1W3C | pdb_00001w3c

Crystal structure of the Hepatitis C Virus NS3 Protease in complex with a peptidomimetic inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1W3C/pdb

• Classification: HYDROLASE
• Organism(s): Hepatitis C virus (isolate 1)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-07-14 Released: 2004-12-09 
• Deposition Author(s): Di Marco, S., Volpari, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.240 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.169 (DCC) 

Starting Model: experimental

Literature

The Design and Enzyme-Bound Crystal Structure of Indoline Based Peptidomimetic Inhibitors of Hepatitis C Virus Ns3 Protease

Ontoria, J.M., Di Marco, S., Conte, I., Di Francesco, M.E., Gardelli, C., Koch, U., Matassa, V.G., Poma, M., Steinkuhler, C., Volpari, C., Harper, S.

(2004) J Med Chem 47: 6443

• PubMed: 15588076 
• DOI: https://doi.org/10.1021/jm049435d
• Primary Citation Related Structures: 
  1W3C


• PubMed Abstract: 
  

  The design of a series of peptidomimetic inhibitors of the hepatitis C virus NS3 protease is described. These inhibitors feature an indoline-2-carboxamide as a novel heterocyclic replacement for the P3 amino acid residue and N-terminal capping group of tripeptide based inhibitors. The crystal structure of the ternary NS3/NS4A/inhibitor complex for the most active molecule in this series highlights its suitability as an N-terminal capping group of a dipeptide inhibitor of the NS3 protease.

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Organizational Affiliation: 
• IRBM-MRL Rome, Via Pontina km 30,600, 00040 Rome, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and 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)

Macromolecule Content 

• Total Structure Weight: 44.01 kDa 
• Atom Count: 2,988 
• Modeled Residue Count: 374 
• Deposited Residue Count: 406 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASE/HELICASE NS3 (P70)	A, B	187	Hepatitis C virus (isolate 1)	Mutation(s): 0  EC: 3.4.22
UniProt
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese)) Explore P26662  Go to UniProtKB:  P26662

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NONSTRUCTURAL PROTEIN NS4A (P4)	C, D	16	Hepatitis C virus (isolate 1)	Mutation(s): 2
UniProt
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese)) Explore P26662  Go to UniProtKB:  P26662

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DN1	E [auth A]	3-({(2S)-2-[({(1R)-1-[({(1R)-1-[(R)-CARBOXY(HYDROXY)METHYL]-3,3-DIFLUOROPROPYL}AMINO)CARBONYL]-3-METHYLBUTYL}AMINO)CARB ONYL]-2,3-DIHYDRO-1H-INDOL-2-YL}METHYL)THIOPHENE-2-CARBOXYLIC ACID C26 H31 F2 N3 O7 S BEFPIHVRQQQFFB-DUFVWYDBSA-N
DN2	F [auth B]	3-({(2S)-2-[({(1S)-1-[({(1S)-1-[(R)-CARBOXY(HYDROXY)METHYL]-3,3-DIFLUOROPROPYL}AMINO)CARBONYL]-3-METHYLBUTYL}AMINO)CARBONYL]-2,3-DIHYDRO-1H-INDOL-2-YL}METHYL)THIOPHENE-2-CARBOXYLIC ACID C26 H31 F2 N3 O7 S BEFPIHVRQQQFFB-QUPVEMFASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.240 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.169 (DCC) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.411	α = 90
b = 92.411	β = 90
c = 80.007	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-09 
Deposition Author(s): Di Marco, S., Volpari, C.

Revision History  

• Version 1.0: 2004-12-09
  Type: Initial release
  
• Version 1.1: 2015-09-16
  Changes: Data collection, Database references, Derived calculations, Other, Source and taxonomy, Structure summary, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary
• Version 1.3: 2024-10-23
  Changes: Structure summary