2A4Q

HCV NS3 protease with NS4a peptide and a covalently bound macrocyclic ketoamide compound.

• PDB DOI: https://doi.org/10.2210/pdb2A4Q/pdb

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


• Deposited: 2005-06-29 Released: 2006-07-04 
• Deposition Author(s): Chen, K.X., Njoroge, F.G., Prongay, A., Pichardo, J., Madison, V., Girijavallabhan, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.274 
• R-Value Work: 0.191 

Literature

Synthesis and Biological Activity of Macrocyclic Inhibitors of Hepatitis C Virus (HCV) NS3 Protease

Chen, K.X., Njoroge, F.G., Prongay, A., Pichardo, J., Madison, V., Girijavallabhan, V.

(2005) Bioorg Med Chem Lett 15: 4475-4478

• PubMed: 16112859 
• DOI: https://doi.org/10.1016/j.bmcl.2005.07.033
• Primary Citation of Related Structures:  
  2A4Q


• PubMed Abstract: 
  

  The 17-membered phenylalanine-based macrocycle 6 was prepared starting from 3-iodo-phenylalanine. Macrocyclization of alkene phenyl iodide 5 was effected through a palladium-catalyzed Heck reaction. The macrocyclic alpha-ketoamides were active inhibitors of the HCV NS3 protease, with the C-terminal acids and amides being more potent than tert-butyl esters.

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Organizational Affiliation: 

Schering-Plough Research Institute, 2015 Galloping Hill Road, K-15-3-3545, Kenilworth, NJ 07033, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.21 kDa 
• Atom Count: 2,953 
• Modelled Residue Count: 370 
• Deposited Residue Count: 446 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS3 protease/helicase'	A, C	200	Hepacivirus hominis	Mutation(s): 0
UniProt
Find proteins for Q91RS4 (Hepacivirus hominis) Explore Q91RS4  Go to UniProtKB:  Q91RS4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NS4a peptide	B, D	23	N/A	Mutation(s): 1
UniProt
Find proteins for O39914 (Hepacivirus hominis) Explore O39914  Go to UniProtKB:  O39914

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FNH	G [auth A]	(2R)-({N-[(3S)-3-({[(3S,6S)-6-CYCLOHEXYL-5,8-DIOXO-4,7-DIAZABICYCLO[14.3.1]ICOSA-1(20),16,18-TRIEN-3-YL]CARBONYL}AMINO)-2-OXOHEXANOYL]GLYCYL}AMINO)(PHENYL)ACETIC ACID C41 H55 N5 O8 MRGBFMHIJSOQIX-IMJQVECRSA-N
BME	F [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
ZN	E [auth A], H [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FNH	PDBBind:  2A4Q	Ki: 66 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.274 
• R-Value Work: 0.191 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 224.923	α = 90
b = 224.923	β = 90
c = 75.317	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
HKL-2000	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-04 
Deposition Author(s): Chen, K.X., Njoroge, F.G., Prongay, A., Pichardo, J., Madison, V., Girijavallabhan, V.

Revision History  

• Version 1.0: 2006-07-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  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