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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Genome polyproteinA, C200hepatitis 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
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
KK-NS4a(21-39)-KKB, D23N/AMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / 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		 Ligand Interaction
BME
Query on BME
Download Ideal Coordinates CCD File 
G [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
E [auth A],
H [auth C]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
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

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Ligand Structure Quality Assessment 


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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