C., Shi, S., Duggal, R., Lewis, C., Fuhrman, S.

(2006) Bioorg Med Chem Lett 16: 4834-4838

• PubMed: 16824756 
• DOI: https://doi.org/10.1016/j.bmcl.2006.06.065
• Primary Citation of Related Structures:  
  2HAI


• PubMed Abstract: 
  

  A novel class of non-nucleoside HCV NS5B polymerase inhibitors has been identified from screening. A co-crystal structure revealed an allosteric binding site in the protein that required a unique conformational change to accommodate inhibitor binding. Herein we report the structure-activity relationships (SARs) of this novel class of dihydropyrone-containing compounds that show potent inhibitory activities against the HCV RNA polymerase in biochemical assays.

---

Organizational Affiliation: 

Pfizer Global Research and Development, La Jolla Laboratories, 10770 Science Center Dr., San Diego, CA 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: 64.63 kDa 
• Atom Count: 4,929 
• Modelled Residue Count: 562 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEPATITIS C VIRUS NS5B RNA POLYMERASE	A	576	Hepacivirus hominis	Mutation(s): 5  Gene Names: NS5B EC: 2.7.7.48
UniProt
Find proteins for Q99AU2 (Hepatitis C virus subtype 1b) Explore Q99AU2  Go to UniProtKB:  Q99AU2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PFI	B [auth A]	(6S)-6-CYCLOPENTYL-6-[2-(3-FLUORO-4-ISOPROPOXYPHENYL)ETHYL]-4-HYDROXY-5,6-DIHYDRO-2H-PYRAN-2-ONE C21 H27 F O4 AKNIHFDXRAOPAI-NRFANRHFSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
PFI	PDBBind:  2HAI	IC50: 530 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.236 
• R-Value Work: 0.215 
• R-Value Observed: 0.215 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.255	α = 90
b = 83.255	β = 90
c = 179.83	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-05 
Deposition Author(s): Li, H., Love, R.L.

Revision History  

• Version 1.0: 2006-09-05
  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: 2024-04-03
  Changes: Data collection, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary