3LON

HCV NS3-4a protease domain with ketoamide inhibitor narlaprevir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.204 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyprotein
A, C
200hepatitis C virus genotype 1aMutation(s): 1 
Gene Names: NS3
UniProt
Find proteins for Q9ELS8 (hepatitis C virus genotype 1a)
Explore Q9ELS8 
Go to UniProtKB:  Q9ELS8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ELS8
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
KK-NS4a(21-39)-KK
B, D
23N/AMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NNA
Query on NNA

Download Ideal Coordinates CCD File 
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
Query on BME

Download Ideal Coordinates CCD File 
G [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.204 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 224.392α = 90
b = 224.392β = 90
c = 75.331γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
X-PLORmodel building
X-PLORrefinement
HKL-2000data reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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