1RTL | pdb_00001rtl

CRYSTAL STRUCTURE OF HCV NS3 PROTEASE DOMAIN: NS4A PEPTIDE COMPLEX WITH COVALENTLY BOUND PYRROLIDINE-5,5-TRANSLACTAM INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb1RTL/pdb

• Classification: Viral protein complex
• Organism(s): Orthohepacivirus hominis, Hepacivirus hominis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-12-10 Released: 2004-12-14 
• Deposition Author(s): Skarzynski, T., Somers, D.O.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.234 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Pyrrolidine-5,5-trans-lactams. 4. Incorporation of a P3/P4 urea leads to potent intracellular inhibitors of hepatitis C virus NS3/4A protease

Slater, M.J., Amphlett, E.M., Andrews, D.M., Bamborough, P., Carey, S.J., Johnson, M.R., Jones, P.S., Mills, G., Parry, N.R., Somers, D.O., Stewart, A.J., Skarzynski, T.

(2003) Org Lett 5: 4627-4630

• PubMed: 14627400 
• DOI: https://doi.org/10.1021/ol035826v
• Primary Citation Related Structures: 
  1RTL


• PubMed Abstract: 
  

  [reaction: see text] In this, the first of two Letters, we describe how a P3/P4 urea linking unit was used to greatly enhance the biochemical and replicon potency of inhibitors based upon the pyrrolidine-5,5-trans-lactam template. Compound 7b demonstrated a 100 nM IC(50) in the replicon cell-based surrogate HCV assay.

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Organizational Affiliation: 
• GlaxoSmithKline Medicines Research Center, Gunnels Wood Road, Stevenage, SG1 2NY, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

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

Macromolecule Content 

• Total Structure Weight: 47.89 kDa 
• Atom Count: 2,868 
• Modeled 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, B	200	Orthohepacivirus hominis	Mutation(s): 1  Gene Names: H STRAIN
UniProt
Find proteins for P26664 (Hepatitis C virus genotype 1a (isolate 1)) Explore P26664  Go to UniProtKB:  P26664

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NS4A COFACTOR	C, D	23	N/A	Mutation(s): 0
UniProt
Find proteins for O39914 (Hepacivirus hominis) Explore O39914  Go to UniProtKB:  O39914

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CPX	F [auth A]	N-[(2R,3S)-1-((2S)-2-{[(CYCLOPENTYLAMINO)CARBONYL]AMINO}-3-METHYLBUTANOYL)-2-(1-FORMYL-1-CYCLOBUTYL)PYRROLIDINYL]CYCLOPROPANECARBOXAMIDE C24 H38 N4 O4 GCDRFILPPBOJLM-UFYCRDLUSA-N
ZN	E [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.234 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 224.082	α = 90
b = 224.082	β = 90
c = 75.694	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-14 
Deposition Author(s): Skarzynski, T., Somers, D.O.N.

Revision History  

• Version 1.0: 2004-12-14
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-20
  Changes: Data collection, Structure summary