3LON | pdb_00003lon

HCV NS3-4a protease domain with ketoamide inhibitor narlaprevir

• PDB DOI: https://doi.org/10.2210/pdb3LON/pdb

• Classification: VIRAL PROTEIN/INHIBITOR
• Organism(s): hepatitis C virus genotype 1a
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-02-04 Released: 2011-01-19 
• Deposition Author(s): Prongay, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.269 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.214 (DCC) 

Starting Model: experimental

Literature

Candidate selection and preclinical evaluation culminating in the discovery of Narlaprevir (SCH 900518): A potent, selective and orally efficacious second generation HCV NS3 serine protease inhibitor

Arasappan, A., Bennett, F., Bogen, S.L., Blackman, M., Chen, K., Hendrata, S., Huang, Y., Huelgas, R.M., Nair, L., Padilla, A.I., Pan, W., Pike, R., Pinto, P., Ruan, S., Sannigrahi, M., Velaquez, F., Vibulbhan, B., Wu, W., Yang, W., Saksena, A.K., Girijavallabhan, V., Shih, N.Y., Kong, J., Meng, T., Jin, Y., Wong, J., McNamara, P., Prongay, A., Madison, V., Piwinski, J.J., Cheng, K.C., Morrison, R., Malcolm, B., Tong, X., Ralston, R., Njoroge, F.G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.17 kDa 
• Atom Count: 3,001 
• Modeled Residue Count: 370 
• Deposited Residue Count: 446 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A, C	200	hepatitis C virus genotype 1a	Mutation(s): 1  Gene Names: NS3
UniProt
Find proteins for Q9ELS8 (hepatitis C virus genotype 1a) Explore Q9ELS8  Go to UniProtKB:  Q9ELS8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
KK-NS4a(21-39)-KK	B, D	23	N/A	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NNA	F [auth A]	(1R,2S,5S)-3-[N-({1-[(tert-butylsulfonyl)methyl]cyclohexyl}carbamoyl)-3-methyl-L-valyl]-N-{(1S)-1-[(1R)-2-(cyclopropylamino)-1-hydroxy-2-oxoethyl]pentyl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide C36 H63 N5 O7 S BZXRATSZUNDEEV-FZFXNXQRSA-N
BME	G [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
ZN	E [auth A], H [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.269 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.214 (DCC) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 224.392	α = 90
b = 224.392	β = 90
c = 75.331	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-19 
Deposition Author(s): Prongay, A.J.

Revision History  

• Version 1.0: 2011-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-04-14
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2021-10-13
  Changes: Database references
• Version 1.4: 2024-04-03
  Changes: Data collection, Refinement description